Starting phenix.real_space_refine on Tue Mar 19 07:30:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi8_12921/03_2024/7oi8_12921_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi8_12921/03_2024/7oi8_12921.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi8_12921/03_2024/7oi8_12921_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/7oi8_12921/03_2024/7oi8_12921_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi8_12921/03_2024/7oi8_12921_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi8_12921/03_2024/7oi8_12921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi8_12921/03_2024/7oi8_12921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi8_12921/03_2024/7oi8_12921_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi8_12921/03_2024/7oi8_12921_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= 0.021 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 1221 5.49 5 Mg 49 5.21 5 S 282 5.16 5 C 54245 2.51 5 N 16896 2.21 5 O 20074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 232": "NH1" <-> "NH2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "E TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "F ASP 191": "OD1" <-> "OD2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "F TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K GLU 123": "OE1" <-> "OE2" Residue "K GLU 143": "OE1" <-> "OE2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "L ARG 37": "NH1" <-> "NH2" 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 TYR 134": "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 GLU 68": "OE1" <-> "OE2" Residue "M TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M ASP 185": "OD1" <-> "OD2" Residue "M GLU 208": "OE1" <-> "OE2" Residue "M ASP 216": "OD1" <-> "OD2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M ASP 246": "OD1" <-> "OD2" Residue "M ARG 259": "NH1" <-> "NH2" Residue "M ASP 287": "OD1" <-> "OD2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "N ASP 201": "OD1" <-> "OD2" Residue "N GLU 206": "OE1" <-> "OE2" Residue "N PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O GLU 51": "OE1" <-> "OE2" Residue "O TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 61": "OD1" <-> "OD2" Residue "O TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 67": "OD1" <-> "OD2" Residue "O ASP 77": "OD1" <-> "OD2" Residue "O PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "P GLU 42": "OE1" <-> "OE2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 75": "NH1" <-> "NH2" Residue "P GLU 76": "OE1" <-> "OE2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "P GLU 126": "OE1" <-> "OE2" Residue "P GLU 174": "OE1" <-> "OE2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "Q ARG 74": "NH1" <-> "NH2" Residue "Q PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q GLU 156": "OE1" <-> "OE2" Residue "Q GLU 161": "OE1" <-> "OE2" Residue "Q PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 165": "OE1" <-> "OE2" Residue "Q GLU 173": "OE1" <-> "OE2" Residue "Q ARG 191": "NH1" <-> "NH2" Residue "Q PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 219": "OE1" <-> "OE2" Residue "Q GLU 234": "OE1" <-> "OE2" Residue "Q PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q ARG 271": "NH1" <-> "NH2" Residue "Q TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 274": "OD1" <-> "OD2" Residue "Q GLU 285": "OE1" <-> "OE2" Residue "Q GLU 287": "OE1" <-> "OE2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "R PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 68": "OD1" <-> "OD2" Residue "S GLU 71": "OE1" <-> "OE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S GLU 126": "OE1" <-> "OE2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 152": "OD1" <-> "OD2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T ASP 85": "OD1" <-> "OD2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "T GLU 123": "OE1" <-> "OE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "T TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 180": "OE1" <-> "OE2" Residue "U PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U TYR 61": "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 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 109": "OD1" <-> "OD2" Residue "U PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 143": "NH1" <-> "NH2" Residue "V ARG 20": "NH1" <-> "NH2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V ASP 53": "OD1" <-> "OD2" Residue "V ASP 69": "OD1" <-> "OD2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "V GLU 112": "OE1" <-> "OE2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "V ASP 124": "OD1" <-> "OD2" Residue "V GLU 132": "OE1" <-> "OE2" 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 200": "OE1" <-> "OE2" Residue "V TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W GLU 57": "OE1" <-> "OE2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X ASP 180": "OD1" <-> "OD2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 200": "OE1" <-> "OE2" Residue "X GLU 209": "OE1" <-> "OE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "Y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y ARG 162": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y ASP 206": "OD1" <-> "OD2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Y GLU 214": "OE1" <-> "OE2" Residue "Y PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 43": "OE1" <-> "OE2" Residue "Z TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "0 GLU 128": "OE1" <-> "OE2" Residue "0 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 GLU 23": "OE1" <-> "OE2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "1 GLU 39": "OE1" <-> "OE2" Residue "1 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 ASP 112": "OD1" <-> "OD2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 GLU 146": "OE1" <-> "OE2" Residue "3 ASP 159": "OD1" <-> "OD2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "5 GLU 32": "OE1" <-> "OE2" Residue "5 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 56": "OE1" <-> "OE2" Residue "5 ARG 80": "NH1" <-> "NH2" Residue "5 GLU 95": "OE1" <-> "OE2" Residue "5 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 130": "OE1" <-> "OE2" Residue "5 GLU 134": "OE1" <-> "OE2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 182": "OD1" <-> "OD2" Residue "5 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "5 GLU 244": "OE1" <-> "OE2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ASP 307": "OD1" <-> "OD2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "5 ASP 379": "OD1" <-> "OD2" Residue "5 TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 27": "NH1" <-> "NH2" Residue "6 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 55": "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 ARG 124": "NH1" <-> "NH2" Residue "6 ARG 136": "NH1" <-> "NH2" Residue "6 GLU 138": "OE1" <-> "OE2" Residue "6 GLU 140": "OE1" <-> "OE2" Residue "6 TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 ARG 364": "NH1" <-> "NH2" Residue "6 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 97": "OE1" <-> "OE2" Residue "7 TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 137": "OE1" <-> "OE2" Residue "7 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 161": "OE1" <-> "OE2" Residue "7 TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 241": "OE1" <-> "OE2" Residue "7 GLU 249": "OE1" <-> "OE2" Residue "7 ARG 250": "NH1" <-> "NH2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "7 TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 279": "OE1" <-> "OE2" Residue "7 PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 96": "OD1" <-> "OD2" Residue "8 GLU 109": "OE1" <-> "OE2" Residue "8 ARG 137": "NH1" <-> "NH2" Residue "8 GLU 141": "OE1" <-> "OE2" Residue "9 ARG 25": "NH1" <-> "NH2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 49": "NH1" <-> "NH2" Residue "9 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 82": "OE1" <-> "OE2" Residue "9 ASP 103": "OD1" <-> "OD2" Residue "9 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 48": "OE1" <-> "OE2" Residue "a TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a ARG 131": "NH1" <-> "NH2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a ARG 142": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b GLU 50": "OE1" <-> "OE2" 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 GLU 44": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ASP 86": "OD1" <-> "OD2" Residue "c GLU 101": "OE1" <-> "OE2" Residue "c GLU 127": "OE1" <-> "OE2" Residue "c PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 176": "OE1" <-> "OE2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "c ASP 217": "OD1" <-> "OD2" Residue "c PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 227": "OE1" <-> "OE2" Residue "c GLU 230": "OE1" <-> "OE2" Residue "c GLU 287": "OE1" <-> "OE2" Residue "c GLU 293": "OE1" <-> "OE2" Residue "c GLU 294": "OE1" <-> "OE2" Residue "c GLU 309": "OE1" <-> "OE2" Residue "c TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 74": "NH1" <-> "NH2" Residue "d PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 158": "OD1" <-> "OD2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "d GLU 187": "OE1" <-> "OE2" Residue "d TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 226": "OD1" <-> "OD2" Residue "d TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 236": "OE1" <-> "OE2" Residue "d TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 104": "OE1" <-> "OE2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "g TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 49": "OE1" <-> "OE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ASP 99": "OD1" <-> "OD2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g GLU 125": "OE1" <-> "OE2" Residue "h ARG 69": "NH1" <-> "NH2" Residue "h TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 106": "OD1" <-> "OD2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "h ASP 125": "OD1" <-> "OD2" Residue "h PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 45": "OD1" <-> "OD2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i GLU 67": "OE1" <-> "OE2" 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 TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j GLU 69": "OE1" <-> "OE2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "j PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j GLU 83": "OE1" <-> "OE2" 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 "l ARG 115": "NH1" <-> "NH2" Residue "l ARG 120": "NH1" <-> "NH2" Residue "l ARG 128": "NH1" <-> "NH2" Residue "l ARG 131": "NH1" <-> "NH2" Residue "m ASP 34": "OD1" <-> "OD2" Residue "o ARG 11": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o GLU 72": "OE1" <-> "OE2" Residue "p TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 113": "OE1" <-> "OE2" Residue "p GLU 138": "OE1" <-> "OE2" Residue "p ASP 149": "OD1" <-> "OD2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q GLU 86": "OE1" <-> "OE2" Residue "q GLU 88": "OE1" <-> "OE2" Residue "q GLU 101": "OE1" <-> "OE2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "q GLU 116": "OE1" <-> "OE2" Residue "q GLU 118": "OE1" <-> "OE2" Residue "q ARG 140": "NH1" <-> "NH2" Residue "r TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 85": "OD1" <-> "OD2" Residue "r PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 116": "OE1" <-> "OE2" Residue "r ARG 132": "NH1" <-> "NH2" Residue "r ARG 153": "NH1" <-> "NH2" Residue "r ARG 168": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "r TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "s GLU 74": "OE1" <-> "OE2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s ASP 103": "OD1" <-> "OD2" Residue "s TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 148": "OD1" <-> "OD2" Residue "s GLU 153": "OE1" <-> "OE2" Residue "s PHE 155": "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 GLU 214": "OE1" <-> "OE2" Residue "s GLU 215": "OE1" <-> "OE2" Residue "s ARG 219": "NH1" <-> "NH2" Residue "s ARG 222": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s ASP 227": "OD1" <-> "OD2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 234": "OD1" <-> "OD2" Residue "s ARG 242": "NH1" <-> "NH2" Residue "s PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 254": "OD1" <-> "OD2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s GLU 309": "OE1" <-> "OE2" Residue "s PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 348": "OE1" <-> "OE2" Residue "s ASP 350": "OD1" <-> "OD2" Residue "s PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 389": "NH1" <-> "NH2" Residue "s GLU 403": "OE1" <-> "OE2" Residue "s GLU 406": "OE1" <-> "OE2" Residue "s PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 93": "OD1" <-> "OD2" Residue "u ASP 95": "OD1" <-> "OD2" Residue "u ASP 122": "OD1" <-> "OD2" Residue "u TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 200": "OD1" <-> "OD2" Residue "v ARG 6": "NH1" <-> "NH2" Residue "v GLU 7": "OE1" <-> "OE2" 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 