Starting phenix.real_space_refine on Wed Mar 20 14:44:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i9r_4434/03_2024/6i9r_4434_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i9r_4434/03_2024/6i9r_4434.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i9r_4434/03_2024/6i9r_4434_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i9r_4434/03_2024/6i9r_4434_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i9r_4434/03_2024/6i9r_4434_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i9r_4434/03_2024/6i9r_4434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i9r_4434/03_2024/6i9r_4434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i9r_4434/03_2024/6i9r_4434_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i9r_4434/03_2024/6i9r_4434_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 3 6.06 5 P 1562 5.49 5 Mg 134 5.21 5 S 281 5.16 5 C 57587 2.51 5 N 18223 2.21 5 O 22484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 108": "OD1" <-> "OD2" Residue "0 ARG 173": "NH1" <-> "NH2" Residue "0 GLU 176": "OE1" <-> "OE2" Residue "0 ARG 179": "NH1" <-> "NH2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "1 ARG 63": "NH1" <-> "NH2" Residue "2 ARG 49": "NH1" <-> "NH2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "4 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 32": "OE1" <-> "OE2" Residue "5 ASP 47": "OD1" <-> "OD2" Residue "5 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 56": "OE1" <-> "OE2" Residue "5 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 110": "NH1" <-> "NH2" Residue "5 GLU 134": "OE1" <-> "OE2" Residue "5 ASP 142": "OD1" <-> "OD2" Residue "5 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 182": "OD1" <-> "OD2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "5 ARG 229": "NH1" <-> "NH2" Residue "5 ASP 264": "OD1" <-> "OD2" Residue "5 GLU 281": "OE1" <-> "OE2" Residue "5 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "6 ARG 27": "NH1" <-> "NH2" Residue "6 ARG 28": "NH1" <-> "NH2" Residue "6 ASP 39": "OD1" <-> "OD2" Residue "6 ARG 47": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 58": "NH1" <-> "NH2" Residue "6 ARG 60": "NH1" <-> "NH2" Residue "6 ARG 72": "NH1" <-> "NH2" Residue "6 ARG 114": "NH1" <-> "NH2" Residue "6 ARG 121": "NH1" <-> "NH2" Residue "6 ARG 126": "NH1" <-> "NH2" Residue "6 ARG 136": "NH1" <-> "NH2" Residue "6 GLU 138": "OE1" <-> "OE2" Residue "6 GLU 153": "OE1" <-> "OE2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 183": "OD1" <-> "OD2" Residue "6 GLU 197": "OE1" <-> "OE2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 ARG 267": "NH1" <-> "NH2" Residue "6 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 283": "OE1" <-> "OE2" Residue "6 ARG 286": "NH1" <-> "NH2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 ASP 302": "OD1" <-> "OD2" Residue "6 ASP 325": "OD1" <-> "OD2" Residue "6 ARG 360": "NH1" <-> "NH2" Residue "6 ARG 364": "NH1" <-> "NH2" Residue "7 ARG 44": "NH1" <-> "NH2" Residue "7 ASP 134": "OD1" <-> "OD2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 GLU 171": "OE1" <-> "OE2" Residue "7 PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 217": "OE1" <-> "OE2" Residue "7 ARG 250": "NH1" <-> "NH2" Residue "7 ASP 259": "OD1" <-> "OD2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "7 TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 295": "NH1" <-> "NH2" Residue "7 ASP 314": "OD1" <-> "OD2" Residue "8 ASP 87": "OD1" <-> "OD2" Residue "8 ARG 137": "NH1" <-> "NH2" Residue "8 GLU 148": "OE1" <-> "OE2" Residue "8 ARG 164": "NH1" <-> "NH2" 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 "D ARG 80": "NH1" <-> "NH2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I GLU 157": "OE1" <-> "OE2" Residue "I ARG 188": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "J ASP 158": "OD1" <-> "OD2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K ASP 136": "OD1" <-> "OD2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "L ARG 37": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M GLU 208": "OE1" <-> "OE2" Residue "M ASP 216": "OD1" <-> "OD2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ASP 77": "OD1" <-> "OD2" Residue "O TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ARG 117": "NH1" <-> "NH2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 53": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P ARG 74": "NH1" <-> "NH2" Residue "P ARG 79": "NH1" <-> "NH2" Residue "P ARG 107": "NH1" <-> "NH2" Residue "P ARG 119": "NH1" <-> "NH2" Residue "Q ARG 74": "NH1" <-> "NH2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 274": "OD1" <-> "OD2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "S ASP 68": "OD1" <-> "OD2" Residue "S PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S GLU 165": "OE1" <-> "OE2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "T ARG 157": "NH1" <-> "NH2" Residue "T ARG 163": "NH1" <-> "NH2" Residue "T GLU 168": "OE1" <-> "OE2" Residue "U PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U ASP 52": "OD1" <-> "OD2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 144": "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 47": "OE1" <-> "OE2" Residue "V ASP 51": "OD1" <-> "OD2" Residue "V ASP 53": "OD1" <-> "OD2" Residue "V ASP 60": "OD1" <-> "OD2" Residue "V GLU 66": "OE1" <-> "OE2" Residue "V ASP 69": "OD1" <-> "OD2" Residue "V ARG 81": "NH1" <-> "NH2" 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 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 145": "NH1" <-> "NH2" Residue "V ARG 149": "NH1" <-> "NH2" Residue "V GLU 168": "OE1" <-> "OE2" Residue "V GLU 180": "OE1" <-> "OE2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "V ARG 208": "NH1" <-> "NH2" Residue "V TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 233": "OE1" <-> "OE2" Residue "Y ASP 70": "OD1" <-> "OD2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y ASP 97": "OD1" <-> "OD2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y ARG 162": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Z ARG 40": "NH1" <-> "NH2" Residue "Z PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a ARG 131": "NH1" <-> "NH2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a ARG 142": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 116": "NH1" <-> "NH2" Residue "b PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 60": "NH1" <-> "NH2" Residue "c ASP 158": "OD1" <-> "OD2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "c TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ASP 127": "OD1" <-> "OD2" Residue "d ASP 129": "OD1" <-> "OD2" Residue "d ASP 158": "OD1" <-> "OD2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "d TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 241": "OD1" <-> "OD2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e ASP 86": "OD1" <-> "OD2" Residue "e ASP 104": "OD1" <-> "OD2" Residue "e GLU 139": "OE1" <-> "OE2" Residue "e ASP 145": "OD1" <-> "OD2" Residue "e GLU 189": "OE1" <-> "OE2" Residue "e ASP 242": "OD1" <-> "OD2" Residue "e PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 278": "OD1" <-> "OD2" Residue "f TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 87": "OE1" <-> "OE2" Residue "f TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "h GLU 64": "OE1" <-> "OE2" Residue "h ARG 69": "NH1" <-> "NH2" Residue "h ASP 93": "OD1" <-> "OD2" Residue "h ASP 106": "OD1" <-> "OD2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "h ASP 128": "OD1" <-> "OD2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j ARG 94": "NH1" <-> "NH2" Residue "j ARG 103": "NH1" <-> "NH2" Residue "j GLU 106": "OE1" <-> "OE2" Residue "k ASP 65": "OD1" <-> "OD2" Residue "k ASP 70": "OD1" <-> "OD2" Residue "k ARG 77": "NH1" <-> "NH2" Residue "l ASP 58": "OD1" <-> "OD2" Residue "l ASP 89": "OD1" <-> "OD2" Residue "l GLU 94": "OE1" <-> "OE2" Residue "l PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 98": "OE1" <-> "OE2" Residue "l ASP 111": "OD1" <-> "OD2" Residue "l ARG 115": "NH1" <-> "NH2" Residue "l ARG 120": "NH1" <-> "NH2" Residue "l ARG 128": "NH1" <-> "NH2" Residue "l ARG 131": "NH1" <-> "NH2" Residue "m TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 72": "NH1" <-> "NH2" Residue "o ARG 23": "NH1" <-> "NH2" Residue "o ARG 38": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o GLU 72": "OE1" <-> "OE2" Residue "o PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 90": "OD1" <-> "OD2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "p ASP 46": "OD1" <-> "OD2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "p GLU 181": "OE1" <-> "OE2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q GLU 84": "OE1" <-> "OE2" Residue "q GLU 89": "OE1" <-> "OE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "q ARG 140": "NH1" <-> "NH2" Residue "q GLU 141": "OE1" <-> "OE2" Residue "q GLU 144": "OE1" <-> "OE2" Residue "q GLU 151": "OE1" <-> "OE2" Residue "r ARG 132": "NH1" <-> "NH2" Residue "r ARG 153": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "r ASP 183": "OD1" <-> "OD2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 158": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s ARG 162": "NH1" <-> "NH2" Residue "s ARG 212": "NH1" <-> "NH2" Residue "s ARG 219": "NH1" <-> "NH2" Residue "s ARG 222": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s ASP 227": "OD1" <-> "OD2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 242": "NH1" <-> "NH2" Residue "s PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s GLU 279": "OE1" <-> "OE2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s ASP 363": "OD1" <-> "OD2" Residue "s PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 407": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 100274 Number of models: 1 Model: "" Number of chains: 63 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: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 439 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "2" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 376 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 341 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain breaks: 1 Chain: "5" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3204 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 32, 'TRANS': 360} Chain breaks: 3 Chain: "6" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2947 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 34, 'TRANS': 319} Chain breaks: 3 Chain: "7" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2365 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 17, 'TRANS': 273} Chain breaks: 3 Chain: "8" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 886 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 11, 'TRANS': 93} Chain: "9" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 996 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 113} Chain: "A" Number of atoms: 31875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1501, 31875 Classifications: {'RNA': 1501} Modifications used: {'rna2p': 2, 'rna2p_pur': 168, 'rna2p_pyr': 115, 'rna3p': 1, 'rna3p_pur': 623, 'rna3p_pyr': 591} Link IDs: {'rna2p': 284, 'rna3p': 1216} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1275 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 30, 'rna3p_pyr': 24} Link IDs: {'rna2p': 6, 'rna3p': 53} Chain breaks: 4 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 breaks: 1 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: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1350 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 15, 'TRANS': 151} Chain: "J" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1294 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} 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: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1778 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 17, 'TRANS': 203} 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: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1164 