ARG 28": "NH1" <-> "NH2" Residue "v GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 92769 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: "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: 23184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 23184 Classifications: {'RNA': 1092} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 89, 'rna3p_pur': 463, 'rna3p_pyr': 422} Link IDs: {'rna2p': 206, 'rna3p': 885} Chain breaks: 22 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: "z" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Inner-chain residues flagged as termini: ['pdbres=" G z 1 "'] Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 25} Link IDs: {'rna2p': 16, 'rna3p': 56} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Unusual residues: {' MG': 48} Classifications: {'undetermined': 48} Link IDs: {None: 47} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31967 SG CYS 0 110 165.628 86.453 173.447 1.00 25.26 S ATOM 31989 SG CYS 0 113 162.796 84.538 175.282 1.00 26.48 S ATOM 32069 SG CYS 0 123 161.929 87.538 173.519 1.00 10.16 S ATOM 32092 SG CYS 0 126 164.208 87.695 176.700 1.00 20.67 S ATOM 7322 SG CYS I 64 141.414 99.171 60.758 1.00 57.90 S ATOM 60618 SG CYS r 70 145.473 98.780 59.919 1.00 47.16 S ATOM 60639 SG CYS r 73 143.141 96.938 60.408 1.00 42.59 S ATOM 60933 SG CYS r 108 143.268 101.258 59.875 1.00 48.01 S Time building chain proxies: 36.36, per 1000 atoms: 0.39 Number of scatterers: 92769 At special positions: 0 Unit cell: (221.136, 223.304, 252.572, 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 282 16.00 P 1221 15.00 Mg 49 11.99 O 20074 8.00 N 16896 7.00 C 54245 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: 32.61 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " 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 0 110 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 73 " 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 " Number of angles added : 12 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15436 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 264 helices and 79 sheets defined 32.1% alpha, 11.9% beta 319 base pairs and 653 stacking pairs defined. Time for finding SS restraints: 31.17 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 Processing helix chain 'E' and resid 55 through 75 Proline residue: E 59 - end of helix 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 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' 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 251 through 254 No H-bonds generated for 'chain 'F' and resid 251 through 254' Processing helix chain 'F' and resid 263 through 274 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 146 removed outlier: 3.658A pdb=" N LEU H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) 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 90 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 168 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 73 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 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 135 through 138 No H-bonds generated for 'chain 'L' and resid 135 through 138' Processing helix chain 'M' and resid 11 through 18 removed outlier: 3.930A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) 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 169 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 190 through 194 Processing helix chain 'M' and resid 211 through 214 No H-bonds generated for 'chain 'M' and resid 211 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 257 Processing helix chain 'M' and resid 288 through 294 Processing helix chain 'N' and resid 99 through 111 Processing helix chain 'N' and resid 169 through 182 removed outlier: 5.013A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 207 Processing helix chain 'N' and resid 215 through 221 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 232 through 237 removed outlier: 3.621A pdb=" N LEU N 235 " --> pdb=" O PRO N 232 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS N 237 " --> pdb=" O ASP N 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 39 Processing helix chain 'O' and resid 46 through 65 removed outlier: 4.060A pdb=" N LEU O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 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 96 No H-bonds generated for 'chain 'O' and resid 93 through 96' Processing helix chain 'O' and resid 144 through 159 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: 4.415A 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 153 No H-bonds generated for 'chain 'P' and resid 150 through 153' Processing helix chain 'P' and resid 156 through 166 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 247 No H-bonds generated for 'chain 'Q' and resid 245 through 247' Processing helix chain 'Q' and resid 251 through 259 Processing helix chain 'Q' and resid 264 through 266 No H-bonds generated for 'chain 'Q' and resid 264 through 266' Processing helix chain 'Q' and resid 277 through 289 Processing helix chain 'R' and resid 17 through 27 removed outlier: 4.829A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 36 No H-bonds generated for 'chain 'R' and resid 34 through 36' Processing helix chain 'R' and resid 39 through 79 removed outlier: 4.554A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 91 Processing helix chain 'R' and resid 99 through 108 Processing helix chain 'R' and resid 110 through 132 Processing helix chain 'S' and resid 69 through 88 Processing helix chain 'T' and resid 50 through 56 removed outlier: 3.546A pdb=" N LYS T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 50 through 56' Processing helix chain 'T' and resid 87 through 93 Processing helix chain 'T' and resid 99 through 107 Processing helix chain 'T' and resid 112 through 130 Processing helix chain 'T' and resid 192 through 205 removed outlier: 3.784A pdb=" N SER T 205 " --> pdb=" O GLN T 201 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 60 Processing helix chain 'U' and resid 127 through 133 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 202 Processing helix chain 'W' and resid 111 through 119 removed outlier: 4.229A pdb=" N ARG W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 16 removed outlier: 4.068A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU X 16 " --> pdb=" O LYS X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 33 Processing helix chain 'X' and resid 73 through 76 Processing helix chain 'X' and resid 129 through 138 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: 4.555A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 208 through 219 Processing helix chain 'X' and resid 226 through 243 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 122 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 194 through 196 No H-bonds generated for 'chain 'Y' and resid 194 through 196' Processing helix chain 'Y' and resid 203 through 237 removed outlier: 4.337A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) 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 88 Processing helix chain 'Z' and resid 104 through 112 Processing helix chain '0' and resid 87 through 94 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 69 No H-bonds generated for 'chain '2' and resid 66 through 69' 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 160 Processing helix chain '3' and resid 164 through 166 No H-bonds generated for 'chain '3' and resid 164 through 166' Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '5' and resid 36 through 38 No H-bonds generated for 'chain '5' and resid 36 through 38' Processing helix chain '5' and resid 85 through 87 No H-bonds generated for 'chain '5' and resid 85 through 87' Processing helix chain '5' and resid 117 through 124 Processing helix chain '5' and resid 134 through 140 removed outlier: 3.971A 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 193 removed outlier: 3.912A pdb=" N CYS 5 177 " --> pdb=" O ARG 5 173 " (cutoff:3.500A) Proline residue: 5 178 - end of helix removed outlier: 5.437A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) Processing helix chain '5' and resid 196 through 199 Processing helix chain '5' and resid 242 through 250 removed outlier: 4.353A 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 409 through 419 Processing helix chain '6' and resid 55 through 65 Processing helix chain '6' and resid 74 through 78 Processing helix chain '6' and resid 100 through 115 Processing helix chain '6' and resid 117 through 125 Processing helix chain '6' and resid 132 through 142 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 295 No H-bonds generated for 'chain '6' and resid 293 through 295' Processing helix chain '6' and resid 300 through 306 Processing helix chain '6' and resid 325 through 333 Processing helix chain '6' and resid 363 through 367 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 100 No H-bonds generated for 'chain '7' and resid 97 through 100' 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: 3.906A pdb=" N SER 7 245 " --> pdb=" O GLU 7 241 " (cutoff:3.500A) removed outlier: 3.912A 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 162 Processing helix chain '9' and resid 28 through 33 Processing helix chain '9' and resid 54 through 56 No H-bonds generated for 'chain '9' and resid 54 through 56' Processing helix chain '9' and resid 88 through 104 Proline residue: 9 98 - end of helix Processing helix chain '9' and resid 115 through 117 No H-bonds generated for 'chain '9' and resid 115 through 117' 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 128 through 133 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 'b' and resid 140 through 142 No H-bonds generated for 'chain 'b' and resid 140 through 142' Processing helix chain 'c' and resid 36 through 52 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 78 Processing helix chain 'c' and resid 85 through 91 Processing helix chain 'c' and resid 95 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 164 through 172 Processing helix chain 'c' and resid 188 through 218 Proline residue: c 208 - end of helix Processing helix chain 'c' and resid 220 through 223 Processing helix chain 'c' and resid 237 through 247 Processing helix chain 'c' and resid 289 through 305 Processing helix chain 'd' and resid 53 through 63 Processing helix chain 'd' and resid 119 through 126 Processing helix chain 'd' and resid 137 through 151 Processing helix chain 'd' and resid 158 through 163 Processing helix chain 'e' and resid 65 through 81 removed outlier: 3.535A pdb=" N ARG e 81 " --> pdb=" O ILE e 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 87 through 91 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 260 through 263 No H-bonds generated for 'chain 'e' and resid 260 through 263' Processing helix chain 'e' and resid 267 through 270 No H-bonds generated for 'chain 'e' and resid 267 through 270' Processing helix chain 'e' and resid 272 through 275 Processing helix chain 'f' and resid 100 through 117 Processing helix chain 'f' and resid 164 through 177 Processing helix chain 'g' and resid 45 through 49 Processing helix chain 'g' and resid 117 through 132 Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 154 through 164 Processing helix chain 'h' and resid 64 through 77 removed outlier: 4.563A pdb=" N GLN h 67 " --> pdb=" O GLU h 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG h 69 " --> pdb=" O LEU h 66 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL h 77 " --> pdb=" O VAL h 74 " (cutoff:3.500A) 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 130 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 72 No H-bonds generated for 'chain 'i' and resid 70 through 72' Processing helix chain 'i' and resid 87 through 101 removed outlier: 6.370A pdb=" N SER i 100 " --> pdb=" O LYS i 96 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG i 101 " --> pdb=" O MET i 97 " (cutoff:3.500A) 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 104 Processing helix chain 'k' and resid 28 through 36 Processing helix chain 'k' and resid 40 through 45 removed outlier: 3.934A pdb=" N THR k 45 " --> pdb=" O LYS k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 84 through 95 Processing helix chain 'l' and resid 115 through 134 removed outlier: 4.195A pdb=" N LYS l 134 " --> pdb=" O ASN l 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 29 through 49 Processing helix chain 'o' and resid 56 through 59 No H-bonds generated for 'chain 'o' and resid 56 through 59' Processing helix chain 'o' and resid 64 through 80 removed outlier: 3.756A pdb=" N SER o 80 " --> pdb=" O ALA o 76 " (cutoff:3.500A) Processing helix chain 'o' and resid 88 through 98 removed outlier: 4.348A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.281A 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 56 through 59 No H-bonds generated for 'chain 'p' and resid 56 through 59' Processing helix chain 'p' and resid 113 through 122 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 176 through 188 Processing helix chain 'q' and resid 54 through 68 removed outlier: 3.521A pdb=" N ALA q 58 " --> pdb=" O PRO q 54 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA q 66 " --> pdb=" O ALA q 62 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ALA q 67 " --> pdb=" O ARG q 63 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER q 68 " --> pdb=" O TYR q 64 " (cutoff:3.500A) Processing helix chain 'q' and resid 72 through 74 No H-bonds generated for 'chain 'q' and resid 72 through 74' 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 168 through 187 removed outlier: 3.669A pdb=" N SER q 172 " --> pdb=" O VAL q 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 71 through 74 No H-bonds generated for 'chain 'r' and resid 71 through 74' Processing helix chain 'r' and resid 86 through 91 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 124 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 179 through 183 removed outlier: 4.305A pdb=" N ASP r 183 " --> pdb=" O LEU r 180 " (cutoff:3.500A) Processing helix chain 's' and resid 56 through 71 removed outlier: 3.576A pdb=" N LEU s 60 " --> pdb=" O LYS s 56 " (cutoff:3.500A) Processing helix chain 's' and resid 76 through 83 Processing helix chain 's' and resid 102 through 110 Processing helix chain 's' and resid 141 through 154 Processing helix chain 's' and resid 168 through 171 No H-bonds generated for 'chain 's' and resid 168 through 171' Processing helix chain 's' and resid 173 through 187 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 317 through 342 Processing helix chain 's' and resid 416 through 426 Processing helix chain 'u' and resid 94 through 103 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 192 No H-bonds generated for 'chain 'u' and resid 190 through 192' Processing helix chain 'v' and resid 6 through 20 Processing helix chain 'v' and resid 28 through 40 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 141 through 150 Processing sheet with id= A, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= B, first strand: chain 'D' and resid 162 through 165 removed outlier: 6.533A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE D 139 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= D, first strand: chain 'D' and resid 233 through 236 removed outlier: 6.379A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU D 216 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 265 through 268 removed outlier: 4.930A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU E 121 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET E 106 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL E 119 " --> pdb=" O MET E 106 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS E 117 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 175 through 181 removed outlier: 6.152A pdb=" N GLY E 148 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL E 129 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 214 through 216 removed outlier: 3.623A pdb=" N GLY E 214 " --> pdb=" O MET E 261 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 259 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 62 through 65 Processing sheet with id= I, first strand: chain 'F' and resid 187 through 190 removed outlier: 6.313A pdb=" N LEU F 259 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET F 190 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU F 261 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 111 through 114 Processing sheet with id= K, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.436A pdb=" N GLU H 57 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU H 82 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 122 through 124 Processing sheet with id= M, first strand: chain 'I' and resid 179 through 181 Processing sheet with id= N, first strand: chain 'J' and resid 110 through 113 Processing sheet with id= O, first strand: chain 'K' and resid 56 through 60 removed outlier: 6.482A pdb=" N GLU K 143 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ASP K 22 " --> pdb=" O GLU K 143 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU K 145 " --> pdb=" O ASP K 22 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 76 through 80 Processing sheet with id= Q, first strand: chain 'L' and resid 105 through 107 removed outlier: 3.811A pdb=" N ILE L 77 " --> pdb=" O GLN L 80 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS L 59 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA L 76 " --> pdb=" O CYS L 57 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N CYS L 57 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'M' and resid 95 through 97 removed outlier: 6.084A pdb=" N GLN M 139 " --> pdb=" O LEU M 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'M' and resid 153 through 156 removed outlier: 6.682A pdb=" N VAL M 173 " --> pdb=" O ILE M 154 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL M 156 " --> pdb=" O VAL M 173 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N THR M 175 " --> pdb=" O VAL M 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'M' and resid 274 through 276 Processing sheet with id= U, first strand: chain 'N' and resid 87 through 92 Processing sheet with id= V, first strand: chain 'N' and resid 95 through 97 Processing sheet with id= W, first strand: chain 'N' and resid 118 through 122 Processing sheet with id= X, first strand: chain 'N' and resid 129 through 132 Processing sheet with id= Y, first strand: chain 'O' and resid 42 through 45 Processing sheet with id= Z, first strand: chain 'P' and resid 79 through 85 removed outlier: 6.155A pdb=" N HIS P 96 " --> pdb=" O VAL P 101 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL P 101 " --> pdb=" O HIS P 96 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 173 through 178 removed outlier: 6.854A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE Q 150 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 104 through 109 removed outlier: 6.091A pdb=" N HIS S 100 " --> pdb=" O VAL S 133 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL S 133 " --> pdb=" O HIS S 100 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'S' and resid 112 through 116 Processing sheet with id= AD, first strand: chain 'S' and resid 127 through 129 removed outlier: 6.160A pdb=" N THR S 159 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE S 195 " --> pdb=" O THR S 159 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'S' and resid 169 through 175 Processing sheet with id= AF, first strand: chain 'T' and resid 72 through 77 removed outlier: 6.538A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE T 142 " --> pdb=" O VAL T 179 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 153 through 155 Processing sheet with id= AH, first strand: chain 'U' and resid 27 through 29 removed outlier: 3.679A pdb=" N GLN U 27 " --> pdb=" O ARG U 43 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'V' and resid 120 through 122 removed outlier: 7.077A pdb=" N VAL V 87 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL V 79 " --> pdb=" O TRP V 85 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TRP V 85 " --> pdb=" O VAL V 79 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'V' and resid 93 through 98 Processing sheet with id= AK, first strand: chain 'V' and resid 133 through 136 Processing sheet with id= AL, first strand: chain 'W' and resid 81 through 83 Processing sheet with id= AM, first strand: chain 'W' and resid 95 through 103 Processing sheet with id= AN, first strand: chain 'X' and resid 50 through 52 Processing sheet with id= AO, first strand: chain 'X' and resid 86 through 91 Processing sheet with id= AP, first strand: chain 'X' and resid 110 through 116 Processing sheet with id= AQ, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id= AR, first strand: chain 'Z' and resid 97 through 101 Processing sheet with id= AS, first strand: chain '0' and resid 107 through 109 Processing sheet with id= AT, first strand: chain '0' and resid 156 through 159 removed outlier: 5.955A pdb=" N ARG 0 173 " --> pdb=" O VAL 0 157 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU 0 159 " --> pdb=" O ARG 0 173 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE 0 175 " --> pdb=" O LEU 0 159 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain '1' and resid 29 through 35 Processing sheet with id= AV, first strand: chain '3' and resid 115 through 117 Processing sheet with id= AW, first strand: chain '5' and resid 266 through 268 Processing sheet with id= AX, first strand: chain '5' and resid 126 through 130 removed outlier: 6.712A pdb=" N ASN 5 372 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE 5 129 " --> pdb=" O ASN 5 372 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA 5 374 " --> pdb=" O ILE 5 129 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N VAL 5 341 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS 5 289 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '5' and resid 385 through 387 Processing sheet with id= AZ, first strand: chain '6' and resid 203 through 205 Processing sheet with id= BA, first strand: chain '6' and resid 249 through 252 removed outlier: 6.888A pdb=" N LEU 6 236 " --> pdb=" O THR 6 251 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR 6 232 " --> pdb=" O SER 6 220 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU 6 236 " --> pdb=" O LEU 6 216 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU 6 216 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR 6 238 " --> pdb=" O TRP 6 214 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP 6 214 " --> pdb=" O THR 6 238 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS 6 274 " --> pdb=" O PRO 6 313 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '7' and resid 77 through 82 removed outlier: 6.966A pdb=" N CYS 7 123 " --> pdb=" O LYS 7 68 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '7' and resid 111 through 114 removed outlier: 6.473A pdb=" N LEU 7 128 " --> pdb=" O ILE 7 104 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain '7' and resid 164 through 168 removed outlier: 7.030A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL 7 300 " --> pdb=" O VAL 7 280 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL 7 280 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '7' and resid 217 through 222 removed outlier: 4.663A pdb=" N LYS 7 253 " --> pdb=" O SER 7 264 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER 7 264 " --> pdb=" O LYS 7 253 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain '9' and resid 42 through 45 Processing sheet with id= BG, first strand: chain 'a' and resid 48 through 51 Processing sheet with id= BH, first strand: chain 'b' and resid 28 through 33 removed outlier: 6.312A pdb=" N VAL b 62 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE b 31 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR b 64 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL b 33 " --> pdb=" O TYR b 64 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN b 66 " --> pdb=" O VAL b 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'b' and resid 74 through 78 Processing sheet with id= BJ, first strand: chain 'c' and resid 254 through 261 removed outlier: 6.699A pdb=" N PHE c 271 " --> pdb=" O THR c 258 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN c 260 " --> pdb=" O LEU c 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU c 269 " --> pdb=" O GLN c 260 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N CYS c 276 " --> pdb=" O LEU c 280 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU c 280 " --> pdb=" O CYS c 276 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'd' and resid 184 through 186 removed outlier: 5.756A pdb=" N GLU d 249 " --> pdb=" O MET d 261 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N MET d 261 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'd' and resid 193 through 198 removed outlier: 6.771A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL d 197 " --> pdb=" O GLN d 211 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN d 211 " --> pdb=" O VAL d 197 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'e' and resid 175 through 177 removed outlier: 7.489A pdb=" N GLY e 228 " --> pdb=" O ARG e 46 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU e 48 " --> pdb=" O GLY e 228 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LYS e 230 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA e 50 " --> pdb=" O LYS e 230 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE e 232 " --> pdb=" O ALA e 50 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS e 52 " --> pdb=" O PHE e 232 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE e 234 " --> pdb=" O CYS e 52 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'e' and resid 161 through 164 Processing