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "Q" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1822 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 14, 'TRANS': 204} 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: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1284 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 148} Chain: "T" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1368 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "U" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1171 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain breaks: 1 Chain: "V" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1652 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 182} Chain breaks: 1 Chain: "W" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "X" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2027 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 17, 'TRANS': 225} Chain: "Y" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 8, 'TRANS': 169} 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: "a" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 693 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 10, 'TRANS': 72} 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: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1736 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} 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: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 999 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 2 Chain: "g" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1085 Classifications: {'peptide': 131} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 115} Chain: "h" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 886 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} 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: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 689 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "k" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "l" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 675 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 8, 'TRANS': 71} Chain: "m" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 499 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "o" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 797 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} 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: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1092 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 14, 'TRANS': 115} Chain: "r" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1256 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 17, 'TRANS': 135} Chain breaks: 3 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: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 73 Unusual residues: {'MHT': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="004 C 7 " pdbres="MHT C 8 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'MHU:plan-3': 1, 'DBB:plan-1': 1, '004:plan-2': 1, 'MHW:plan-2': 1, 'MHV:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 189 Unusual residues: {' MG': 128, 'H8T': 1} Classifications: {'RNA': 1, 'undetermined': 129} Modifications used: {'rna3p_pur': 1} Link IDs: {'MG-O1P': 1, None: 128} Not linked: pdbres=" MG A3301 " pdbres=" MG A3302 " Not linked: pdbres=" MG A3302 " pdbres=" MG A3303 " Not linked: pdbres=" MG A3303 " pdbres=" MG A3304 " Not linked: pdbres=" MG A3304 " pdbres=" MG A3305 " Not linked: pdbres=" MG A3305 " pdbres=" MG A3306 " ... (remaining 123 not shown) Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 264 SG CYS 0 110 181.866 147.680 162.090 1.00 71.78 S ATOM 366 SG CYS 0 123 182.735 146.923 158.590 1.00 71.42 S ATOM 389 SG CYS 0 126 186.283 148.383 159.292 1.00 76.27 S ATOM 2643 SG CYS 4 79 108.315 65.139 165.836 1.00 74.62 S ATOM 2767 SG CYS 4 92 110.683 63.155 168.436 1.00 74.18 S ATOM 95984 SG CYS r 70 82.841 89.359 179.653 1.00 87.12 S Time building chain proxies: 39.24, per 1000 atoms: 0.39 Number of scatterers: 100274 At special positions: 0 Unit cell: (252, 223.65, 226.8, 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 3 29.99 S 281 16.00 P 1562 15.00 Mg 134 11.99 O 22484 8.00 N 18223 7.00 C 57587 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: 37.39 Conformation dependent library (CDL) restraints added in 9.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb=" ZN 4 200 " pdb="ZN ZN 4 200 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" SG CYS r 70 " 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB DBB C 3 " pdb=" CB PRO C 4 " Number of C-beta restraints generated: 15468 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 267 helices and 78 sheets defined 40.8% alpha, 12.6% beta 366 base pairs and 817 stacking pairs defined. Time for finding SS restraints: 58.77 Creating SS restraints... Processing helix chain '0' and resid 86 through 96 Processing helix chain '0' and resid 123 through 146 Processing helix chain '2' and resid 56 through 64 Processing helix chain '2' and resid 65 through 73 Proline residue: 2 73 - end of helix Processing helix chain '2' and resid 74 through 86 removed outlier: 4.326A pdb=" N VAL 2 78 " --> pdb=" O ALA 2 74 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE 2 79 " --> pdb=" O GLY 2 75 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU 2 80 " --> pdb=" O VAL 2 76 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG 2 82 " --> pdb=" O VAL 2 78 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU 2 84 " --> pdb=" O LEU 2 80 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS 2 85 " --> pdb=" O ARG 2 81 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 114 removed outlier: 4.387A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 3.843A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 137' Processing helix chain '3' and resid 138 through 147 removed outlier: 5.742A pdb=" N PHE 3 147 " --> pdb=" O ARG 3 143 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 5.281A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 4.567A pdb=" N ASP 3 182 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 5.278A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 53 removed outlier: 4.503A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) Proline residue: 5 53 - end of helix No H-bonds generated for 'chain '5' and resid 48 through 53' Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 142 removed outlier: 4.403A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP 5 142 " --> pdb=" O SER 5 138 " (cutoff:3.500A) Processing helix chain '5' and resid 150 through 163 removed outlier: 3.628A pdb=" N LEU 5 163 " --> pdb=" O SER 5 159 " (cutoff:3.500A) Processing helix chain '5' and resid 172 through 196 Proline residue: 5 178 - end of helix removed outlier: 3.547A pdb=" N VAL 5 181 " --> pdb=" O CYS 5 177 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU 5 184 " --> pdb=" O ILE 5 180 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS 5 194 " --> pdb=" O SER 5 190 " (cutoff:3.500A) Proline residue: 5 196 - end of helix Processing helix chain '5' and resid 241 through 252 removed outlier: 3.555A pdb=" N ILE 5 245 " --> pdb=" O SER 5 241 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 330 Processing helix chain '5' and resid 407 through 420 removed outlier: 4.462A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 5.282A pdb=" N LEU 6 48 " --> pdb=" O ASN 6 44 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 44 through 49' Processing helix chain '6' and resid 53 through 68 removed outlier: 3.530A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 73 through 79 removed outlier: 4.038A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 116 removed outlier: 3.543A pdb=" N GLU 6 112 " --> pdb=" O GLN 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 117 through 126 removed outlier: 4.390A pdb=" N ARG 6 121 " --> pdb=" O VAL 6 117 " (cutoff:3.500A) Processing helix chain '6' and resid 131 through 143 removed outlier: 3.577A pdb=" N ARG 6 141 " --> pdb=" O ALA 6 137 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 156 Processing helix chain '6' and resid 157 through 162 Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 292 through 298 removed outlier: 5.972A pdb=" N PHE 6 298 " --> pdb=" O ALA 6 294 " (cutoff:3.500A) Processing helix chain '6' and resid 299 through 307 Processing helix chain '6' and resid 324 through 333 Processing helix chain '6' and resid 364 through 370 removed outlier: 4.001A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 Proline residue: 7 60 - end of helix Processing helix chain '7' and resid 87 through 96 Processing helix chain '7' and resid 97 through 103 Processing helix chain '7' and resid 135 through 158 removed outlier: 3.750A pdb=" N MET 7 150 " --> pdb=" O CYS 7 146 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY 7 151 " --> pdb=" O ALA 7 147 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS 7 152 " --> pdb=" O MET 7 148 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 191 removed outlier: 4.044A pdb=" N ASP 7 190 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLU 7 191 " --> pdb=" O SER 7 187 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 186 through 191' Processing helix chain '7' and resid 195 through 213 removed outlier: 3.732A pdb=" N ASP 7 213 " --> pdb=" O LEU 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 222 through 231 Processing helix chain '7' and resid 233 through 248 Proline residue: 7 248 - end of helix Processing helix chain '7' and resid 309 through 322 removed outlier: 3.548A pdb=" N GLU 7 318 " --> pdb=" O ASP 7 314 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 4.123A pdb=" N ILE 7 274 " --> pdb=" O ARG 7 271 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 91 through 98 removed outlier: 4.772A pdb=" N LEU 8 95 " --> pdb=" O PRO 8 91 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP 8 96 " --> pdb=" O LEU 8 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS 8 97 " --> pdb=" O LYS 8 93 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALA 8 98 " --> pdb=" O PHE 8 94 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 91 through 98' Processing helix chain '8' and resid 107 through 154 Processing helix chain '8' and resid 155 through 164 removed outlier: 5.406A pdb=" N ALA 8 159 " --> pdb=" O PRO 8 155 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 165 through 171 removed outlier: 4.365A pdb=" N PHE 8 169 " --> pdb=" O ASP 8 165 " (cutoff:3.500A) Proline residue: 8 170 - end of helix No H-bonds generated for 'chain '8' and resid 165 through 171' Processing helix chain '9' and resid 27 through 34 Processing helix chain '9' and resid 53 through 58 Proline residue: 9 58 - end of helix Processing helix chain '9' and resid 87 through 95 Processing helix chain '9' and resid 96 through 106 Processing helix chain '9' and resid 113 through 118 removed outlier: 4.737A pdb=" N TYR 9 117 " --> pdb=" O ASN 9 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 188 Proline residue: D 188 - end of helix Processing helix chain 'D' and resid 259 through 267 removed outlier: 4.036A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 4.650A pdb=" N HIS E 52 " --> pdb=" O TRP E 48 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU E 53 " --> pdb=" O TRP E 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 53' Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 5.077A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 4.009A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 306 through 311 removed outlier: 4.835A pdb=" N ASP E 309 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU E 310 " --> pdb=" O TYR E 307 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY E 311 " --> pdb=" O LYS E 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 306 through 311' Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 109 removed outlier: 4.792A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 5.900A pdb=" N ARG F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 removed outlier: 3.735A pdb=" N LEU F 178 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR F 179 " --> pdb=" O LYS F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 211 Processing helix chain 'F' and resid 227 through 238 removed outlier: 4.438A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 3.738A pdb=" N MET F 253 " --> pdb=" O ASN F 249 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 Processing helix chain 'H' and resid 74 through 79 Processing helix chain 'H' and resid 85 through 90 removed outlier: 6.515A pdb=" N ARG H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Proline residue: H 90 - end of helix No H-bonds generated for 'chain 'H' and resid 85 through 90' Processing helix chain 'H' and resid 115 through 122 removed outlier: 3.622A pdb=" N ASN H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 147 removed outlier: 5.112A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 52 removed outlier: 4.620A pdb=" N GLU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.743A pdb=" N ARG I 80 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE I 90 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP I 92 " --> pdb=" O ALA I 88 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 Processing helix chain 'I' and resid 127 through 139 Proline residue: I 133 - end of helix Processing helix chain 'I' and resid 140 through 147 Proline residue: I 145 - end of helix Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.728A pdb=" N ILE I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 196 Processing helix chain 'J' and resid 33 through 43 Proline residue: J 37 - end of helix removed outlier: 3.642A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY J 43 " --> pdb=" O LEU J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.041A pdb=" N ARG J 56 " --> pdb=" O GLU J 52 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE J 60 " --> pdb=" O ARG J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.611A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY J 96 " --> pdb=" O LYS J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 128 removed outlier: 4.044A pdb=" N GLN J 126 " --> pdb=" O ARG J 122 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP J 127 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLU J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 134 removed outlier: 4.902A pdb=" N ASP J 134 " --> pdb=" O PHE J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 3.519A pdb=" N GLY J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 187 removed outlier: 4.538A pdb=" N PHE J 165 " --> pdb=" O GLU J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 41 removed outlier: 3.517A pdb=" N LEU K 31 " --> pdb=" O PRO K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.642A pdb=" N LYS K 105 " --> pdb=" O VAL K 101 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) Proline residue: K 113 - end of helix Processing helix chain 'K' and resid 115 through 126 removed outlier: 4.577A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.594A pdb=" N ASN K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 159 removed outlier: 5.613A pdb=" N THR K 159 " --> pdb=" O LEU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 167 Proline residue: K 167 - end of helix Processing helix chain 'L' and resid 44 through 49 Processing helix chain 'L' and resid 127 through 132 removed outlier: 4.577A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLY L 132 " --> pdb=" O ARG L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 132' Processing helix chain 'L' and resid 134 through 142 removed outlier: 3.603A pdb=" N LEU L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA L 139 " --> pdb=" O SER L 135 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA L 141 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 134 through 142' Processing helix chain 'M' and resid 10 through 20 removed outlier: 4.155A pdb=" N LEU M 15 " --> pdb=" O ARG M 11 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU M 16 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.516A pdb=" N ARG M 77 " --> pdb=" O PRO M 73 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 73 through 78' Processing helix chain 'M' and resid 97 through 108 Processing helix chain 'M' and resid 117 through 125 Processing helix chain 'M' and resid 160 through 171 Processing helix chain 'M' and resid 180 through 190 removed outlier: 3.869A pdb=" N ILE M 186 " --> pdb=" O ARG M 182 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL M 187 " --> pdb=" O SER M 183 " (cutoff:3.500A) Proline residue: M 190 - end of helix Processing helix chain 'M' and resid 191 through 197 Processing helix chain 'M' and resid 210 through 216 Processing helix chain 'M' and resid 225 through 241 removed outlier: 3.953A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix Processing helix chain 'M' and resid 252 through 258 Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.617A pdb=" N TYR M 293 " --> pdb=" O ASN M 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 74 removed outlier: 5.228A pdb=" N GLY N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 170 through 184 removed outlier: 3.641A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN N 178 " --> pdb=" O GLY N 174 " (cutoff:3.500A) Proline residue: N 184 - end of helix Processing helix chain 'N' and resid 191 through 209 removed outlier: 3.575A pdb=" N GLN N 202 " --> pdb=" O MET N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 226 through 231 removed outlier: 4.857A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.570A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 removed outlier: 3.810A pdb=" N ILE O 26 " --> pdb=" O PRO O 22 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS O 27 " --> pdb=" O GLU O 23 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG O 38 " --> pdb=" O THR O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 65 removed outlier: 4.679A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 4.698A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 98 Proline residue: O 87 - end of helix removed outlier: 4.431A pdb=" N ALA O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Proline residue: O 95 - end of helix Processing helix chain 'O' and resid 143 through 160 removed outlier: 3.644A pdb=" N ARG O 153 " --> pdb=" O LEU O 149 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN O 154 " --> pdb=" O GLN O 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 59 removed outlier: 4.398A pdb=" N LEU P 55 " --> pdb=" O ASN P 51 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU P 56 " --> pdb=" O PRO P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 116 removed outlier: 5.117A pdb=" N HIS P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU P 115 " --> pdb=" O ILE P 111 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 139 Processing helix chain 'P' and resid 148 through 154 Processing helix chain 'P' and resid 155 through 168 removed outlier: 3.675A pdb=" N MET P 164 " --> pdb=" O LEU P 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR P 165 " --> pdb=" O GLN P 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 106 removed outlier: 4.159A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 194 removed outlier: 5.238A pdb=" N LEU Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 Processing helix chain 'Q' and resid 250 through 269 removed outlier: 3.960A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Proline residue: Q 263 - end of helix removed outlier: 4.882A pdb=" N GLU Q 266 " --> pdb=" O GLN Q 262 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N MET Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 292 Processing helix chain 'R' and resid 16 through 29 removed outlier: 3.508A pdb=" N ILE R 21 " --> pdb=" O ARG R 17 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 38 removed outlier: 4.487A pdb=" N ARG R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 68 removed outlier: 3.581A pdb=" N LYS R 55 " --> pdb=" O VAL R 51 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 79 Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 98 through 109 removed outlier: 3.546A pdb=" N ALA R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR R 108 " --> pdb=" O ASP R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 134 Processing helix chain 'S' and resid 54 through 59 removed outlier: 4.668A pdb=" N SER S 58 " --> pdb=" O THR S 54 " (cutoff:3.500A) Proline residue: S 59 - end of helix No H-bonds generated for 'chain 'S' and resid 54 through 59' Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.950A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 150 through 155' Processing helix chain 'T' and resid 49 through 57 removed outlier: 3.883A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE T 57 " --> pdb=" O LYS T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 95 removed outlier: 3.607A pdb=" N MET T 87 " --> pdb=" O SER T 83 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 109 removed outlier: 3.513A pdb=" N ALA T 104 " --> pdb=" O ASP T 100 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN T 105 " --> pdb=" O GLN T 101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU T 107 " --> pdb=" O LEU T 103 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 4.381A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL T 120 " --> pdb=" O ILE T 116 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU T 121 " --> pdb=" O ILE T 117 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU T 123 " --> pdb=" O GLU T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 207 removed outlier: 6.130A pdb=" N THR T 207 " --> pdb=" O LEU T 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 125 through 138 removed outlier: 5.625A pdb=" N GLN U 138 " --> pdb=" O ARG U 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 36 Proline residue: V 36 - end of helix Processing helix chain 'V' and resid 116 through 121 removed outlier: 4.962A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 184 Processing helix chain 'V' and resid 193 through 203 removed outlier: 3.588A pdb=" N GLU V 200 " --> pdb=" O GLU V 196 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA V 201 " --> pdb=" O GLU V 197 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 121 removed outlier: 3.601A pdb=" N LEU W 116 " --> pdb=" O GLU W 112 " (cutoff:3.500A) Proline residue: W 121 - end of helix Processing helix chain 'X' and resid 7 through 19 removed outlier: 4.026A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 25 removed outlier: 4.316A pdb=" N LEU X 24 " --> pdb=" O ILE X 20 " (cutoff:3.500A) Proline residue: X 25 - end of helix No H-bonds generated for 'chain 'X' and resid 20 through 25' Processing helix chain 'X' and resid 26 through 34 Processing helix chain 'X' and resid 72 through 79 removed outlier: 3.801A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 139 removed outlier: 3.510A pdb=" N ASP X 136 " --> pdb=" O LEU X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 148 removed outlier: 4.026A pdb=" N TYR X 144 " --> pdb=" O GLY X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 196 removed outlier: 3.966A pdb=" N LYS X 190 " --> pdb=" O ALA X 186 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU X 193 " --> pdb=" O ASP X 189 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE X 194 " --> pdb=" O LYS X 190 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA X 195 " --> pdb=" O TYR X 191 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE X 196 " --> pdb=" O LYS X 192 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 205 removed outlier: 5.659A pdb=" N GLY X 205 " --> pdb=" O ALA X 201 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 removed outlier: 3.500A pdb=" N GLU X 213 " --> pdb=" O GLU X 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 225 through 244 Processing helix chain 'Y' and resid 64 through 69 