sheet with id= BO, first strand: chain 'e' and resid 199 through 204 removed outlier: 6.071A pdb=" N LYS e 203 " --> pdb=" O LEU e 238 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU e 238 " --> pdb=" O LYS e 203 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= BQ, first strand: chain 'g' and resid 84 through 86 Processing sheet with id= BR, first strand: chain 'g' and resid 96 through 101 Processing sheet with id= BS, first strand: chain 'k' and resid 51 through 55 removed outlier: 6.309A pdb=" N VAL k 16 " --> pdb=" O ILE k 52 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASP k 54 " --> pdb=" O VAL k 16 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL k 18 " --> pdb=" O ASP k 54 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'm' and resid 52 through 57 Processing sheet with id= BU, first strand: chain 'p' and resid 77 through 81 Processing sheet with id= BV, first strand: chain 'r' and resid 36 through 41 Processing sheet with id= BW, first strand: chain 's' and resid 90 through 94 removed outlier: 6.814A pdb=" N ARG s 230 " --> pdb=" O TYR s 91 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL s 93 " --> pdb=" O ARG s 230 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLN s 232 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 's' and resid 112 through 116 removed outlier: 7.039A pdb=" N ASN s 391 " --> pdb=" O VAL s 113 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU s 115 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS s 393 " --> pdb=" O LEU s 115 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 's' and resid 199 through 202 removed outlier: 5.424A pdb=" N ILE s 243 " --> pdb=" O GLY s 295 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY s 295 " --> pdb=" O ILE s 243 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 's' and resid 214 through 216 Processing sheet with id= CA, first strand: chain 'u' and resid 108 through 113 2137 hydrogen bonds defined for protein. 6051 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 773 hydrogen bonds 1334 hydrogen bond angles 0 basepair planarities 319 basepair parallelities 653 stacking parallelities Total time for adding SS restraints: 43.22 Time building geometry restraints manager: 35.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 12401 1.31 - 1.44: 33314 1.44 - 1.57: 48797 1.57 - 1.69: 2415 1.69 - 1.82: 449 Bond restraints: 97376 Sorted by residual: bond pdb=" C GLN 7 290 " pdb=" N PRO 7 291 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.20e-02 6.94e+03 1.32e+01 bond pdb=" CA ARG U 43 " pdb=" CB ARG U 43 " ideal model delta sigma weight residual 1.529 1.481 0.048 1.38e-02 5.25e+03 1.20e+01 bond pdb=" CA ARG H 75 " pdb=" C ARG H 75 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.37e-02 5.33e+03 8.55e+00 bond pdb=" N3 U A 340 " pdb=" C4 U A 340 " ideal model delta sigma weight residual 1.380 1.323 0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C LYS Q 225 " pdb=" N PRO Q 226 " ideal model delta sigma weight residual 1.331 1.364 -0.032 1.21e-02 6.83e+03 7.14e+00 ... (remaining 97371 not shown) Histogram of bond angle deviations from ideal: 93.31 - 102.38: 1770 102.38 - 111.44: 48047 111.44 - 120.51: 53119 120.51 - 129.57: 33163 129.57 - 138.64: 1310 Bond angle restraints: 137409 Sorted by residual: angle pdb=" CA ARG 6 52 " pdb=" CB ARG 6 52 " pdb=" CG ARG 6 52 " ideal model delta sigma weight residual 114.10 128.14 -14.04 2.00e+00 2.50e-01 4.93e+01 angle pdb=" C ARG 6 52 " pdb=" CA ARG 6 52 " pdb=" CB ARG 6 52 " ideal model delta sigma weight residual 110.72 121.59 -10.87 1.69e+00 3.50e-01 4.14e+01 angle pdb=" C ARG g 76 " pdb=" N ASP g 77 " pdb=" CA ASP g 77 " ideal model delta sigma weight residual 122.06 133.08 -11.02 1.78e+00 3.16e-01 3.83e+01 angle pdb=" CA LYS 9 69 " pdb=" CB LYS 9 69 " pdb=" CG LYS 9 69 " ideal model delta sigma weight residual 114.10 126.36 -12.26 2.00e+00 2.50e-01 3.76e+01 angle pdb=" C GLU 8 148 " pdb=" N GLU 8 149 " pdb=" CA GLU 8 149 " ideal model delta sigma weight residual 122.54 112.44 10.10 1.65e+00 3.67e-01 3.75e+01 ... (remaining 137404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 56453 35.97 - 71.94: 2992 71.94 - 107.91: 430 107.91 - 143.88: 7 143.88 - 179.85: 31 Dihedral angle restraints: 59913 sinusoidal: 36085 harmonic: 23828 Sorted by residual: dihedral pdb=" C4' U A1438 " pdb=" C3' U A1438 " pdb=" C2' U A1438 " pdb=" C1' U A1438 " ideal model delta sinusoidal sigma weight residual -35.00 29.90 -64.90 1 8.00e+00 1.56e-02 8.64e+01 dihedral pdb=" O4' C A 143 " pdb=" C1' C A 143 " pdb=" N1 C A 143 " pdb=" C2 C A 143 " ideal model delta sinusoidal sigma weight residual 200.00 22.85 177.15 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 709 " pdb=" C1' C A 709 " pdb=" N1 C A 709 " pdb=" C2 C A 709 " ideal model delta sinusoidal sigma weight residual 200.00 24.39 175.61 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 59910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 14445 0.087 - 0.174: 1417 0.174 - 0.262: 94 0.262 - 0.349: 9 0.349 - 0.436: 7 Chirality restraints: 15972 Sorted by residual: 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 2.21 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" C3' A A 787 " pdb=" C4' A A 787 " pdb=" O3' A A 787 " pdb=" C2' A A 787 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CB ILE u 159 " pdb=" CA ILE u 159 " pdb=" CG1 ILE u 159 " pdb=" CG2 ILE u 159 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 15969 not shown) Planarity restraints: 13135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP 6 139 " -0.046 2.00e-02 2.50e+03 3.57e-02 3.19e+01 pdb=" CG TRP 6 139 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP 6 139 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP 6 139 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP 6 139 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP 6 139 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP 6 139 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP 6 139 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP 6 139 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP 6 139 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 8 121 " -0.028 2.00e-02 2.50e+03 3.41e-02 2.90e+01 pdb=" CG TRP 8 121 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP 8 121 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP 8 121 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP 8 121 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP 8 121 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP 8 121 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP 8 121 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP 8 121 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP 8 121 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 6 235 " -0.040 2.00e-02 2.50e+03 3.32e-02 2.76e+01 pdb=" CG TRP 6 235 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP 6 235 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP 6 235 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP 6 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP 6 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP 6 235 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP 6 235 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP 6 235 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP 6 235 " -0.001 2.00e-02 2.50e+03 ... (remaining 13132 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 987 2.58 - 3.16: 69527 3.16 - 3.74: 160700 3.74 - 4.32: 219378 4.32 - 4.90: 333488 Nonbonded interactions: 784080 Sorted by model distance: nonbonded pdb=" OP1 C A1245 " pdb="MG MG A1636 " model vdw 1.998 2.170 nonbonded pdb=" OP1 U A 365 " pdb="MG MG A1636 " model vdw 2.057 2.170 nonbonded pdb=" OP1 A A 623 " pdb="MG MG A1639 " model vdw 2.073 2.170 nonbonded pdb=" OP1 C A 366 " pdb="MG MG A1629 " model vdw 2.074 2.170 nonbonded pdb=" OP2 G A 106 " pdb="MG MG A1606 " model vdw 2.075 2.170 ... (remaining 784075 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: 2.060 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: 0.080 Extract box with map and model: 13.640 Check model and map are aligned: 1.060 Set scattering table: 0.660 Process input model: 228.940 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.250 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:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 251.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.006 0.117 97376 Z= 0.402 Angle : 0.993 16.113 137409 Z= 0.532 Chirality : 0.052 0.436 15972 Planarity : 0.007 0.113 13135 Dihedral : 19.444 179.848 44477 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 0.03 % Allowed : 0.58 % Favored : 99.39 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.78 (0.09), residues: 8025 helix: -0.92 (0.09), residues: 2688 sheet: -1.19 (0.15), residues: 1014 loop : -1.30 (0.09), residues: 4323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.003 TRP 6 139 HIS 0.026 0.002 HIS s 423 PHE 0.067 0.003 PHE 9 128 TYR 0.031 0.003 TYR e 84 ARG 0.035 0.001 ARG O 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1566 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1564 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 63 GLN cc_start: 0.6355 (mt0) cc_final: 0.5675 (mt0) REVERT: F 162 TYR cc_start: 0.9112 (t80) cc_final: 0.8758 (t80) REVERT: F 184 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8521 (mm-40) REVERT: I 152 MET cc_start: 0.2008 (tpp) cc_final: -0.0360 (mpp) REVERT: J 30 MET cc_start: 0.5558 (mmm) cc_final: 0.4935 (mmp) REVERT: K 61 ASN cc_start: 0.8063 (m-40) cc_final: 0.7821 (m110) REVERT: M 30 ASN cc_start: 0.8392 (t0) cc_final: 0.7973 (t0) REVERT: M 106 ASP cc_start: 0.7900 (t0) cc_final: 0.7503 (t0) REVERT: M 253 PHE cc_start: 0.8205 (t80) cc_final: 0.8001 (t80) REVERT: N 140 MET cc_start: 0.6342 (ttm) cc_final: 0.5818 (ppp) REVERT: P 158 MET cc_start: 0.7840 (mpp) cc_final: 0.7614 (mmt) REVERT: Q 275 THR cc_start: 0.8433 (m) cc_final: 0.8146 (m) REVERT: U 81 ASP cc_start: 0.6995 (m-30) cc_final: 0.6760 (m-30) REVERT: W 49 ARG cc_start: 0.7919 (mtm180) cc_final: 0.7573 (mmm-85) REVERT: W 60 TYR cc_start: 0.8990 (t80) cc_final: 0.8777 (t80) REVERT: W 92 LEU cc_start: 0.9038 (mt) cc_final: 0.8412 (mt) REVERT: X 75 SER cc_start: 0.9022 (t) cc_final: 0.8706 (t) REVERT: X 129 MET cc_start: 0.7650 (mmm) cc_final: 0.7332 (mmm) REVERT: Y 133 ASP cc_start: 0.8116 (p0) cc_final: 0.7823 (p0) REVERT: Z 87 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7648 (tttt) REVERT: 1 20 MET cc_start: 0.8046 (tpt) cc_final: 0.7839 (tpt) REVERT: 5 309 LEU cc_start: 0.8165 (tp) cc_final: 0.7929 (tp) REVERT: 5 331 ASN cc_start: 0.8021 (p0) cc_final: 0.7774 (p0) REVERT: b 106 ASP cc_start: 0.8101 (m-30) cc_final: 0.7630 (m-30) REVERT: c 287 GLU cc_start: 0.7697 (pm20) cc_final: 0.7351 (pm20) REVERT: d 160 LEU cc_start: 0.8702 (mt) cc_final: 0.8219 (tt) REVERT: d 217 HIS cc_start: 0.7192 (t70) cc_final: 0.6953 (t70) REVERT: d 281 MET cc_start: 0.8471 (tmm) cc_final: 0.7889 (ttt) REVERT: e 70 MET cc_start: 0.5284 (ppp) cc_final: 0.4837 (ppp) REVERT: e 243 PHE cc_start: 0.1374 (t80) cc_final: 0.1048 (m-80) REVERT: h 61 THR cc_start: 0.9197 (t) cc_final: 0.8928 (p) REVERT: i 72 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7024 (mm-30) REVERT: i 115 ARG cc_start: 0.7798 (ttm170) cc_final: 0.7547 (mtm-85) REVERT: j 60 MET cc_start: 0.8203 (mtm) cc_final: 0.7972 (ptp) REVERT: j 71 GLU cc_start: 0.7713 (tp30) cc_final: 0.7370 (tp30) REVERT: o 99 LYS cc_start: 0.8525 (ttmm) cc_final: 0.8218 (mtpt) outliers start: 2 outliers final: 1 residues processed: 1565 average time/residue: 0.8924 time to fit residues: 2346.5387 Evaluate side-chains 1264 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1262 time to evaluate : 6.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain S residue 118 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 914 random chunks: chunk 771 optimal weight: 20.0000 chunk 692 optimal weight: 0.0030 chunk 384 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 467 optimal weight: 0.0870 chunk 370 optimal weight: 0.7980 chunk 716 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 435 optimal weight: 8.9990 chunk 533 optimal weight: 2.9990 chunk 830 optimal weight: 10.0000 overall best weight: 0.7570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 227 GLN E 125 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN K 26 GLN K 147 GLN L 48 ASN L 52 HIS L 113 ASN N 173 GLN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 HIS P 162 GLN Q 139 GLN Q 175 GLN ** S 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 GLN V 73 GLN V 82 GLN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN ** Y 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN 2 51 ASN 6 174 HIS 6 266 HIS 7 277 GLN 9 52 GLN 9 123 GLN c 193 GLN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 92 ASN ** f 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 158 GLN f 189 HIS ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 63 GLN o 58 GLN p 53 GLN r 79 HIS r 91 GLN ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 97376 Z= 0.171 Angle : 0.621 10.689 137409 Z= 0.316 Chirality : 0.040 0.259 15972 Planarity : 0.005 0.075 13135 Dihedral : 20.385 179.426 27201 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 1.19 % Allowed : 9.88 % Favored : 88.92 % 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: -1.09 (0.09), residues: 8025 helix: -0.04 (0.10), residues: 2670 sheet: -1.07 (0.15), residues: 1037 loop : -1.02 (0.09), residues: 4318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP 6 139 HIS 0.009 0.001 HIS s 423 PHE 0.065 0.001 PHE e 128 TYR 0.023 0.001 TYR d 245 ARG 0.014 0.000 ARG W 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1498 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1412 time to evaluate : 6.