removed outlier: 4.560A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 64 through 69' Processing helix chain 'Y' and resid 70 through 75 removed outlier: 3.703A pdb=" N TRP Y 74 " --> pdb=" O ASP Y 70 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 70 through 75' Processing helix chain 'Y' and resid 86 through 94 removed outlier: 5.437A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.542A pdb=" N HIS Y 99 " --> pdb=" O ASN Y 95 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.061A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS Y 134 " --> pdb=" O GLU Y 130 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL Y 135 " --> pdb=" O ARG Y 131 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA Y 141 " --> pdb=" O ASP Y 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA Y 152 " --> pdb=" O GLU Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 3.764A pdb=" N ASN Y 191 " --> pdb=" O PRO Y 187 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 187 through 192' Processing helix chain 'Y' and resid 193 through 198 removed outlier: 3.946A pdb=" N LYS Y 197 " --> pdb=" O ARG Y 193 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 193 through 198' Processing helix chain 'Y' and resid 202 through 239 removed outlier: 4.114A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU Y 234 " --> pdb=" O LYS Y 230 " (cutoff:3.500A) Proline residue: Y 239 - end of helix Processing helix chain 'Z' and resid 42 through 47 removed outlier: 4.459A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 47' Processing helix chain 'Z' and resid 49 through 57 Processing helix chain 'Z' and resid 79 through 90 removed outlier: 3.538A pdb=" N ILE Z 85 " --> pdb=" O TRP Z 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE Z 86 " --> pdb=" O GLU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 114 removed outlier: 3.914A pdb=" N LYS Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL Z 112 " --> pdb=" O ALA Z 108 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 73 removed outlier: 4.356A pdb=" N THR a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS a 73 " --> pdb=" O TYR a 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 68 through 73' Processing helix chain 'a' and resid 104 through 117 removed outlier: 3.510A pdb=" N GLU a 110 " --> pdb=" O GLY a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 135 removed outlier: 6.010A pdb=" N ASN a 135 " --> pdb=" O ARG a 131 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.499A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ARG b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 40 through 50 Processing helix chain 'b' and resid 51 through 59 Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 108 removed outlier: 5.443A pdb=" N SER b 108 " --> pdb=" O LEU b 104 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 53 removed outlier: 5.303A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 59 through 64 Proline residue: c 64 - end of helix Processing helix chain 'c' and resid 67 through 80 Processing helix chain 'c' and resid 84 through 94 removed outlier: 5.618A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 107 Processing helix chain 'c' and resid 122 through 146 Proline residue: c 146 - end of helix Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 163 through 174 Processing helix chain 'c' and resid 175 through 180 removed outlier: 5.332A pdb=" N LEU c 180 " --> pdb=" O GLU c 176 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 227 removed outlier: 3.569A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY c 225 " --> pdb=" O THR c 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS c 226 " --> pdb=" O GLN c 222 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU c 227 " --> pdb=" O MET c 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 Processing helix chain 'c' and resid 288 through 306 removed outlier: 3.518A pdb=" N LYS c 303 " --> pdb=" O VAL c 299 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 71 Processing helix chain 'd' and resid 115 through 130 removed outlier: 3.536A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 155 removed outlier: 4.629A pdb=" N PHE d 137 " --> pdb=" O LYS d 133 " (cutoff:3.500A) Proline residue: d 138 - end of helix Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.512A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 173 Proline residue: d 170 - end of helix Processing helix chain 'e' and resid 64 through 82 removed outlier: 3.523A pdb=" N MET e 70 " --> pdb=" O LEU e 66 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA e 71 " --> pdb=" O GLN e 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER e 72 " --> pdb=" O GLU e 68 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU e 80 " --> pdb=" O GLN e 76 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 104 removed outlier: 3.665A pdb=" N ALA e 103 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 132 removed outlier: 4.874A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 144 removed outlier: 3.878A pdb=" N LYS e 143 " --> pdb=" O GLU e 139 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 196 Processing helix chain 'e' and resid 256 through 264 removed outlier: 3.637A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR e 263 " --> pdb=" O GLU e 259 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU e 264 " --> pdb=" O LEU e 260 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 3.882A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.780A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 59 through 64' Processing helix chain 'f' and resid 99 through 118 Processing helix chain 'f' and resid 164 through 178 removed outlier: 3.510A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE f 169 " --> pdb=" O THR f 165 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 53 removed outlier: 4.075A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU g 49 " --> pdb=" O TYR g 45 " (cutoff:3.500A) Proline residue: g 53 - end of helix Processing helix chain 'g' and resid 116 through 133 removed outlier: 3.696A pdb=" N LEU g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 Processing helix chain 'h' and resid 65 through 79 removed outlier: 4.400A pdb=" N GLY h 79 " --> pdb=" O LYS h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 108 Processing helix chain 'h' and resid 113 through 121 removed outlier: 3.562A pdb=" N LEU h 117 " --> pdb=" O PRO h 113 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 133 removed outlier: 3.732A pdb=" N VAL h 126 " --> pdb=" O ARG h 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Proline residue: h 133 - end of helix Processing helix chain 'h' and resid 138 through 147 removed outlier: 5.158A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 54 Processing helix chain 'i' and resid 59 through 64 Processing helix chain 'i' and resid 69 through 74 removed outlier: 4.329A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 74' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 Processing helix chain 'j' and resid 24 through 32 removed outlier: 3.526A pdb=" N GLN j 31 " --> pdb=" O TRP j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 36 through 41 removed outlier: 4.531A pdb=" N TYR j 40 " --> pdb=" O ASN j 36 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY j 41 " --> pdb=" O PRO j 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 36 through 41' Processing helix chain 'j' and resid 60 through 108 Processing helix chain 'k' and resid 2 through 9 removed outlier: 3.629A pdb=" N LEU k 8 " --> pdb=" O ALA k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 27 through 39 Processing helix chain 'k' and resid 40 through 47 removed outlier: 4.140A pdb=" N ASN k 46 " --> pdb=" O VAL k 42 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU k 47 " --> pdb=" O ARG k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 96 Processing helix chain 'l' and resid 64 through 71 Processing helix chain 'l' and resid 93 through 99 Processing helix chain 'l' and resid 106 through 111 removed outlier: 3.539A pdb=" N LEU l 110 " --> pdb=" O THR l 106 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASP l 111 " --> pdb=" O LEU l 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 106 through 111' Processing helix chain 'l' and resid 114 through 136 removed outlier: 3.638A pdb=" N TRP l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 94 Processing helix chain 'm' and resid 36 through 41 removed outlier: 4.897A pdb=" N SER m 39 " --> pdb=" O SER m 36 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU m 40 " --> pdb=" O ARG m 37 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR m 41 " --> pdb=" O ALA m 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 36 through 41' Processing helix chain 'o' and resid 28 through 51 removed outlier: 3.502A pdb=" N ARG o 37 " --> pdb=" O GLN o 33 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 61 removed outlier: 5.952A pdb=" N GLY o 61 " --> pdb=" O GLU o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 81 removed outlier: 4.903A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 4.566A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS o 100 " --> pdb=" O ASN o 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 49 Processing helix chain 'p' and resid 54 through 60 removed outlier: 4.077A pdb=" N ALA p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 77 removed outlier: 4.901A pdb=" N THR p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) Processing helix chain 'p' and resid 112 through 124 removed outlier: 3.605A pdb=" N GLN p 117 " --> pdb=" O GLU p 113 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS p 118 " --> pdb=" O PRO p 114 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 163 Processing helix chain 'p' and resid 174 through 190 removed outlier: 3.589A pdb=" N ARG p 189 " --> pdb=" O ARG p 185 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 54 removed outlier: 4.325A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) Proline residue: q 54 - end of helix Processing helix chain 'q' and resid 55 through 65 Processing helix chain 'q' and resid 71 through 76 removed outlier: 4.411A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP q 76 " --> pdb=" O PRO q 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 71 through 76' Processing helix chain 'q' and resid 78 through 93 Processing helix chain 'q' and resid 95 through 154 removed outlier: 3.511A pdb=" N ARG q 117 " --> pdb=" O LYS q 113 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS q 127 " --> pdb=" O GLU q 123 " (cutoff:3.500A) Proline residue: q 129 - end of helix removed outlier: 4.115A pdb=" N ARG q 152 " --> pdb=" O ALA q 148 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 76 Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.363A pdb=" N LEU r 89 " --> pdb=" O ASP r 85 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ARG r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 126 Processing helix chain 'r' and resid 178 through 183 removed outlier: 4.167A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP r 183 " --> pdb=" O PRO r 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 178 through 183' Processing helix chain 's' and resid 55 through 73 removed outlier: 3.562A pdb=" N ARG s 65 " --> pdb=" O ARG s 61 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP s 66 " --> pdb=" O ARG s 62 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 removed outlier: 3.662A pdb=" N ILE s 82 " --> pdb=" O GLU s 78 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR s 84 " --> pdb=" O LEU s 80 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 111 removed outlier: 3.792A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 140 through 155 removed outlier: 3.643A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) Processing helix chain 's' and resid 171 through 193 Proline residue: s 175 - end of helix Proline residue: s 190 - end of helix Proline residue: s 193 - end of