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 162 TYR cc_start: 0.9123 (t80) cc_final: 0.8863 (t80) REVERT: F 179 THR cc_start: 0.9040 (m) cc_final: 0.8682 (t) REVERT: I 152 MET cc_start: 0.1781 (tpp) cc_final: -0.0576 (mpp) REVERT: J 30 MET cc_start: 0.5722 (mmm) cc_final: 0.5386 (mmp) REVERT: M 186 ILE cc_start: 0.9318 (mp) cc_final: 0.9093 (mp) REVERT: M 253 PHE cc_start: 0.8304 (t80) cc_final: 0.8031 (t80) REVERT: N 140 MET cc_start: 0.6052 (ttm) cc_final: 0.5494 (ppp) REVERT: R 32 ARG cc_start: 0.7838 (ttt90) cc_final: 0.7409 (ttm110) REVERT: T 130 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7484 (ttp80) REVERT: T 198 GLU cc_start: 0.6714 (tt0) cc_final: 0.6396 (mt-10) REVERT: V 109 ILE cc_start: 0.8787 (tp) cc_final: 0.8536 (tt) REVERT: X 75 SER cc_start: 0.8965 (t) cc_final: 0.8707 (t) REVERT: X 129 MET cc_start: 0.7495 (mmm) cc_final: 0.7260 (mmm) REVERT: Y 143 ASP cc_start: 0.7843 (t0) cc_final: 0.7569 (t0) REVERT: Y 157 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7944 (mm110) REVERT: Z 87 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7860 (tttt) REVERT: 3 175 ASP cc_start: 0.6696 (t0) cc_final: 0.6402 (t0) REVERT: 5 137 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8267 (mp) REVERT: 5 309 LEU cc_start: 0.8315 (tp) cc_final: 0.8103 (tp) REVERT: 6 51 TYR cc_start: 0.7228 (m-80) cc_final: 0.6733 (m-80) REVERT: 7 66 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7240 (tm-30) REVERT: 9 90 GLN cc_start: 0.7596 (tm-30) cc_final: 0.7240 (tm-30) REVERT: 9 133 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.8070 (mtm110) REVERT: c 287 GLU cc_start: 0.7651 (pm20) cc_final: 0.7294 (pm20) REVERT: d 172 MET cc_start: 0.7859 (tpp) cc_final: 0.7596 (ttm) REVERT: d 217 HIS cc_start: 0.7203 (t70) cc_final: 0.6940 (t70) REVERT: e 243 PHE cc_start: 0.1334 (t80) cc_final: 0.0989 (m-80) REVERT: g 45 TYR cc_start: 0.8385 (t80) cc_final: 0.7970 (t80) REVERT: g 141 ASN cc_start: 0.8125 (t0) cc_final: 0.7876 (t0) REVERT: h 61 THR cc_start: 0.9144 (t) cc_final: 0.8828 (p) REVERT: j 71 GLU cc_start: 0.7600 (tp30) cc_final: 0.7384 (tp30) REVERT: o 99 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8293 (mtpt) REVERT: u 118 MET cc_start: 0.5995 (mmt) cc_final: 0.5767 (mmp) REVERT: u 135 LEU cc_start: 0.6623 (mt) cc_final: 0.6415 (mp) REVERT: u 142 VAL cc_start: 0.7405 (p) cc_final: 0.4762 (m) outliers start: 86 outliers final: 48 residues processed: 1439 average time/residue: 0.9411 time to fit residues: 2289.5989 Evaluate side-chains 1311 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1262 time to evaluate : 6.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 235 LEU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 5 residue 104 CYS Chi-restraints excluded: chain 5 residue 137 LEU Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 235 TRP Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 193 MET Chi-restraints excluded: chain 7 residue 241 GLU Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 9 residue 101 GLU Chi-restraints excluded: chain c residue 199 ILE Chi-restraints excluded: chain e residue 121 GLU Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain p residue 181 GLU Chi-restraints excluded: chain r residue 185 VAL Chi-restraints excluded: chain s residue 360 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 914 random chunks: chunk 461 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 690 optimal weight: 0.0980 chunk 565 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 831 optimal weight: 5.9990 chunk 898 optimal weight: 20.0000 chunk 740 optimal weight: 5.9990 chunk 824 optimal weight: 4.9990 chunk 283 optimal weight: 0.9980 chunk 667 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN K 26 GLN L 33 GLN L 48 ASN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 HIS ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 ASN T 62 GLN T 173 HIS ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN W 70 GLN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 51 ASN 6 174 HIS ** 7 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 277 GLN ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 GLN b 135 ASN ** c 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 175 GLN ** f 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 112 ASN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 135 GLN j 99 GLN k 19 GLN o 33 GLN s 87 GLN ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 97376 Z= 0.368 Angle : 0.680 11.613 137409 Z= 0.342 Chirality : 0.043 0.321 15972 Planarity : 0.005 0.077 13135 Dihedral : 20.240 179.465 27196 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.17 % Favored : 94.82 % Rotamer: Outliers : 2.47 % Allowed : 12.60 % Favored : 84.93 % 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: -0.90 (0.09), residues: 8025 helix: 0.23 (0.10), residues: 2704 sheet: -1.08 (0.15), residues: 1045 loop : -0.97 (0.09), residues: 4276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP 6 139 HIS 0.009 0.001 HIS T 195 PHE 0.042 0.002 PHE N 169 TYR 0.033 0.002 TYR u 146 ARG 0.011 0.001 ARG Y 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1304 time to evaluate : 6.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 GLU cc_start: 0.6943 (tp30) cc_final: 0.6724 (tp30) REVERT: F 162 TYR cc_start: 0.9066 (t80) cc_final: 0.8770 (t80) REVERT: J 30 MET cc_start: 0.5689 (mmm) cc_final: 0.5460 (mmp) REVERT: K 61 ASN cc_start: 0.8146 (m110) cc_final: 0.7919 (m-40) REVERT: M 39 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6275 (ptm-80) REVERT: M 253 PHE cc_start: 0.8451 (t80) cc_final: 0.8146 (t80) REVERT: P 97 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7698 (tm-30) REVERT: P 162 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8278 (mp10) REVERT: V 57 PHE cc_start: 0.8674 (m-80) cc_final: 0.8076 (m-80) REVERT: V 109 ILE cc_start: 0.8644 (tp) cc_final: 0.8388 (tt) REVERT: X 75 SER cc_start: 0.8946 (t) cc_final: 0.8698 (t) REVERT: Y 133 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7916 (p0) REVERT: Y 137 ASP cc_start: 0.7870 (m-30) cc_final: 0.7651 (m-30) REVERT: Y 143 ASP cc_start: 0.7980 (t0) cc_final: 0.7730 (t0) REVERT: Z 87 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7895 (tttt) REVERT: 0 82 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7403 (ttmt) REVERT: 1 58 GLU cc_start: 0.7445 (pt0) cc_final: 0.7186 (pt0) REVERT: 5 137 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8308 (mp) REVERT: 7 85 ILE cc_start: 0.8652 (mm) cc_final: 0.8398 (mm) REVERT: 9 90 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7189 (tm-30) REVERT: b 106 ASP cc_start: 0.8045 (m-30) cc_final: 0.7530 (m-30) REVERT: d 57 MET cc_start: 0.4570 (tpp) cc_final: 0.2875 (tmm) REVERT: d 172 MET cc_start: 0.7892 (tpp) cc_final: 0.7597 (ttm) REVERT: g 45 TYR cc_start: 0.8486 (t80) cc_final: 0.7997 (t80) REVERT: g 141 ASN cc_start: 0.8260 (t0) cc_final: 0.7992 (t0) REVERT: h 61 THR cc_start: 0.9193 (t) cc_final: 0.8840 (p) REVERT: j 71 GLU cc_start: 0.7633 (tp30) cc_final: 0.7432 (tp30) REVERT: o 28 SER cc_start: 0.8522 (p) cc_final: 0.8181 (p) REVERT: o 47 TYR cc_start: 0.9144 (t80) cc_final: 0.8931 (t80) REVERT: p 128 ASN cc_start: 0.8059 (t0) cc_final: 0.7705 (t0) REVERT: q 82 LEU cc_start: 0.9377 (tt) cc_final: 0.9162 (tp) REVERT: s 86 MET cc_start: 0.8047 (mtp) cc_final: 0.7740 (mtm) outliers start: 178 outliers final: 125 residues processed: 1398 average time/residue: 0.9629 time to fit residues: 2302.0598 Evaluate side-chains 1364 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1235 time to evaluate : 7.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain P residue 121 ASN Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 247 LEU Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 133 ASP Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Y residue 235 LEU Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain 0 residue 82 LYS Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 2 residue 51 ASN Chi-restraints excluded: chain 2 residue 72 THR Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 5 residue 104 CYS Chi-restraints excluded: chain 5 residue 137 LEU Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 235 TRP Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 153 VAL Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 193 MET Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 64 ASP Chi-restraints excluded: chain 9 residue 75 SER Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 94 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain c residue 86 ASP Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 205 SER Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 208 VAL Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 19 GLN Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain p residue 181 GLU Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain r residue 185 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 145 VAL Chi-restraints excluded: chain s residue 181 VAL Chi-restraints excluded: chain s residue 284 VAL Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 381 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 914 random chunks: chunk 821 optimal weight: 3.9990 chunk 625 optimal weight: 20.0000 chunk 431 optimal weight: 0.0980 chunk 92 optimal weight: 20.0000 chunk 396 optimal weight: 0.9980 chunk 558 optimal weight: 6.9990 chunk 834 optimal weight: 4.9990 chunk 883 optimal weight: 10.0000 chunk 435 optimal weight: 10.0000 chunk 790 optimal weight: 10.0000 chunk 238 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 HIS ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 GLN U 23 ASN V 82 GLN W 70 GLN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 277 GLN 9 52 GLN 9 123 GLN b 24 GLN c 193 GLN c 310 ASN f 112 ASN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 ASN h 110 HIS h 135 GLN s 191 HIS ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 97376 Z= 0.377 Angle : 0.671 12.534 137409 Z= 0.337 Chirality : 0.043 0.318 15972 Planarity : 0.005 0.077 13135 Dihedral : 20.208 179.978 27196 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.12 % Favored : 94.87 % Rotamer: Outliers : 2.86 % Allowed : 14.85 % Favored : 82.29 % 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: 8025 helix: 0.39 (0.10), residues: 2697 sheet: -1.05 (0.15), residues: 1060 loop : -0.93 (0.09), residues: 4268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 6 139 HIS 0.007 0.001 HIS d 262 PHE 0.027 0.002 PHE 7 179 TYR 0.022 0.002 TYR 5 176 ARG 0.008 0.001 ARG S 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1281 time to evaluate : 7.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 162 TYR cc_start: 0.9088 (t80) cc_final: 0.8828 (t80) REVERT: J 30 MET cc_start: 0.5960 (mmm) cc_final: 0.5580 (mmp) REVERT: K 61 ASN cc_start: 0.8163 (m110) cc_final: 0.7922 (m-40) REVERT: M 155 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6497 (tm-30) REVERT: M 253 PHE cc_start: 0.8449 (t80) cc_final: 0.8126 (t80) REVERT: O 30 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8299 (ptp-170) REVERT: P 97 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7730 (tm-30) REVERT: P 151 TRP cc_start: 0.8336 (p90) cc_final: 0.8082 (p90) REVERT: V 57 PHE cc_start: 0.8682 (m-80) cc_final: 0.8452 (m-80) REVERT: V 109 ILE cc_start: 0.8756 (tp) cc_final: 0.8491 (tt) REVERT: W 70 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8747 (pm20) REVERT: X 75 SER cc_start: 0.8908 (t) cc_final: 0.8689 (t) REVERT: Y 133 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7913 (p0) REVERT: Y 143 ASP cc_start: 0.8036 (t0) cc_final: 0.7800 (t0) REVERT: Z 87 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7863 (tttt) REVERT: 0 82 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7343 (ttmt) REVERT: 5 137 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8315 (mp) REVERT: 9 94 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6573 (pt0) REVERT: 9 115 GLU cc_start: 0.7345 (pp20) cc_final: 0.7062 (pp20) REVERT: b 106 ASP cc_start: 0.8038 (m-30) cc_final: 0.7591 (m-30) REVERT: d 57 MET cc_start: 0.4560 (tpp) cc_final: 0.2854 (tmm) REVERT: g 45 TYR cc_start: 0.8533 (t80) cc_final: 0.8014 (t80) REVERT: h 61 THR cc_start: 0.9189 (t) cc_final: 0.8802 (p) REVERT: o 28 SER cc_start: 0.8506 (p) cc_final: 0.8165 (p) REVERT: o 47 TYR cc_start: 0.9155 (t80) cc_final: 0.8940 (t80) REVERT: o 99 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8283 (mtpt) REVERT: p 128 ASN cc_start: 0.8018 (t0) cc_final: 0.7681 (t0) REVERT: q 82 LEU cc_start: 0.9381 (tt) cc_final: 0.9158 (tp) REVERT: s 86 MET cc_start: 0.8070 (mtp) cc_final: 0.7760 (mtm) outliers start: 206 outliers final: 145 residues processed: 1393 average time/residue: 0.9579 time to fit residues: 2275.7587 Evaluate side-chains 1388 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1236 time to evaluate : 6.