helix Processing helix chain 's' and resid 307 through 315 removed outlier: 3.543A pdb=" N ASN s 315 " --> pdb=" O LEU s 311 " (cutoff:3.500A) Processing helix chain 's' and resid 318 through 344 removed outlier: 4.110A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 388 removed outlier: 4.156A pdb=" N GLN s 385 " --> pdb=" O THR s 381 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN s 387 " --> pdb=" O ALA s 383 " (cutoff:3.500A) Proline residue: s 388 - end of helix Processing helix chain 's' and resid 414 through 427 Processing sheet with id= 1, first strand: chain '0' and resid 107 through 111 removed outlier: 3.638A pdb=" N ASP 0 108 " --> pdb=" O LYS 0 117 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS 0 115 " --> pdb=" O CYS 0 110 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '0' and resid 155 through 161 removed outlier: 3.689A pdb=" N THR 0 161 " --> pdb=" O ARG 0 177 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1' and resid 42 through 46 Processing sheet with id= 4, first strand: chain '4' and resid 79 through 83 removed outlier: 6.414A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '5' and resid 126 through 130 removed outlier: 3.673A pdb=" N SER 5 344 " --> pdb=" O LEU 5 355 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU 5 291 " --> pdb=" O GLN 5 343 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '5' and resid 208 through 212 removed outlier: 5.163A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '6' and resid 183 through 187 removed outlier: 3.999A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '6' and resid 231 through 234 removed outlier: 6.619A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP 6 235 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '6' and resid 265 through 273 removed outlier: 3.560A pdb=" N HIS 6 266 " --> pdb=" O CYS 6 321 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '7' and resid 77 through 82 removed outlier: 4.888A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS 7 123 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '7' and resid 178 through 184 Processing sheet with id= 12, first strand: chain '7' and resid 217 through 221 removed outlier: 3.663A pdb=" N GLU 7 217 " --> pdb=" O ARG 7 256 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '9' and resid 42 through 45 Processing sheet with id= 14, first strand: chain 'D' and resid 128 through 131 removed outlier: 3.575A pdb=" N GLN D 128 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY D 179 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU D 164 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 214 through 217 removed outlier: 4.268A pdb=" N LEU D 217 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU D 237 " --> pdb=" O TYR D 295 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 139 through 144 removed outlier: 3.579A pdb=" N GLY D 144 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 147 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 98 through 101 Processing sheet with id= 18, first strand: chain 'E' and resid 105 through 111 removed outlier: 4.511A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 127 through 130 removed outlier: 4.486A pdb=" N HIS E 128 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY E 149 " --> pdb=" O THR E 175 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR E 175 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E' and resid 205 through 209 Processing sheet with id= 21, first strand: chain 'E' and resid 275 through 278 removed outlier: 8.162A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 46 through 49 removed outlier: 4.881A pdb=" N VAL F 47 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY F 78 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'F' and resid 186 through 189 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 258 through 261 current: chain 'F' and resid 216 through 220 Processing sheet with id= 24, first strand: chain 'H' and resid 111 through 114 Processing sheet with id= 25, first strand: chain 'I' and resid 94 through 100 Processing sheet with id= 26, first strand: chain 'J' and resid 18 through 26 removed outlier: 5.048A pdb=" N GLY J 18 " --> pdb=" O VAL J 72 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE J 64 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 17 through 22 Processing sheet with id= 28, first strand: chain 'K' and resid 77 through 81 removed outlier: 3.718A pdb=" N THR K 81 " --> pdb=" O GLY K 86 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLY K 86 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'L' and resid 35 through 38 removed outlier: 3.672A pdb=" N THR L 36 " --> pdb=" O CYS L 57 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL L 38 " --> pdb=" O PRO L 55 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'L' and resid 72 through 77 Processing sheet with id= 31, first strand: chain 'L' and resid 87 through 90 removed outlier: 4.521A pdb=" N GLY L 88 " --> pdb=" O ASN L 104 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N CYS L 90 " --> pdb=" O SER L 102 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER L 102 " --> pdb=" O CYS L 90 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 33, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 34, first strand: chain 'N' and resid 88 through 92 removed outlier: 6.470A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 94 through 97 Processing sheet with id= 36, first strand: chain 'N' and resid 119 through 123 removed outlier: 6.083A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.002A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 79 through 84 removed outlier: 6.456A pdb=" N VAL P 89 " --> pdb=" O THR P 106 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Q' and resid 129 through 136 removed outlier: 4.611A pdb=" N LYS Q 129 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Q' and resid 139 through 142 removed outlier: 4.217A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 105 through 109 removed outlier: 4.277A pdb=" N LEU S 135 " --> pdb=" O VAL S 98 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE S 141 " --> pdb=" O ALA S 138 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'S' and resid 113 through 117 removed outlier: 6.911A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 162 through 165 removed outlier: 3.666A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 168 through 175 removed outlier: 4.313A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'T' and resid 71 through 78 removed outlier: 5.451A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN T 139 " --> pdb=" O GLY T 181 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'T' and resid 151 through 159 removed outlier: 4.401A pdb=" N GLN T 151 " --> pdb=" O TYR T 171 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR T 171 " --> pdb=" O GLN T 151 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG T 163 " --> pdb=" O HIS T 159 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'U' and resid 39 through 44 removed outlier: 5.447A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR U 92 " --> pdb=" O GLN U 73 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 61 through 65 Processing sheet with id= 49, first strand: chain 'V' and resid 78 through 81 Processing sheet with id= 50, first strand: chain 'V' and resid 92 through 99 removed outlier: 6.479A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE V 98 " --> pdb=" O THR V 107 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR V 107 " --> pdb=" O ILE V 98 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'W' and resid 80 through 83 removed outlier: 7.806A pdb=" N HIS W 80 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'W' and resid 97 through 103 Processing sheet with id= 53, first strand: chain 'X' and resid 49 through 52 removed outlier: 5.026A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'X' and resid 85 through 91 Processing sheet with id= 55, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 56, first strand: chain 'Z' and resid 97 through 102 removed outlier: 6.566A pdb=" N LYS Z 65 " --> pdb=" O ASN Z 102 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Z' and resid 137 through 140 removed outlier: 3.501A pdb=" N CYS Z 138 " --> pdb=" O VAL Z 146 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU Z 144 " --> pdb=" O LYS Z 140 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'a' and resid 44 through 52 removed outlier: 7.198A pdb=" N ASN a 44 " --> pdb=" O VAL a 65 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'b' and resid 61 through 68 removed outlier: 6.467A pdb=" N VAL b 33 " --> pdb=" O ASN b 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL b 75 " --> pdb=" O GLU b 87 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR b 79 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA b 83 " --> pdb=" O TYR b 79 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'c' and resid 254 through 257 removed outlier: 3.649A pdb=" N ARG c 259 " --> pdb=" O PHE c 271 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'c' and resid 269 through 274 removed outlier: 4.033A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'd' and resid 192 through 195 removed outlier: 6.869A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN d 196 " --> pdb=" O THR d 213 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'd' and resid 259 through 262 removed outlier: 7.098A pdb=" N VAL d 247 " --> pdb=" O HIS d 262 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'd' and resid 210 through 218 Processing sheet with id= 65, first strand: chain 'e' and resid 175 through 178 removed outlier: 5.600A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU e 159 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'e' and resid 211 through 217 removed outlier: 3.623A pdb=" N GLY e 211 " --> pdb=" O PHE e 233 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU e 227 " --> pdb=" O PHE e 217 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'e' and resid 44 through 53 Processing sheet with id= 68, first strand: chain 'f' and resid 123 through 127 removed outlier: 4.364A pdb=" N GLU f 123 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'f' and resid 129 through 137 removed outlier: 3.671A pdb=" N LYS f 130 " --> pdb=" O THR f 152 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'g' and resid 96 through 101 removed outlier: 3.508A pdb=" N ILE g 110 " --> pdb=" O LEU g 147 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'k' and resid 49 through 56 Processing sheet with id= 72, first strand: chain 'm' and resid 62 through 67 removed outlier: 4.774A pdb=" N SER m 62 " --> pdb=" O LYS m 58 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'p' and resid 78 through 83 Processing sheet with id= 74, first strand: chain 'r' and resid 35 through 41 removed outlier: 4.946A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 's' and resid 90 through 93 Processing sheet with id= 76, first strand: chain 's' and resid 112 through 116 removed outlier: 3.542A pdb=" N ILE s 392 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE s 369 " --> pdb=" O THR s 396 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS s 300 " --> pdb=" O VAL s 360 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR s 362 " --> pdb=" O HIS s 300 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 's' and resid 198 through 202 Processing sheet with id= 78, first strand: chain 's' and resid 365 through 368 removed outlier: 8.785A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU s 401 " --> pdb=" O LYS s 365 " (cutoff:3.500A) 2427 hydrogen bonds defined for protein. 7206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 885 hydrogen bonds 1562 hydrogen bond angles 0 basepair planarities 366 basepair parallelities 817 stacking parallelities Total time for adding SS restraints: 74.52 Time building geometry restraints manager: 40.