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 99 LEU 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 285 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 30 ARG Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 121 ASN Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 198 GLU Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain W residue 70 GLN Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain Y residue 133 ASP Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Y residue 235 LEU Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain 0 residue 82 LYS Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 2 residue 72 THR Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 104 CYS Chi-restraints excluded: chain 5 residue 137 LEU Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 208 THR Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 309 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 182 ASP Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 6 residue 235 TRP Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 153 VAL Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 193 MET Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 94 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain c residue 86 ASP Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 205 SER Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 208 VAL Chi-restraints excluded: chain e residue 121 GLU Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain r residue 119 VAL Chi-restraints excluded: chain r residue 185 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 145 VAL Chi-restraints excluded: chain s residue 181 VAL Chi-restraints excluded: chain s residue 284 VAL Chi-restraints excluded: chain s residue 336 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 381 THR Chi-restraints excluded: chain s residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 914 random chunks: chunk 735 optimal weight: 0.3980 chunk 501 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 657 optimal weight: 0.5980 chunk 364 optimal weight: 3.9990 chunk 753 optimal weight: 0.9990 chunk 610 optimal weight: 50.0000 chunk 1 optimal weight: 0.8980 chunk 451 optimal weight: 3.9990 chunk 792 optimal weight: 7.9990 chunk 222 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 GLN F 103 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 HIS Q 153 ASN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN T 173 HIS ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 255 HIS 7 277 GLN 9 123 GLN ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 112 ASN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 135 GLN ** s 319 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: 0.7616 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 97376 Z= 0.161 Angle : 0.583 10.602 137409 Z= 0.293 Chirality : 0.039 0.261 15972 Planarity : 0.004 0.065 13135 Dihedral : 20.108 179.678 27196 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.31 % Favored : 95.68 % Rotamer: Outliers : 2.22 % Allowed : 17.13 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.09), residues: 8025 helix: 0.64 (0.10), residues: 2702 sheet: -0.99 (0.15), residues: 1073 loop : -0.76 (0.09), residues: 4250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP 6 139 HIS 0.007 0.001 HIS E 197 PHE 0.024 0.001 PHE N 169 TYR 0.017 0.001 TYR e 84 ARG 0.010 0.000 ARG r 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1319 time to evaluate : 7.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 292 MET cc_start: 0.6192 (tpt) cc_final: 0.5665 (mmm) REVERT: E 139 ASN cc_start: 0.3195 (OUTLIER) cc_final: 0.2490 (m-40) REVERT: F 101 MET cc_start: 0.7804 (mmm) cc_final: 0.7430 (mmm) REVERT: F 179 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8795 (t) REVERT: F 274 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8755 (mm) REVERT: I 53 TYR cc_start: 0.8270 (t80) cc_final: 0.8037 (t80) REVERT: K 61 ASN cc_start: 0.7985 (m110) cc_final: 0.7740 (m-40) REVERT: M 30 ASN cc_start: 0.8318 (t0) cc_final: 0.8001 (t0) REVERT: M 39 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6695 (ptm-80) REVERT: M 155 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6175 (tm-30) REVERT: N 139 ARG cc_start: 0.3800 (ttm110) cc_final: 0.1999 (ttp-170) REVERT: O 75 MET cc_start: 0.8115 (tpp) cc_final: 0.7394 (tpp) REVERT: P 151 TRP cc_start: 0.8227 (p90) cc_final: 0.7984 (p90) REVERT: R 32 ARG cc_start: 0.7870 (ttt90) cc_final: 0.7382 (ttm110) REVERT: T 130 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7440 (ttp80) REVERT: T 198 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6436 (mt-10) REVERT: V 57 PHE cc_start: 0.8477 (m-80) cc_final: 0.8152 (m-80) REVERT: V 95 TYR cc_start: 0.7743 (m-80) cc_final: 0.7516 (m-80) REVERT: V 202 MET cc_start: 0.8059 (mtp) cc_final: 0.7678 (ttm) REVERT: W 56 MET cc_start: 0.8651 (mmt) cc_final: 0.8036 (mmt) REVERT: Y 123 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.7305 (mmm160) REVERT: Y 133 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7993 (p0) REVERT: Y 143 ASP cc_start: 0.8018 (t0) cc_final: 0.7750 (t0) REVERT: 0 82 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7306 (ttmt) REVERT: 0 144 GLN cc_start: 0.7853 (mm110) cc_final: 0.7466 (mm110) REVERT: 5 137 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8276 (mp) REVERT: 5 324 GLN cc_start: 0.6869 (tm-30) cc_final: 0.6630 (tm-30) REVERT: 7 85 ILE cc_start: 0.8634 (mm) cc_final: 0.8353 (mm) REVERT: 9 115 GLU cc_start: 0.7306 (pp20) cc_final: 0.7038 (pp20) REVERT: d 57 MET cc_start: 0.4588 (tpp) cc_final: 0.2944 (tmm) REVERT: d 217 HIS cc_start: 0.7289 (t70) cc_final: 0.6988 (t70) REVERT: g 141 ASN cc_start: 0.8211 (t0) cc_final: 0.7990 (t0) REVERT: o 99 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8149 (mtpt) REVERT: p 128 ASN cc_start: 0.7863 (t0) cc_final: 0.7620 (t0) REVERT: q 82 LEU cc_start: 0.9334 (tt) cc_final: 0.9104 (tp) REVERT: r 153 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7729 (ttp-170) REVERT: s 86 MET cc_start: 0.7965 (mtp) cc_final: 0.7607 (mtm) REVERT: s 165 ARG cc_start: 0.8074 (tmm160) cc_final: 0.7672 (tmm-80) REVERT: u 97 MET cc_start: 0.6507 (mmm) cc_final: 0.6040 (mmp) outliers start: 160 outliers final: 111 residues processed: 1409 average time/residue: 0.8851 time to fit residues: 2113.1365 Evaluate side-chains 1363 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1243 time to evaluate : 6.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 338 CYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain K residue 123 GLU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 62 TYR Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 247 LEU Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 198 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain Y residue 88 GLN Chi-restraints excluded: chain Y residue 133 ASP Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 235 LEU Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain 0 residue 82 LYS Chi-restraints excluded: chain 0 residue 106 ASN Chi-restraints excluded: chain 2 residue 72 THR Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 137 LEU Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 381 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 235 TRP Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 64 ASP Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain e residue 121 GLU Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 148 LEU Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain r residue 185 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 914 random chunks: chunk 297 optimal weight: 0.5980 chunk 795 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 518 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 884 optimal weight: 5.9990 chunk 734 optimal weight: 7.9990 chunk 409 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 chunk 464 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 GLN E 286 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN ** S 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 HIS V 73 GLN V 82 GLN Y 88 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 195 ASN 6 147 HIS ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 255 HIS 7 277 GLN 9 123 GLN b 135 ASN ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 193 GLN d 211 GLN f 115 ASN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 135 GLN j 63 GLN j 99 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 191 HIS ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 97376 Z= 0.351 Angle : 0.648 11.989 137409 Z= 0.324 Chirality : 0.042 0.314 15972 Planarity : 0.005 0.078 13135 Dihedral : 20.047 179.473 27196 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.13 % Favored : 94.85 % Rotamer: Outliers : 3.05 % Allowed : 17.48 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.09), residues: 8025 helix: 0.63 (0.10), residues: 2704 sheet: -0.99 (0.15), residues: 1039 loop : -0.77 (0.09), residues: 4282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 183 HIS 0.007 0.001 HIS T 195 PHE 0.021 0.002 PHE 7 179 TYR 0.026 0.002 TYR V 216 ARG 0.011 0.001 ARG r 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1268 time to evaluate : 6.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 292 MET cc_start: 0.6452 (tpt) cc_final: 0.5906 (mmm) REVERT: E 139 ASN cc_start: 0.3246 (OUTLIER) cc_final: 0.2452 (m-40) REVERT: F 274 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8844 (mm) REVERT: I 53 TYR cc_start: 0.8315 (t80) cc_final: 0.8043 (t80) REVERT: K 61 ASN cc_start: 0.8148 (m110) cc_final: 0.7926 (m-40) REVERT: M 39 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6285 (ptm-80) REVERT: M 155 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: N 139 ARG cc_start: 0.3864 (ttm110) cc_final: 0.2071 (ttp-170) REVERT: P 97 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7807 (tm-30) REVERT: P 167 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: R 32 ARG cc_start: 0.8060 (ttt90) cc_final: 0.7511 (ttm110) REVERT: U 129 MET cc_start: 0.4195 (mpp) cc_final: 0.3538 (mpp) REVERT: V 57 PHE cc_start: 0.8586 (m-80) cc_final: 0.8231 (m-80) REVERT: Y 123 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7343 (mmm160) REVERT: Y 143 ASP cc_start: 0.8076 (t0) cc_final: 0.7802 (t0) REVERT: Y 209 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8682 (mp) REVERT: Z 134 MET cc_start: 0.6538 (ttp) cc_final: 0.6285 (ttm) REVERT: 0 82 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7312 (ttmt) REVERT: 0 144 GLN cc_start: 0.7956 (mm110) cc_final: 0.7491 (mm110) REVERT: 5 137 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8353 (mp) REVERT: 5 324 GLN cc_start: 0.6985 (tm-30) cc_final: 0.6756 (tm-30) REVERT: 9 115 GLU cc_start: 0.7318 (pp20) cc_final: 0.7023 (pp20) REVERT: b 106 ASP cc_start: 0.8029 (m-30) cc_final: 0.7578 (m-30) REVERT: d 57 MET cc_start: 0.4586 (tpp) cc_final: 0.2925 (tmm) REVERT: d 217 HIS cc_start: 0.7372 (t70) cc_final: 0.7098 (t70) REVERT: e 243 PHE cc_start: 0.1535 (t80) cc_final: 0.1025 (m-80) REVERT: g 45 TYR cc_start: 0.8613 (t80) cc_final: 0.8023 (t80) REVERT: g 141 ASN cc_start: 0.8263 (t0) cc_final: 0.8031 (t0) REVERT: o 28 SER cc_start: 0.8502 (p) cc_final: 0.8162 (p) REVERT: o 99 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8188 (mtpt) REVERT: q 82 LEU cc_start: 0.9366 (tt) cc_final: 0.9138 (tp) REVERT: r 153 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7745 (ttp-170) outliers start: 220 outliers final: 161 residues processed: 1403 average time/residue: 0.8861 time to fit residues: 2109.6784 Evaluate side-chains 1389 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1220 time to evaluate : 6.