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 12063 1.28 - 1.41: 31764 1.41 - 1.55: 58187 1.55 - 1.68: 3226 1.68 - 1.81: 453 Bond restraints: 105693 Sorted by residual: bond pdb=" N PRO F 129 " pdb=" CA PRO F 129 " ideal model delta sigma weight residual 1.466 1.703 -0.237 1.24e-02 6.50e+03 3.65e+02 bond pdb=" C4' 2MU A3039 " pdb=" O4' 2MU A3039 " ideal model delta sigma weight residual 1.617 1.315 0.302 2.00e-02 2.50e+03 2.28e+02 bond pdb=" C5 5MU A2602 " pdb=" C6 5MU A2602 " ideal model delta sigma weight residual 1.155 1.454 -0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" C4' 2MU A3039 " pdb=" C3' 2MU A3039 " ideal model delta sigma weight residual 1.332 1.630 -0.298 2.00e-02 2.50e+03 2.23e+02 bond pdb=" O4' 2MU A3039 " pdb=" C1' 2MU A3039 " ideal model delta sigma weight residual 1.287 1.574 -0.287 2.00e-02 2.50e+03 2.07e+02 ... (remaining 105688 not shown) Histogram of bond angle deviations from ideal: 97.43 - 105.43: 8849 105.43 - 113.43: 61209 113.43 - 121.43: 54649 121.43 - 129.44: 24092 129.44 - 137.44: 1587 Bond angle restraints: 150386 Sorted by residual: angle pdb=" C TRP F 128 " pdb=" N PRO F 129 " pdb=" CA PRO F 129 " ideal model delta sigma weight residual 119.78 137.44 -17.66 1.03e+00 9.43e-01 2.94e+02 angle pdb=" CA PRO F 129 " pdb=" N PRO F 129 " pdb=" CD PRO F 129 " ideal model delta sigma weight residual 112.00 97.43 14.57 1.40e+00 5.10e-01 1.08e+02 angle pdb=" C1' 2MA A2990 " pdb=" N9 2MA A2990 " pdb=" C8 2MA A2990 " ideal model delta sigma weight residual 106.32 126.92 -20.60 3.00e+00 1.11e-01 4.71e+01 angle pdb=" C3' U A2987 " pdb=" O3' U A2987 " pdb=" P C A2988 " ideal model delta sigma weight residual 120.20 130.15 -9.95 1.50e+00 4.44e-01 4.40e+01 angle pdb=" C3' A A2297 " pdb=" O3' A A2297 " pdb=" P A A2298 " ideal model delta sigma weight residual 120.20 129.44 -9.24 1.50e+00 4.44e-01 3.79e+01 ... (remaining 150381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 61553 35.62 - 71.24: 3212 71.24 - 106.85: 516 106.85 - 142.47: 7 142.47 - 178.09: 16 Dihedral angle restraints: 65304 sinusoidal: 41427 harmonic: 23877 Sorted by residual: dihedral pdb=" C MHW C 1 " pdb=" N MHW C 1 " pdb=" CA MHW C 1 " pdb=" CB MHW C 1 " ideal model delta harmonic sigma weight residual -122.60 -178.41 55.81 0 2.50e+00 1.60e-01 4.98e+02 dihedral pdb=" N MHW C 1 " pdb=" C MHW C 1 " pdb=" CA MHW C 1 " pdb=" CB MHW C 1 " ideal model delta harmonic sigma weight residual 122.80 178.40 -55.60 0 2.50e+00 1.60e-01 4.95e+02 dihedral pdb=" CA PRO C 4 " pdb=" C PRO C 4 " pdb=" N MHU C 5 " pdb=" CA MHU C 5 " ideal model delta harmonic sigma weight residual 180.00 97.31 82.69 0 5.00e+00 4.00e-02 2.73e+02 ... (remaining 65301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.061: 17678 1.061 - 2.121: 0 2.121 - 3.182: 0 3.182 - 4.242: 0 4.242 - 5.303: 2 Chirality restraints: 17680 Sorted by residual: chirality pdb=" CA PRO C 4 " pdb=" N PRO C 4 " pdb=" C PRO C 4 " pdb=" CB PRO C 4 " both_signs ideal model delta sigma weight residual False 2.72 -2.58 5.30 2.00e-01 2.50e+01 7.03e+02 chirality pdb=" CB THR C 2 " pdb=" CA THR C 2 " pdb=" OG1 THR C 2 " pdb=" CG2 THR C 2 " both_signs ideal model delta sigma weight residual False 2.55 -2.58 5.13 2.00e-01 2.50e+01 6.57e+02 chirality pdb=" CA PRO F 129 " pdb=" N PRO F 129 " pdb=" C PRO F 129 " pdb=" CB PRO F 129 " both_signs ideal model delta sigma weight residual False 2.72 3.07 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 17677 not shown) Planarity restraints: 13535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A2625 " -0.034 2.00e-02 2.50e+03 5.54e-01 6.92e+03 pdb=" C4' 5MC A2625 " -0.426 2.00e-02 2.50e+03 pdb=" O4' 5MC A2625 " -0.578 2.00e-02 2.50e+03 pdb=" C3' 5MC A2625 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 5MC A2625 " 0.551 2.00e-02 2.50e+03 pdb=" C2' 5MC A2625 " 0.207 2.00e-02 2.50e+03 pdb=" O2' 5MC A2625 " -0.899 2.00e-02 2.50e+03 pdb=" C1' 5MC A2625 " -0.242 2.00e-02 2.50e+03 pdb=" N1 5MC A2625 " 0.829 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A2602 " 0.647 2.00e-02 2.50e+03 4.74e-01 5.05e+03 pdb=" C4' 5MU A2602 " -0.259 2.00e-02 2.50e+03 pdb=" O4' 5MU A2602 " -0.447 2.00e-02 2.50e+03 pdb=" C3' 5MU A2602 " 0.260 2.00e-02 2.50e+03 pdb=" O3' 5MU A2602 " -0.775 2.00e-02 2.50e+03 pdb=" C2' 5MU A2602 " 0.578 2.00e-02 2.50e+03 pdb=" O2' 5MU A2602 " 0.408 2.00e-02 2.50e+03 pdb=" C1' 5MU A2602 " -0.407 2.00e-02 2.50e+03 pdb=" N1 5MU A2602 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 H8T A3431 " -0.251 2.00e-02 2.50e+03 2.56e-01 1.48e+03 pdb=" C2 H8T A3431 " -0.309 2.00e-02 2.50e+03 pdb=" C3 H8T A3431 " 0.060 2.00e-02 2.50e+03 pdb=" C37 H8T A3431 " 0.526 2.00e-02 2.50e+03 pdb=" C4 H8T A3431 " 0.197 2.00e-02 2.50e+03 pdb=" C6 H8T A3431 " -0.075 2.00e-02 2.50e+03 pdb=" C8 H8T A3431 " 0.180 2.00e-02 2.50e+03 pdb=" N5 H8T A3431 " -0.055 2.00e-02 2.50e+03 pdb=" O7 H8T A3431 " -0.271 2.00e-02 2.50e+03 ... (remaining 13532 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 160 2.19 - 2.87: 32526 2.87 - 3.54: 145675 3.54 - 4.22: 265908 4.22 - 4.90: 405381 Nonbonded interactions: 849650 Sorted by model distance: nonbonded pdb=" OP2 A A2720 " pdb="MG MG A3397 " model vdw 1.512 2.170 nonbonded pdb=" P C A1672 " pdb=" O3' G A3429 " model vdw 1.607 3.400 nonbonded pdb=" O2 C A1905 " pdb=" N2 G A2018 " model vdw 1.752 2.520 nonbonded pdb=" O2' 2MA A2990 " pdb=" O18 H8T A3431 " model vdw 1.753 2.440 nonbonded pdb=" C2 C A1905 " pdb=" N2 G A2018 " model vdw 1.797 3.340 ... (remaining 849645 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: 6.070 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: 27.220 Check model and map are aligned: 1.140 Set scattering table: 0.720 Process input model: 304.600 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.310 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:2.520 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 345.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.005 0.302 105693 Z= 0.285 Angle : 0.608 20.600 150386 Z= 0.312 Chirality : 0.065 5.303 17680 Planarity : 0.008 0.554 13535 Dihedral : 18.291 178.087 49836 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 0.01 % Allowed : 2.59 % Favored : 97.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.01 % Twisted Proline : 0.18 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.08), residues: 8037 helix: -2.55 (0.07), residues: 2642 sheet: -2.40 (0.14), residues: 1000 loop : -2.00 (0.09), residues: 4395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP S 106 HIS 0.012 0.001 HIS F 138 PHE 0.019 0.001 PHE F 106 TYR 0.018 0.001 TYR T 82 ARG 0.005 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2969 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2968 time to evaluate : 6.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 168 GLN cc_start: 0.8525 (tm-30) cc_final: 0.7949 (tm-30) REVERT: 1 50 VAL cc_start: 0.8461 (t) cc_final: 0.7940 (t) REVERT: 3 118 HIS cc_start: 0.8215 (t-90) cc_final: 0.7758 (t-170) REVERT: 3 135 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7527 (ptmm) REVERT: 4 93 LYS cc_start: 0.8662 (mmtp) cc_final: 0.8106 (mtpp) REVERT: 5 364 LEU cc_start: 0.8246 (mm) cc_final: 0.7832 (mm) REVERT: 5 401 VAL cc_start: 0.9129 (t) cc_final: 0.8815 (p) REVERT: 6 44 ASN cc_start: 0.8042 (t0) cc_final: 0.7818 (t0) REVERT: 6 185 MET cc_start: 0.7646 (tpp) cc_final: 0.6557 (tpp) REVERT: 6 272 LEU cc_start: 0.8045 (tt) cc_final: 0.7636 (tt) REVERT: 6 362 PRO cc_start: 0.9171 (Cg_endo) cc_final: 0.8945 (Cg_exo) REVERT: 7 51 GLU cc_start: 0.7974 (tp30) cc_final: 0.7636 (tp30) REVERT: 7 84 ASN cc_start: 0.8051 (m110) cc_final: 0.7561 (m110) REVERT: 7 264 SER cc_start: 0.7613 (p) cc_final: 0.7142 (p) REVERT: 7 306 LEU cc_start: 0.7666 (pt) cc_final: 0.7263 (pp) REVERT: 8 125 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8189 (mmtp) REVERT: 9 44 LEU cc_start: 0.8445 (tp) cc_final: 0.8148 (tt) REVERT: 9 74 VAL cc_start: 0.8317 (t) cc_final: 0.7865 (p) REVERT: D 65 SER cc_start: 0.9054 (t) cc_final: 0.8827 (t) REVERT: D 132 ASP cc_start: 0.8585 (t0) cc_final: 0.8373 (t0) REVERT: D 151 ILE cc_start: 0.8306 (tt) cc_final: 0.8079 (tt) REVERT: D 197 GLU cc_start: 0.7527 (pt0) cc_final: 0.6950 (pm20) REVERT: E 77 LEU cc_start: 0.8803 (mt) cc_final: 0.8346 (tt) REVERT: E 87 ILE cc_start: 0.8377 (mt) cc_final: 0.8174 (mt) REVERT: E 122 LEU cc_start: 0.9230 (mt) cc_final: 0.8999 (mp) REVERT: F 67 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7545 (mm-30) REVERT: F 108 ARG cc_start: 0.8275 (ttt180) cc_final: 0.7678 (ttt90) REVERT: F 114 THR cc_start: 0.9051 (p) cc_final: 0.8776 (t) REVERT: F 192 SER cc_start: 0.7591 (m) cc_final: 0.6294 (p) REVERT: F 194 GLU cc_start: 0.7883 (mp0) cc_final: 0.6836 (mp0) REVERT: I 80 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7472 (mtt180) REVERT: I 84 ARG cc_start: 0.5879 (mtm110) cc_final: 0.5521 (ptp-170) REVERT: I 119 HIS cc_start: 0.6458 (m-70) cc_final: 0.5720 (m-70) REVERT: J 58 LYS cc_start: 0.6154 (mmtt) cc_final: 0.5820 (mmtt) REVERT: J 177 LYS cc_start: 0.5173 (ptpp) cc_final: 0.4720 (tptt) REVERT: K 4 PHE cc_start: 0.7904 (m-80) cc_final: 0.7337 (m-80) REVERT: K 101 VAL cc_start: 0.9043 (t) cc_final: 0.8777 (p) REVERT: L 111 ASN cc_start: 0.8515 (p0) cc_final: 0.8172 (p0) REVERT: L 125 THR cc_start: 0.8778 (p) cc_final: 0.8482 (p) REVERT: M 39 ARG cc_start: 0.7888 (mtp-110) cc_final: 0.6859 (mtm-85) REVERT: M 143 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7653 (tm-30) REVERT: N 71 ASP cc_start: 0.8449 (p0) cc_final: 0.8124 (p0) REVERT: N 83 THR cc_start: 0.8499 (p) cc_final: 0.7755 (p) REVERT: N 86 ASN cc_start: 0.8896 (m110) cc_final: 0.8546 (m-40) REVERT: N 117 ASN cc_start: 0.8419 (m110) cc_final: 0.8206 (m-40) REVERT: O 150 GLN cc_start: 0.8525 (tp40) cc_final: 0.8321 (tp40) REVERT: P 99 LYS cc_start: 0.9165 (ttpt) cc_final: 0.8853 (ttpp) REVERT: Q 172 GLN cc_start: 0.8454 (mm110) cc_final: 0.8184 (mp10) REVERT: Q 217 VAL cc_start: 0.8765 (t) cc_final: 0.8498 (p) REVERT: Q 264 TRP cc_start: 0.7684 (p90) cc_final: 0.7240 (p90) REVERT: R 36 ASN cc_start: 0.9121 (p0) cc_final: 0.8767 (p0) REVERT: R 76 SER cc_start: 0.8669 (p) cc_final: 0.8323 (t) REVERT: R 90 LEU cc_start: 0.9006 (mt) cc_final: 0.8779 (mt) REVERT: S 152 ASP cc_start: 0.8120 (p0) cc_final: 0.7717 (t0) REVERT: S 159 THR cc_start: 0.8697 (m) cc_final: 0.8432 (p) REVERT: T 87 MET cc_start: 0.7833 (pmm) cc_final: 0.7387 (ptm) REVERT: T 132 HIS cc_start: 0.6021 (m90) cc_final: 0.5606 (m90) REVERT: T 177 LYS cc_start: 0.8845 (tttt) cc_final: 0.8611 (tttm) REVERT: U 76 SER cc_start: 0.9049 (t) cc_final: 0.8735 (p) REVERT: V 85 TRP cc_start: 0.8377 (m-10) cc_final: 0.7907 (m-10) REVERT: V 134 GLU cc_start: 0.3898 (pt0) cc_final: 0.3033 (mp0) REVERT: V 216 TYR cc_start: 0.8298 (p90) cc_final: 0.7988 (p90) REVERT: W 74 ARG cc_start: 0.8709 (ttt180) cc_final: 0.7832 (mtt180) REVERT: W 93 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7790 (mm-30) REVERT: X 5 LYS cc_start: 0.8767 (tptm) cc_final: 0.8561 (tppt) REVERT: X 21 CYS cc_start: 0.8689 (p) cc_final: 0.8288 (p) REVERT: X 90 ILE cc_start: 0.9288 (tp) cc_final: 0.9045 (tt) REVERT: X 109 LEU cc_start: 0.9062 (mt) cc_final: 0.8612 (mt) REVERT: X 149 SER cc_start: 0.7517 (m) cc_final: 0.6799 (t) REVERT: X 238 LEU cc_start: 0.7353 (mm) cc_final: 0.7090 (tp) REVERT: Y 111 MET cc_start: 0.8246 (tmm) cc_final: 0.7779 (tmm) REVERT: Y 160 GLN cc_start: 0.8638 (mp-120) cc_final: 0.7396 (mp10) REVERT: Y 165 PRO cc_start: 0.9008 (Cg_exo) cc_final: 0.8768 (Cg_endo) REVERT: Y 214 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8029 (mt-10) REVERT: Z 44 LYS cc_start: 0.7663 (tmmt) cc_final: 0.7371 (pttm) REVERT: Z 73 LYS cc_start: 0.8818 (tptm) cc_final: 0.8522 (tttm) REVERT: Z 136 ASN cc_start: 0.7600 (p0) cc_final: 0.6998 (p0) REVERT: a 137 ASN cc_start: 0.7834 (p0) cc_final: 0.7207 (p0) REVERT: b 6 THR cc_start: 0.8824 (m) cc_final: 0.8559 (p) REVERT: b 30 SER cc_start: 0.9015 (m) cc_final: 0.8648 (t) REVERT: b 32 SER cc_start: 0.8687 (m) cc_final: 0.8062 (p) REVERT: b 68 ARG cc_start: 0.8491 (ptt-90) cc_final: 0.8203 (ptt90) REVERT: b 98 SER cc_start: 0.9078 (m) cc_final: 0.8817 (t) REVERT: b 99 THR cc_start: 0.9464 (p) cc_final: 0.9199 (p) REVERT: b 103 LYS cc_start: 0.8398 (ptmm) cc_final: 0.8109 (pttt) REVERT: c 88 LEU cc_start: 0.6886 (mt) cc_final: 0.6536 (mt) REVERT: c 97 TYR cc_start: 0.6767 (t80) cc_final: 0.6109 (t80) REVERT: c 308 THR cc_start: 0.8717 (p) cc_final: 0.8321 (t) REVERT: d 172 MET cc_start: 0.8364 (ttm) cc_final: 0.8137 (ttp) REVERT: d 196 GLN cc_start: 0.7568 (pt0) cc_final: 0.6713 (pp30) REVERT: d 202 MET cc_start: 0.3478 (tpt) cc_final: 0.2037 (ptt) REVERT: d 279 THR cc_start: 0.8452 (p) cc_final: 0.7983 (p) REVERT: d 282 ILE cc_start: 0.8436 (pt) cc_final: 0.7820 (mp) REVERT: e 120 LEU cc_start: 0.8233 (mt) cc_final: 0.8033 (mt) REVERT: e 124 TRP cc_start: 0.7483 (m-10) cc_final: 0.6922 (m-10) REVERT: e 126 GLN cc_start: 0.7411 (mp10) cc_final: 0.7113 (pt0) REVERT: e 154 ASP cc_start: 0.9099 (p0) cc_final: 0.8879 (p0) REVERT: e 205 LEU cc_start: 0.8270 (pp) cc_final: 0.7886 (mt) REVERT: f 122 GLU cc_start: 0.7456 (mp0) cc_final: 0.6906 (mp0) REVERT: g 68 THR cc_start: 0.7366 (m) cc_final: 0.7042 (p) REVERT: i 56 VAL cc_start: 0.9219 (t) cc_final: 0.8820 (p) REVERT: j 92 GLN cc_start: 0.8053 (mt0) cc_final: 0.7628 (mt0) REVERT: j 100 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7750 (tm-30) REVERT: k 19 GLN cc_start: 0.7607 (pt0) cc_final: 0.7208 (pt0) REVERT: l 128 ARG cc_start: 0.8196 (ptm160) cc_final: 0.7880 (ttm170) REVERT: m 56 LEU cc_start: 0.9272 (tt) cc_final: 0.8949 (tp) REVERT: m 57 VAL cc_start: 0.8304 (t) cc_final: 0.7873 (p) REVERT: m 79 ILE cc_start: 0.7749 (mp) cc_final: 0.7520 (mm) REVERT: p 152 GLN cc_start: 0.8177 (tp40) cc_final: 0.7878 (tp40) REVERT: q 112 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7947 (tm-30) REVERT: q 120 HIS cc_start: 0.6450 (t70) cc_final: 0.6019 (t-170) REVERT: q 130 GLN cc_start: 0.7827 (tp40) cc_final: 0.7509 (tp40) REVERT: q 131 MET cc_start: 0.8257 (ptp) cc_final: 0.7937 (ptp) REVERT: q 134 ASN cc_start: 0.8104 (m110) cc_final: 0.7334 (m110) REVERT: q 140 ARG cc_start: 0.7156 (mmp-170) cc_final: 0.6315 (mtm-85) REVERT: r 109 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7644 (tm-30) REVERT: r 181 LEU cc_start: 0.8360 (pt) cc_final: 0.8117 (pt) REVERT: s 174 LEU cc_start: 0.8530 (tt) cc_final: 0.8289 (tt) REVERT: s 232 GLN cc_start: 0.7825 (tp40) cc_final: 0.7583 (tp40) REVERT: s 274 PHE cc_start: 0.9079 (m-80) cc_final: 0.8536 (m-80) REVERT: s 318 ASP cc_start: 0.8218 (p0) cc_final: 0.8015 (t0) REVERT: s 419 LEU cc_start: 0.8249 (pp) cc_final: 0.8008 (tp) outliers start: 1 outliers final: 0 residues processed: 2968 average time/residue: 1.0245 time to fit residues: 4987.5046 Evaluate side-chains 1731 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1731 time to evaluate : 6.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 807 optimal weight: 0.0370 chunk 724 optimal weight: 0.9990 chunk 402 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 488 optimal weight: 20.0000 chunk 387 optimal weight: 3.9990 chunk 749 optimal weight: 1.9990 chunk 289 optimal weight: 6.9990 chunk 455 optimal weight: 3.9990 chunk 557 optimal weight: 0.0770 chunk 868 optimal weight: 1.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN 2 62 ASN ** 3 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 324 GLN 5 331 ASN ** 5 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 GLN 6 63 GLN 6 191 ASN 7 49 ASN 7 255 HIS 7 298 GLN 8 144 GLN 9 52 GLN D 168 HIS ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN E 174 GLN E 180 ASN E 339 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 115 ASN ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 ASN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 HIS Q 139 GLN Q 175 GLN R 22 GLN R 30 HIS ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 105 GLN T 210 HIS V 18 HIS Y 92 ASN Z 62 ASN a 62 HIS b 24 GLN b 25 GLN ** b 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 ASN c 122 ASN d 193 HIS e 67 GLN e 150 ASN f 61 HIS f 108 GLN h 103 HIS j 96 GLN k 15 GLN k 57 HIS l 125 ASN o 58 GLN p 104 HIS r 96 HIS r 148 ASN ** r 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 238 ASN s 382 GLN s 414 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 105693 Z= 0.212 Angle : 0.651 14.055 150386 Z= 0.321 Chirality : 0.038 0.330 17680 Planarity : 0.005 0.122 13535 Dihedral : 19.696 178.247 32483 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.71 % Favored : 96.28 % Rotamer: Outliers : 3.04 % Allowed : 15.51 % Favored : 81.44 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % 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: -1.80 (0.09), residues: 8037 helix: -0.56 (0.09), residues: 2733 sheet: -1.64 (0.14), residues: 1012 loop : -1.47 (0.09), residues: 4292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP j 91 HIS 0.013 0.001 HIS K 48 PHE 0.026 0.002 PHE e 165 TYR 0.032 0.002 TYR h 73 ARG 0.009 0.001 ARG H 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2130 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1910 time to evaluate : 7.048 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: 0 172 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8119 (mtmt) REVERT: 0 178 ASP cc_start: 0.6747 (p0) cc_final: 0.6467 (p0) REVERT: 1 20 MET cc_start: 0.7891 (mtm) cc_final: 0.7638 (mtm) REVERT: 1 60 LYS cc_start: 0.6601 (ptpt) cc_final: 0.6366 (ptmm) REVERT: 3 146 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7966 (mm-30) REVERT: 4 93 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8140 (mtpp) REVERT: 5 159 SER cc_start: 0.8096 (t) cc_final: 0.7455 (p) REVERT: 5 384 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7593 (tp-100) REVERT: 6 27 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7304 (ptm-80) REVERT: 6 41 ASP cc_start: 0.7507 (p0) cc_final: 0.6518 (p0) REVERT: 6 44 ASN cc_start: 0.8042 (t0) cc_final: 0.7378 (p0) REVERT: 6 116 ASN cc_start: 0.5639 (m110) cc_final: 0.4801 (m-40) REVERT: 7 149 MET cc_start: 0.8725 (ptt) cc_final: 0.8520 (ptp) REVERT: 7 179 PHE cc_start: 0.7440 (p90) cc_final: 0.7181 (p90) REVERT: 7 235 TYR cc_start: 0.7585 (m-80) cc_final: 0.7317 (m-80) REVERT: 7 317 LEU cc_start: 0.8484 (mp) cc_final: 0.8160 (tp) REVERT: 8 121 TRP cc_start: 0.8174 (t60) cc_final: 0.7956 (t60) REVERT: 8 143 GLN cc_start: 0.7715 (mt0) cc_final: 0.7431 (mt0) REVERT: 9 44 LEU cc_start: 0.8667 (tp) cc_final: 0.8250 (pp) REVERT: 9 94 GLU cc_start: 0.6754 (pp20) cc_final: 0.6327 (pp20) REVERT: D 132 ASP cc_start: 0.8538 (t0) cc_final: 0.8278 (t0) REVERT: D 155 GLU cc_start: 0.7852 (pm20) cc_final: 0.7631 (pm20) REVERT: D 197 GLU cc_start: 0.7699 (pt0) cc_final: 0.7017 (pm20) REVERT: E 77 LEU cc_start: 0.8938 (mt) cc_final: 0.8509 (tt) REVERT: E 227 GLN cc_start: 0.8125 (mp10) cc_final: 0.7613 (mp10) REVERT: E 344 SER cc_start: 0.8573 (p) cc_final: 0.7740 (p) REVERT: F 67 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7608 (mm-30) REVERT: F 103 GLN cc_start: 0.9171 (pt0) cc_final: 0.8730 (pt0) REVERT: F 108 ARG cc_start: 0.8657 (ttt180) cc_final: 0.8021 (ttt90) REVERT: F 114 THR cc_start: 0.9032 (p) cc_final: 0.8720 (t) REVERT: F 192 SER cc_start: 0.8237 (m) cc_final: 0.6993 (p) REVERT: F 194 GLU cc_start: 0.8063 (mp0) cc_final: 0.7078 (mp0) REVERT: F 226 MET cc_start: 0.7091 (mtm) cc_final: 0.6774 (mtt) REVERT: H 115 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8299 (mtpt) REVERT: I 84 ARG cc_start: 0.5741 (mtm110) cc_final: 0.4867 (ptp-170) REVERT: I 123 MET cc_start: 0.6495 (pmm) cc_final: 0.6295 (pmm) REVERT: J 49 PHE cc_start: 0.7562 (t80) cc_final: 0.7274 (t80) REVERT: J 142 ARG cc_start: 0.6945 (mtm180) cc_final: 0.6326 (mtm180) REVERT: J 177 LYS cc_start: 0.5062 (ptpp) cc_final: 0.4670 (tptt) REVERT: K 128 PHE cc_start: 0.8838 (m-80) cc_final: 0.8488 (m-10) REVERT: L 111 ASN cc_start: 0.8604 (p0) cc_final: 0.8057 (p0) REVERT: L 117 THR cc_start: 0.8772 (p) cc_final: 0.7996 (t) REVERT: L 118 ARG cc_start: 0.7902 (mpp-170) cc_final: 0.6946 (mpp-170) REVERT: L 125 THR cc_start: 0.8967 (p) cc_final: 0.8685 (p) REVERT: M 143 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7448 (tm-30) REVERT: M 248 THR cc_start: 0.8448 (m) cc_final: 0.8135 (p) REVERT: M 273 TRP cc_start: 0.7243 (m100) cc_final: 0.6390 (m100) REVERT: M 284 LYS cc_start: 0.6651 (mppt) cc_final: 0.6137 (mttm) REVERT: N 87 PHE cc_start: 0.7833 (m-80) cc_final: 0.7605 (m-10) REVERT: N 118 MET cc_start: 0.8984 (ptp) cc_final: 0.8436 (ptp) REVERT: N 169 PHE cc_start: 0.8222 (t80) cc_final: 0.8019 (t80) REVERT: N 200 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8582 (mttt) REVERT: N 247 MET cc_start: 0.8279 (mpp) cc_final: 0.7846 (mtt) REVERT: P 56 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8596 (tm-30) REVERT: P 57 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8566 (mm) REVERT: P 64 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6496 (mt-10) REVERT: P 99 LYS cc_start: 0.9126 (ttpt) cc_final: 0.8820 (ttpp) REVERT: P 116 TYR cc_start: 0.8614 (t80) cc_final: 0.7190 (t80) REVERT: Q 123 ASP cc_start: 0.8020 (t0) cc_final: 0.7645 (t0) REVERT: Q 172 GLN cc_start: 0.8419 (mm110) cc_final: 0.8010 (mm110) REVERT: Q 276 SER cc_start: 0.8145 (p) cc_final: 0.7905 (t) REVERT: R 41 LEU cc_start: 0.8761 (mp) cc_final: 0.7631 (mp) REVERT: S 85 GLU cc_start: 0.7905 (pp20) cc_final: 0.7399 (pp20) REVERT: S 152 ASP cc_start: 0.8070 (p0) cc_final: 0.7356 (t0) REVERT: T 74 TYR cc_start: 0.8921 (m-80) cc_final: 0.8287 (m-80) REVERT: T 82 TYR cc_start: 0.8575 (t80) cc_final: 0.8221 (t80) REVERT: T 87 MET cc_start: 0.7840 (pmm) cc_final: 0.7314 (ptm) REVERT: T 97 MET cc_start: 0.5186 (ptt) cc_final: 0.4661 (ptt) REVERT: T 173 HIS cc_start: 0.6925 (m-70) cc_final: 0.6453 (m-70) REVERT: T 177 LYS cc_start: 0.9049 (tttt) cc_final: 0.8471 (ttmm) REVERT: U 48 MET cc_start: 0.8587 (mtm) cc_final: 0.8338 (mtm) REVERT: U 76 SER cc_start: 0.9097 (t) cc_final: 0.8878 (p) REVERT: U 92 TYR cc_start: 0.8859 (p90) cc_final: 0.8581 (p90) REVERT: V 194 LEU cc_start: 0.7963 (tt) cc_final: 0.7691 (tp) REVERT: V 216 TYR cc_start: 0.8392 (p90) cc_final: 0.7900 (p90) REVERT: W 74 ARG cc_start: 0.8873 (ttt180) cc_final: 0.8248 (ttt180) REVERT: X 5 LYS cc_start: 0.8830 (tptm) cc_final: 0.8562 (tppt) REVERT: X 21 CYS cc_start: 0.8654 (p) cc_final: 0.8297 (p) REVERT: X 80 TRP cc_start: 0.8467 (m-10) cc_final: 0.7894 (m-10) REVERT: Y 111 MET cc_start: 0.8423 (tmm) cc_final: 0.7914 (tmm) REVERT: Y 160 GLN cc_start: 0.8903 (mp-120) cc_final: 0.8552 (mp10) REVERT: Z 73 LYS cc_start: 0.8975 (tptm) cc_final: 0.8718 (tttm) REVERT: Z 136 ASN cc_start: 0.7805 (p0) cc_final: 0.7201 (p0) REVERT: a 137 ASN cc_start: 0.7636 (p0) cc_final: 0.7382 (p0) REVERT: b 14 VAL cc_start: 0.8218 (t) cc_final: 0.7973 (t) REVERT: b 25 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8849 (tp40) REVERT: b 32 SER cc_start: 0.8648 (m) cc_final: 0.8362 (t) REVERT: c 308 THR cc_start: 0.8938 (p) cc_final: 0.8386 (t) REVERT: d 160 LEU cc_start: 0.8859 (tt) cc_final: 0.8620 (tt) REVERT: d 171 ASP cc_start: 0.8510 (m-30) cc_final: 0.8152 (m-30) REVERT: d 172 MET cc_start: 0.8547 (ttm) cc_final: 0.8291 (ttp) REVERT: d 202 MET cc_start: 0.3291 (tpt) cc_final: 0.2083 (ptt) REVERT: e 124 TRP cc_start: 0.7337 (m-10) cc_final: 0.7100 (m-10) REVERT: e 189 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7814 (tp30) REVERT: e 205 LEU cc_start: 0.8396 (pp) cc_final: 0.7994 (mt) REVERT: f 122 GLU cc_start: 0.7561 (mp0) cc_final: 0.7002 (mp0) REVERT: f 173 ILE cc_start: 0.8979 (tp) cc_final: 0.8776 (mt) REVERT: g 68 THR cc_start: 0.7792 (m) cc_final: 0.7032 (p) REVERT: g 99 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: i 32 ILE cc_start: 0.6065 (mm) cc_final: 0.5744 (mm) REVERT: i 56 VAL cc_start: 0.9290 (t) cc_final: 0.9036 (p) REVERT: i 110 LEU cc_start: 0.9141 (tp) cc_final: 0.8795 (tp) REVERT: j 53 ASP cc_start: 0.7876 (p0) cc_final: 0.7608 (p0) REVERT: j 97 LYS cc_start: 0.8196 (mtpp) cc_final: 0.7822 (mtmm) REVERT: k 82 THR cc_start: 0.7313 (t) cc_final: 0.6574 (p) REVERT: k 84 LEU cc_start: 0.6967 (pt) cc_final: 0.6650 (mp) REVERT: l 99 MET cc_start: 0.2744 (ttm) cc_final: 0.2120 (ptm) REVERT: l 124 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: m 48 TYR cc_start: 0.6916 (p90) cc_final: 0.6173 (p90) REVERT: m 52 TYR cc_start: 0.6749 (m-80) cc_final: 0.6463 (m-80) REVERT: m 73 ARG cc_start: 0.7478 (mtt90) cc_final: 0.6955 (mtt90) REVERT: m 74 MET cc_start: 0.8284 (ppp) cc_final: 0.7994 (ppp) REVERT: m 79 ILE cc_start: 0.7728 (mp) cc_final: 0.7471 (mm) REVERT: m 90 ARG cc_start: 0.5987 (ptt90) cc_final: 0.5763 (ptt90) REVERT: o 49 LEU cc_start: 0.8193 (pt) cc_final: 0.7973 (pt) REVERT: p 80 TYR cc_start: 0.7857 (m-10) cc_final: 0.7642 (m-10) REVERT: p 152 GLN cc_start: 0.8528 (tp40) cc_final: 0.8177 (tp40) REVERT: p 157 MET cc_start: 0.7628 (mtp) cc_final: 0.7318 (mtp) REVERT: q 56 TYR cc_start: 0.7772 (t80) cc_final: 0.7236 (t80) REVERT: q 120 HIS cc_start: 0.6484 (t70) cc_final: 0.6085 (t-170) REVERT: q 131 MET cc_start: 0.8229 (ptp) cc_final: 0.7927 (ptp) REVERT: q 140 ARG cc_start: 0.7221 (mmp-170) cc_final: 0.6264 (mtm-85) REVERT: r 117 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7567 (tm-30) REVERT: s 232 GLN cc_start: 0.7773 (tp40) cc_final: 0.7475 (tp40) REVERT: s 269 ASP cc_start: 0.8242 (m-30) cc_final: 0.7725 (t0) REVERT: s 274 PHE cc_start: 0.9174 (m-80) cc_final: 0.8683 (m-80) REVERT: s 318 ASP cc_start: 0.8332 (p0) cc_final: 0.8042 (t0) outliers start: 220 outliers final: 131 residues processed: 2009 average time/residue: 0.9374 time to fit residues: 3219.5164 Evaluate side-chains 1735 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1600 time to evaluate : 6.