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 338 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 165 GLU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 198 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Y residue 209 LEU Chi-restraints excluded: chain Y residue 235 LEU Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain 0 residue 82 LYS Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 72 THR Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 37 SER Chi-restraints excluded: chain 5 residue 137 LEU Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 208 THR Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 381 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 6 residue 235 TRP Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 193 MET Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 113 ARG Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain c residue 86 ASP Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 205 SER Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain e residue 121 GLU Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 148 LEU Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 119 ILE Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain r residue 185 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 247 LEU Chi-restraints excluded: chain s residue 261 ILE Chi-restraints excluded: chain s residue 284 VAL Chi-restraints excluded: chain s residue 336 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 381 THR Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 417 VAL Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 914 random chunks: chunk 852 optimal weight: 6.9990 chunk 99 optimal weight: 40.0000 chunk 503 optimal weight: 4.9990 chunk 645 optimal weight: 7.9990 chunk 500 optimal weight: 4.9990 chunk 744 optimal weight: 5.9990 chunk 493 optimal weight: 5.9990 chunk 880 optimal weight: 10.0000 chunk 551 optimal weight: 1.9990 chunk 537 optimal weight: 0.9990 chunk 406 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 GLN E 72 GLN F 103 GLN H 93 ASN ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 ASN W 70 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 51 ASN ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 277 GLN 9 123 GLN a 46 ASN b 135 ASN ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 193 GLN d 77 HIS d 211 GLN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 63 GLN j 99 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 191 HIS ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 97376 Z= 0.317 Angle : 0.642 11.661 137409 Z= 0.320 Chirality : 0.042 0.304 15972 Planarity : 0.005 0.071 13135 Dihedral : 20.051 179.787 27196 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.91 % Favored : 95.08 % Rotamer: Outliers : 3.40 % Allowed : 17.81 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.09), residues: 8025 helix: 0.69 (0.10), residues: 2687 sheet: -1.00 (0.15), residues: 1046 loop : -0.74 (0.09), residues: 4292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 90 HIS 0.009 0.001 HIS d 262 PHE 0.050 0.002 PHE e 128 TYR 0.027 0.002 TYR 0 127 ARG 0.008 0.000 ARG 9 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1502 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1257 time to evaluate : 6.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 292 MET cc_start: 0.6609 (tpt) cc_final: 0.5991 (mmm) REVERT: E 126 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: E 139 ASN cc_start: 0.3179 (OUTLIER) cc_final: 0.2296 (m-40) REVERT: F 274 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8820 (mm) REVERT: I 53 TYR cc_start: 0.8332 (t80) cc_final: 0.8064 (t80) REVERT: K 61 ASN cc_start: 0.8139 (m110) cc_final: 0.7911 (m-40) REVERT: L 34 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8063 (mmmm) REVERT: M 39 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6349 (ptm-80) REVERT: M 155 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: N 139 ARG cc_start: 0.3887 (ttm110) cc_final: 0.2102 (ttp-170) REVERT: O 73 MET cc_start: 0.8971 (tpp) cc_final: 0.8770 (tpt) REVERT: O 109 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: P 97 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7830 (tm-30) REVERT: R 32 ARG cc_start: 0.8054 (ttt90) cc_final: 0.7501 (ttm110) REVERT: T 130 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7341 (ttp80) REVERT: U 129 MET cc_start: 0.4318 (mpp) cc_final: 0.3673 (mpp) REVERT: V 57 PHE cc_start: 0.8594 (m-80) cc_final: 0.8213 (m-80) REVERT: V 95 TYR cc_start: 0.7743 (m-80) cc_final: 0.7346 (m-80) REVERT: W 109 ARG cc_start: 0.7574 (ptp90) cc_final: 0.7150 (ptt90) REVERT: Y 123 ARG cc_start: 0.7729 (mmm-85) cc_final: 0.7234 (mmm160) REVERT: Y 143 ASP cc_start: 0.8106 (t0) cc_final: 0.7866 (t0) REVERT: Y 209 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8684 (mp) REVERT: Z 134 MET cc_start: 0.6705 (ttp) cc_final: 0.6466 (ttm) REVERT: 0 82 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7286 (ttmt) REVERT: 0 144 GLN cc_start: 0.7970 (mm110) cc_final: 0.7507 (mm110) REVERT: 7 85 ILE cc_start: 0.8776 (mm) cc_final: 0.8496 (mm) REVERT: 7 143 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.7834 (m-90) REVERT: 9 115 GLU cc_start: 0.7365 (pp20) cc_final: 0.7080 (pp20) REVERT: b 103 LYS cc_start: 0.8245 (tttp) cc_final: 0.7761 (tttp) REVERT: b 106 ASP cc_start: 0.8037 (m-30) cc_final: 0.7586 (m-30) REVERT: d 57 MET cc_start: 0.4768 (tpp) cc_final: 0.2827 (tmm) REVERT: d 217 HIS cc_start: 0.7461 (t70) cc_final: 0.7194 (t70) REVERT: g 45 TYR cc_start: 0.8602 (t80) cc_final: 0.8030 (t80) REVERT: g 141 ASN cc_start: 0.8247 (t0) cc_final: 0.8024 (t0) REVERT: h 120 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6735 (ptp) REVERT: o 28 SER cc_start: 0.8502 (p) cc_final: 0.8159 (p) REVERT: o 99 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8245 (mtpt) REVERT: r 153 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7742 (ttp-170) REVERT: s 86 MET cc_start: 0.8017 (mtp) cc_final: 0.7769 (mtp) outliers start: 245 outliers final: 186 residues processed: 1406 average time/residue: 0.8764 time to fit residues: 2089.4724 Evaluate side-chains 1413 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1217 time to evaluate : 6.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 338 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 109 GLN Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 198 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain W residue 70 GLN Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Y residue 209 LEU Chi-restraints excluded: chain Y residue 235 LEU Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain 0 residue 82 LYS Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 51 ASN Chi-restraints excluded: chain 2 residue 72 THR Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 208 THR Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 309 LEU Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 381 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 182 ASP Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 6 residue 235 TRP Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 43 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 193 MET Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 113 ARG Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 54 LYS Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 86 ASP Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain c residue 310 ASN Chi-restraints excluded: chain d residue 77 HIS Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 208 VAL Chi-restraints excluded: chain e residue 76 GLN Chi-restraints excluded: chain e residue 121 GLU Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 135 GLN Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 148 LEU Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain r residue 185 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 145 VAL Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 247 LEU Chi-restraints excluded: chain s residue 261 ILE Chi-restraints excluded: chain s residue 284 VAL Chi-restraints excluded: chain s residue 336 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 381 THR Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 914 random chunks: chunk 545 optimal weight: 0.2980 chunk 351 optimal weight: 0.9990 chunk 526 optimal weight: 0.0970 chunk 265 optimal weight: 0.7980 chunk 173 optimal weight: 0.0060 chunk 170 optimal weight: 5.9990 chunk 560 optimal weight: 0.9990 chunk 600 optimal weight: 50.0000 chunk 435 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 692 optimal weight: 0.4980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN E 63 GLN E 72 GLN E 88 HIS ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN ** T 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 277 GLN 9 123 GLN a 46 ASN ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 HIS ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 ASN j 99 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 87 GLN ** s 319 GLN ** 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: 0.7588 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 97376 Z= 0.147 Angle : 0.583 12.249 137409 Z= 0.292 Chirality : 0.038 0.248 15972 Planarity : 0.004 0.059 13135 Dihedral : 19.976 179.291 27196 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.01 % Favored : 95.98 % Rotamer: Outliers : 2.22 % Allowed : 19.16 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.09), residues: 8025 helix: 0.82 (0.10), residues: 2703 sheet: -0.91 (0.15), residues: 1055 loop : -0.60 (0.10), residues: 4267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 5 122 HIS 0.045 0.001 HIS d 77 PHE 0.052 0.001 PHE e 128 TYR 0.020 0.001 TYR u 146 ARG 0.020 0.000 ARG W 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1319 time to evaluate : 6.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 292 MET cc_start: 0.6237 (tpt) cc_final: 0.5485 (mmm) REVERT: F 101 MET cc_start: 0.7903 (mmm) cc_final: 0.7233 (mmm) REVERT: F 179 THR cc_start: 0.9138 (m) cc_final: 0.8831 (t) REVERT: F 274 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8775 (mm) REVERT: M 30 ASN cc_start: 0.8305 (t0) cc_final: 0.8010 (t0) REVERT: M 39 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6696 (ptm-80) REVERT: M 155 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6250 (tm-30) REVERT: N 139 ARG cc_start: 0.4031 (ttm110) cc_final: 0.2077 (ttp-170) REVERT: O 62 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7263 (t80) REVERT: P 97 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7692 (tm-30) REVERT: P 151 TRP cc_start: 0.8107 (p90) cc_final: 0.7845 (p90) REVERT: Q 99 MET cc_start: 0.6816 (mtm) cc_final: 0.6576 (mtm) REVERT: T 139 ASN cc_start: 0.8899 (t0) cc_final: 0.8689 (t0) REVERT: U 129 MET cc_start: 0.4130 (mpp) cc_final: 0.3538 (mpp) REVERT: V 57 PHE cc_start: 0.8458 (m-80) cc_final: 0.8210 (m-80) REVERT: V 202 MET cc_start: 0.8018 (mtp) cc_final: 0.7701 (ttm) REVERT: W 56 MET cc_start: 0.8956 (mmt) cc_final: 0.8508 (mmt) REVERT: Y 123 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7191 (mmm160) REVERT: Y 143 ASP cc_start: 0.8038 (t0) cc_final: 0.7788 (t0) REVERT: Y 235 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8326 (tt) REVERT: 2 52 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7675 (mt-10) REVERT: 6 35 MET cc_start: 0.8016 (mmt) cc_final: 0.7780 (mmt) REVERT: 6 170 ARG cc_start: 0.5558 (mtt90) cc_final: 0.5229 (mtt180) REVERT: 7 85 ILE cc_start: 0.8647 (mm) cc_final: 0.8350 (mm) REVERT: 7 143 TRP cc_start: 0.8450 (OUTLIER) cc_final: 0.7747 (m-90) REVERT: 9 115 GLU cc_start: 0.7343 (pp20) cc_final: 0.7112 (pp20) REVERT: b 103 LYS cc_start: 0.8113 (tttp) cc_final: 0.7643 (ttpp) REVERT: d 57 MET cc_start: 0.4755 (tpp) cc_final: 0.3096 (tmm) REVERT: d 217 HIS cc_start: 0.7311 (t70) cc_final: 0.7028 (t70) REVERT: g 141 ASN cc_start: 0.8084 (t0) cc_final: 0.7865 (t0) REVERT: o 71 PHE cc_start: 0.8673 (t80) cc_final: 0.8296 (t80) REVERT: q 106 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8487 (mtmt) REVERT: r 153 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7599 (ttp-170) REVERT: s 86 MET cc_start: 0.7869 (mtp) cc_final: 0.7483 (mtp) REVERT: u 95 ASP cc_start: 0.5881 (OUTLIER) cc_final: 0.5631 (p0) outliers start: 160 outliers final: 121 residues processed: 1412 average time/residue: 0.8949 time to fit residues: 2148.9660 Evaluate side-chains 1390 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1262 time to evaluate : 6.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 338 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 62 TYR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 198 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 235 LEU Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 147 ILE Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 381 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 157 LEU Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 235 TRP Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 43 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 193 MET Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 9 residue 54 LYS Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain a residue 46 ASN Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 51 VAL 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 113 ILE Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 310 ASN Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 143 ASP Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain e residue 121 GLU Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 148 LEU Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 151 GLU Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 336 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain u residue 95 ASP Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 914 random chunks: chunk 801 optimal weight: 5.9990 chunk 843 optimal weight: 5.9990 chunk 770 optimal weight: 20.0000 chunk 820 optimal weight: 5.9990 chunk 494 optimal weight: 4.9990 chunk 357 optimal weight: 0.7980 chunk 644 optimal weight: 4.9990 chunk 251 optimal weight: 0.9980 chunk 741 optimal weight: 9.9990 chunk 776 optimal weight: 10.0000 chunk 818 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN E 57 ASN E 63 GLN E 72 GLN F 103 GLN H 93 ASN ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 HIS ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 GLN W 70 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 GLN ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 55 GLN 7 277 GLN 7 298 GLN 9 123 GLN a 46 ASN ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 HIS j 99 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 176 GLN s 87 GLN s 191 HIS ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 97376 Z= 0.388 Angle : 0.675 13.385 137409 Z= 0.336 Chirality : 0.043 0.329 15972 Planarity : 0.005 0.089 13135 Dihedral : 19.935 179.428 27196 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.05 % Favored : 94.94 % Rotamer: Outliers : 2.53 % Allowed : 19.32 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.09), residues: 8025 helix: 0.76 (0.10), residues: 2708 sheet: -0.93 (0.15), residues: 1048 loop : -0.67 (0.10), residues: 4269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 5 122 HIS 0.007 0.001 HIS T 195 PHE 0.050 0.002 PHE e 128 TYR 0.035 0.002 TYR u 146 ARG 0.009 0.001 ARG 9 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1253 time to evaluate : 6.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 ASN cc_start: 0.6362 (m-40) cc_final: 0.5682 (p0) REVERT: E 126 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: F 101 MET cc_start: 0.8258 (mmm) cc_final: 0.7450 (mmm) REVERT: F 103 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: F 274 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8840 (mm) REVERT: M 39 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6318 (ptm-80) REVERT: M 155 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: N 139 ARG cc_start: 0.3922 (ttm110) cc_final: 0.2157 (ttp-170) REVERT: P 97 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7787 (tm-30) REVERT: T 130 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7377 (ttp80) REVERT: U 129 MET cc_start: 0.4329 (mpp) cc_final: 0.3645 (mpp) REVERT: V 57 PHE cc_start: 0.8560 (m-80) cc_final: 0.8246 (m-80) REVERT: W 109 ARG cc_start: 0.7564 (ptp90) cc_final: 0.7152 (ptt90) REVERT: X 116 SER cc_start: 0.8374 (t) cc_final: 0.8122 (t) REVERT: Y 123 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7247 (mmm160) REVERT: Y 143 ASP cc_start: 0.8062 (t0) cc_final: 0.7819 (t0) REVERT: 0 185 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: 6 170 ARG cc_start: 0.5599 (mtt90) cc_final: 0.5268 (mtt180) REVERT: 7 143 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.7808 (m-90) REVERT: 9 115 GLU cc_start: 0.7452 (pp20) cc_final: 0.7207 (pp20) REVERT: b 103 LYS cc_start: 0.8301 (ttpp) cc_final: 0.7894 (tttp) REVERT: b 106 ASP cc_start: 0.8020 (m-30) cc_final: 0.7588 (m-30) REVERT: d 57 MET cc_start: 0.4854 (tpp) cc_final: 0.3038 (tmm) REVERT: g 45 TYR cc_start: 0.8531 (t80) cc_final: 0.7970 (t80) REVERT: g 141 ASN cc_start: 0.8210 (t0) cc_final: 0.8000 (t0) REVERT: o 28 SER cc_start: 0.8496 (p) cc_final: 0.8152 (p) REVERT: r 153 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7733 (ttp-170) REVERT: s 86 MET cc_start: 0.8052 (mtp) cc_final: 0.7696 (mtp) outliers start: 182 outliers final: 150 residues processed: 1367 average time/residue: 0.9159 time to fit residues: 2127.7461 Evaluate side-chains 1382 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1225 time to evaluate : 7.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 338 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 198 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Y residue 206 ASP Chi-restraints excluded: chain Y residue 235 LEU Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 208 THR Chi-restraints excluded: chain 5 residue 253 LEU Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 381 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 235 TRP Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 43 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 193 MET Chi-restraints excluded: chain 7 residue 198 ASN Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain a residue 46 ASN Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 24 GLN Chi-restraints excluded: chain b residue 51 VAL 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 113 ILE Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 205 SER Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain c residue 310 ASN Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 143 ASP Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain e residue 76 GLN Chi-restraints excluded: chain e residue 121 GLU Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 148 LEU Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 96 LEU Chi-restraints excluded: chain q residue 151 GLU Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 336 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 381 THR Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 914 random chunks: chunk 539 optimal weight: 0.8980 chunk 868 optimal weight: 8.9990 chunk 529 optimal weight: 8.9990 chunk 411 optimal weight: 2.9990 chunk 603 optimal weight: 10.0000 chunk 910 optimal weight: 60.0000 chunk 838 optimal weight: 50.0000 chunk 725 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 560 optimal weight: 0.9990 chunk 444 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 GLN E 72 GLN ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN H 93 ASN K 61 ASN L 33 GLN ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 GLN ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 277 GLN 9 123 GLN ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 191 HIS ** s 319 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: 0.7658 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 97376 Z= 0.236 Angle : 0.621 13.072 137409 Z= 0.309 Chirality : 0.040 0.285 15972 Planarity : 0.004 0.057 13135 Dihedral : 19.949 179.724 27196 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.59 % Favored : 95.40 % Rotamer: Outliers : 2.19 % Allowed : 19.92 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 8025 helix: 0.82 (0.10), residues: 2708 sheet: -0.96 (0.16), residues: 1041 loop : -0.61 (0.10), residues: 4276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 5 122 HIS 0.007 0.001 HIS d 262 PHE 0.050 0.001 PHE e 128 TYR 0.024 0.001 TYR 0 127 ARG 0.009 0.000 ARG 9 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16050 Ramachandran restraints generated. 8025 Oldfield, 0 Emsley, 8025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1263 time to evaluate : 6.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 ASN cc_start: 0.6472 (m-40) cc_final: 0.5819 (p0) REVERT: E 126 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: E 139 ASN cc_start: 0.3081 (OUTLIER) cc_final: 0.2219 (m-40) REVERT: F 179 THR cc_start: 0.9144 (m) cc_final: 0.8795 (t) REVERT: F 274 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8823 (mm) REVERT: K 61 ASN cc_start: 0.7948 (m-40) cc_final: 0.7715 (m-40) REVERT: M 39 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6362 (ptm-80) REVERT: M 155 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: N 139 ARG cc_start: 0.4064 (ttm110) cc_final: 0.2272 (ttp-170) REVERT: P 97 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7765 (tm-30) REVERT: U 129 MET cc_start: 0.4241 (mpp) cc_final: 0.3568 (mpp) REVERT: V 57 PHE cc_start: 0.8589 (m-80) cc_final: 0.8292 (m-80) REVERT: W 56 MET cc_start: 0.8955 (mmt) cc_final: 0.8375 (mmt) REVERT: Y 123 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7148 (mmm160) REVERT: Y 143 ASP cc_start: 0.8110 (t0) cc_final: 0.7858 (t0) REVERT: Y 235 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8363 (tt) REVERT: 0 185 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: 2 52 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7456 (mt-10) REVERT: 6 170 ARG cc_start: 0.5567 (mtt90) cc_final: 0.5330 (mtt180) REVERT: 7 85 ILE cc_start: 0.8698 (mm) cc_final: 0.8417 (mm) REVERT: 7 143 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.7756 (m-90) REVERT: 9 115 GLU cc_start: 0.7486 (pp20) cc_final: 0.7233 (pp20) REVERT: b 106 ASP cc_start: 0.7986 (m-30) cc_final: 0.7542 (m-30) REVERT: c 97 TYR cc_start: 0.8360 (t80) cc_final: 0.7924 (t80) REVERT: d 57 MET cc_start: 0.4779 (tpp) cc_final: 0.2951 (tmm) REVERT: d 217 HIS cc_start: 0.7410 (t70) cc_final: 0.7073 (t70) REVERT: g 45 TYR cc_start: 0.8476 (t80) cc_final: 0.7921 (t80) REVERT: g 141 ASN cc_start: 0.8160 (t0) cc_final: 0.7952 (t0) REVERT: o 28 SER cc_start: 0.8504 (p) cc_final: 0.8163 (p) REVERT: q 106 LYS cc_start: 0.8893 (mtmm) cc_final: 0.8660 (mtmt) REVERT: r 153 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7750 (ttp-170) REVERT: u 95 ASP cc_start: 0.5883 (OUTLIER) cc_final: 0.5549 (p0) outliers start: 158 outliers final: 141 residues processed: 1357 average time/residue: 0.9090 time to fit residues: 2097.6769 Evaluate side-chains 1391 residues out of total 7226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1241 time to evaluate : 6.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 338 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 198 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 70 GLN Chi-restraints excluded: chain W residue 86 ASN Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Y residue 206 ASP Chi-restraints excluded: chain Y residue 235 LEU Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 72 THR Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 104 CYS Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 253 LEU Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 381 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 235 TRP Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 43 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 193 MET Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 51 VAL 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 113 ILE Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 310 ASN Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain e residue 76 GLN Chi-restraints excluded: chain e residue 121 GLU Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 148 LEU Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 96 LEU Chi-restraints excluded: chain q residue 151 GLU Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 336 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 95 ASP Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 914 random chunks: chunk 575 optimal weight: 20.0000 chunk 772 optimal weight: 30.0000 chunk 222 optimal weight: 10.0000 chunk 668 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 201 optimal weight: 0.7980 chunk 726 optimal weight: 8.9990 chunk 303 optimal weight: 6.9990 chunk 745 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN E 63 GLN E 72 GLN E 88 HIS ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN M 102 GLN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 ASN W 70 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 277 GLN 9 123 GLN ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 191 HIS ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125595 restraints weight = 130408.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121075 restraints weight = 234442.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.118692 restraints weight = 173257.425| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.302 97376 Z= 0.307 Angle : 0.656 65.900 137409 Z= 0.333 Chirality : 0.041 0.601 15972 Planarity : 0.005 0.179 13135 Dihedral : 19.947 179.705 27196 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.69 % Favored : 95.30 % Rotamer: Outliers : 2.40 % Allowed : 19.77 % Favored : 77.83 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.09), residues: 8025 helix: 0.81 (0.10), residues: 2708 sheet: -0.97 (0.16), residues: 1047 loop : -0.61 (0.10), residues: 4270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 5 122 HIS 0.006 0.001 HIS E 197 PHE 0.046 0.001 PHE e 128 TYR 0.023 0.001 TYR 0 127 ARG 0.009 0.000 ARG 6 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28634.12 seconds wall clock time: 502 minutes 16.93 seconds (30136.93 seconds total)