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 153 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 1 residue 35 ASN Chi-restraints excluded: chain 3 residue 137 THR Chi-restraints excluded: chain 3 residue 155 SER Chi-restraints excluded: chain 4 residue 68 ASN Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 5 residue 331 ASN Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 396 VAL Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 6 residue 92 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 140 GLU Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 291 TYR Chi-restraints excluded: chain 7 residue 46 ASP Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 186 ASP Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 98 HIS Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 63 LYS Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain Q residue 155 ILE Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 283 TRP Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 143 ASP Chi-restraints excluded: chain Y residue 145 VAL Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 152 LYS Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 234 ILE Chi-restraints excluded: chain c residue 283 GLU Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 238 VAL Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 69 GLU Chi-restraints excluded: chain e residue 272 VAL Chi-restraints excluded: chain g residue 51 LEU Chi-restraints excluded: chain g residue 99 ASP Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 121 CYS Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 153 LYS Chi-restraints excluded: chain h residue 154 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain p residue 134 ILE Chi-restraints excluded: chain p residue 180 ILE Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 123 GLU Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 214 GLU Chi-restraints excluded: chain s residue 414 ASN Chi-restraints excluded: chain s residue 424 PHE Chi-restraints excluded: chain s residue 426 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 482 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 722 optimal weight: 1.9990 chunk 591 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 869 optimal weight: 0.6980 chunk 939 optimal weight: 3.9990 chunk 774 optimal weight: 7.9990 chunk 862 optimal weight: 7.9990 chunk 296 optimal weight: 8.9990 chunk 697 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 96 HIS ** 5 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 66 GLN 6 249 GLN 7 49 ASN 8 158 HIS D 156 ASN D 182 HIS ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 ASN K 160 GLN M 198 GLN ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 GLN ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 HIS P 96 GLN ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN Q 175 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 HIS S 105 GLN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN T 62 GLN ** T 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS W 132 HIS Y 179 HIS Y 183 GLN Y 189 HIS Y 240 HIS Z 62 ASN ** Z 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 123 ASN d 153 ASN e 87 HIS i 124 HIS ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 48 ASN k 57 HIS l 125 ASN m 44 HIS p 104 HIS ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 130 GLN q 134 ASN r 79 HIS r 123 HIS s 154 HIS ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 343 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.164 105693 Z= 0.410 Angle : 0.763 13.442 150386 Z= 0.389 Chirality : 0.044 0.351 17680 Planarity : 0.006 0.113 13535 Dihedral : 19.855 178.057 32483 Min Nonbonded Distance : 0.868 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.80 % Favored : 95.18 % Rotamer: Outliers : 5.85 % Allowed : 17.93 % Favored : 76.22 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.09), residues: 8037 helix: -0.00 (0.09), residues: 2723 sheet: -1.18 (0.15), residues: 1013 loop : -1.16 (0.09), residues: 4301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP l 118 HIS 0.013 0.002 HIS E 292 PHE 0.038 0.003 PHE Y 238 TYR 0.047 0.003 TYR F 280 ARG 0.020 0.001 ARG e 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2267 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 423 poor density : 1844 time to evaluate : 7.375 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: 0 102 LYS cc_start: 0.8778 (mtmm) cc_final: 0.8439 (pttp) REVERT: 1 33 LYS cc_start: 0.9116 (ptmt) cc_final: 0.8891 (ptmm) REVERT: 2 66 TRP cc_start: 0.8894 (t-100) cc_final: 0.8630 (t-100) REVERT: 3 164 SER cc_start: 0.9549 (OUTLIER) cc_final: 0.9314 (t) REVERT: 4 93 LYS cc_start: 0.8770 (mmtp) cc_final: 0.8283 (mtpp) REVERT: 4 102 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: 5 210 SER cc_start: 0.8787 (t) cc_final: 0.8556 (p) REVERT: 5 314 ILE cc_start: 0.9107 (pt) cc_final: 0.8893 (mt) REVERT: 6 103 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8764 (tt) REVERT: 6 105 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7618 (tm-30) REVERT: 6 120 GLU cc_start: 0.7410 (tp30) cc_final: 0.6774 (tp30) REVERT: 6 356 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7787 (ttp80) REVERT: 7 51 GLU cc_start: 0.7738 (tp30) cc_final: 0.7398 (mm-30) REVERT: 8 120 LYS cc_start: 0.8561 (mtmm) cc_final: 0.8274 (mtmm) REVERT: 9 18 MET cc_start: 0.8747 (mmm) cc_final: 0.8519 (mpp) REVERT: 9 44 LEU cc_start: 0.9013 (tp) cc_final: 0.8559 (tt) REVERT: 9 69 LYS cc_start: 0.7425 (pttm) cc_final: 0.7221 (tppt) REVERT: 9 126 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8080 (ttpt) REVERT: D 155 GLU cc_start: 0.8643 (pm20) cc_final: 0.8394 (pm20) REVERT: D 177 ARG cc_start: 0.8107 (mtm180) cc_final: 0.7194 (ttp-110) REVERT: D 235 GLN cc_start: 0.8785 (tp40) cc_final: 0.8462 (mm-40) REVERT: E 77 LEU cc_start: 0.9004 (mt) cc_final: 0.8682 (tt) REVERT: E 183 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8700 (p0) REVERT: E 203 TYR cc_start: 0.8445 (m-10) cc_final: 0.8185 (m-10) REVERT: E 227 GLN cc_start: 0.8784 (mp10) cc_final: 0.8211 (mp10) REVERT: E 344 SER cc_start: 0.9192 (p) cc_final: 0.8900 (p) REVERT: F 98 GLN cc_start: 0.8893 (mt0) cc_final: 0.8686 (mt0) REVERT: F 103 GLN cc_start: 0.9406 (pt0) cc_final: 0.9033 (pt0) REVERT: F 182 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9150 (tt) REVERT: F 190 MET cc_start: 0.8519 (mpp) cc_final: 0.7807 (mtp) REVERT: F 192 SER cc_start: 0.8947 (m) cc_final: 0.8608 (m) REVERT: F 194 GLU cc_start: 0.8200 (mp0) cc_final: 0.7836 (mp0) REVERT: F 280 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7022 (t80) REVERT: H 80 TYR cc_start: 0.9339 (m-80) cc_final: 0.9116 (m-80) REVERT: H 95 GLU cc_start: 0.8202 (pp20) cc_final: 0.7922 (pp20) REVERT: H 96 LEU cc_start: 0.8383 (mt) cc_final: 0.8082 (mt) REVERT: H 115 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8244 (mtpt) REVERT: I 112 MET cc_start: 0.8451 (ttp) cc_final: 0.8075 (tmm) REVERT: I 123 MET cc_start: 0.6703 (pmm) cc_final: 0.6414 (mpp) REVERT: I 144 LEU cc_start: 0.7230 (mt) cc_final: 0.6902 (mt) REVERT: J 52 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6350 (mm-30) REVERT: J 177 LYS cc_start: 0.4760 (ptpp) cc_final: 0.4231 (tptt) REVERT: K 22 ASP cc_start: 0.8404 (t0) cc_final: 0.7961 (t0) REVERT: K 62 THR cc_start: 0.9622 (p) cc_final: 0.9406 (t) REVERT: K 99 ASP cc_start: 0.7992 (t0) cc_final: 0.7585 (t0) REVERT: K 109 TYR cc_start: 0.8899 (t80) cc_final: 0.8245 (t80) REVERT: K 116 LEU cc_start: 0.9147 (mt) cc_final: 0.8837 (mm) REVERT: K 147 GLN cc_start: 0.8421 (mt0) cc_final: 0.8179 (mt0) REVERT: K 150 LYS cc_start: 0.8817 (mppt) cc_final: 0.8565 (mtpp) REVERT: L 33 GLN cc_start: 0.8246 (pt0) cc_final: 0.7988 (pt0) REVERT: L 111 ASN cc_start: 0.8753 (p0) cc_final: 0.8505 (p0) REVERT: L 117 THR cc_start: 0.8807 (p) cc_final: 0.8242 (t) REVERT: L 118 ARG cc_start: 0.8078 (mpp-170) cc_final: 0.7421 (mpp-170) REVERT: M 111 ASP cc_start: 0.7716 (t0) cc_final: 0.7193 (t70) REVERT: M 143 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7269 (tm-30) REVERT: N 118 MET cc_start: 0.9207 (ptp) cc_final: 0.8455 (ptp) REVERT: N 226 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8754 (mp) REVERT: N 247 MET cc_start: 0.8546 (mpp) cc_final: 0.8127 (mtt) REVERT: O 50 ASP cc_start: 0.8247 (t0) cc_final: 0.8040 (t0) REVERT: O 57 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8517 (mm-30) REVERT: O 84 ASP cc_start: 0.8925 (p0) cc_final: 0.8665 (p0) REVERT: P 56 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8711 (tm-30) REVERT: P 57 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8609 (mm) REVERT: P 96 GLN cc_start: 0.8794 (tp40) cc_final: 0.8311 (tp40) REVERT: P 99 LYS cc_start: 0.9266 (ttpt) cc_final: 0.9041 (ttpp) REVERT: Q 123 ASP cc_start: 0.8272 (t0) cc_final: 0.7929 (t0) REVERT: Q 259 LYS cc_start: 0.8306 (pptt) cc_final: 0.7778 (mtmt) REVERT: Q 276 SER cc_start: 0.8401 (p) cc_final: 0.8090 (t) REVERT: Q 279 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: R 44 ARG cc_start: 0.9119 (mpp80) cc_final: 0.8693 (mtt180) REVERT: R 55 LYS cc_start: 0.9079 (ptpp) cc_final: 0.8315 (mttm) REVERT: R 64 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8346 (mmm) REVERT: R 76 SER cc_start: 0.9439 (m) cc_final: 0.8736 (t) REVERT: R 89 ASN cc_start: 0.8803 (m110) cc_final: 0.8562 (m110) REVERT: S 81 LYS cc_start: 0.8569 (tmmt) cc_final: 0.7986 (tppt) REVERT: S 85 GLU cc_start: 0.8225 (pp20) cc_final: 0.7660 (pp20) REVERT: S 152 ASP cc_start: 0.7844 (p0) cc_final: 0.7485 (t0) REVERT: S 165 GLU cc_start: 0.8009 (pt0) cc_final: 0.7758 (pt0) REVERT: T 87 MET cc_start: 0.8438 (pmm) cc_final: 0.8238 (ptm) REVERT: T 105 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8723 (mm-40) REVERT: T 135 GLU cc_start: 0.8134 (tt0) cc_final: 0.7823 (tt0) REVERT: T 173 HIS cc_start: 0.8545 (m-70) cc_final: 0.8038 (m-70) REVERT: U 12 LEU cc_start: 0.8441 (mm) cc_final: 0.8031 (tp) REVERT: U 16 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7623 (tm-30) REVERT: U 17 LEU cc_start: 0.9333 (tp) cc_final: 0.8893 (tp) REVERT: U 55 ASN cc_start: 0.8984 (m-40) cc_final: 0.8780 (m-40) REVERT: U 78 LYS cc_start: 0.9226 (tttp) cc_final: 0.8567 (ttpt) REVERT: U 104 THR cc_start: 0.7746 (m) cc_final: 0.7314 (t) REVERT: V 51 ASP cc_start: 0.7838 (m-30) cc_final: 0.7143 (p0) REVERT: V 115 LEU cc_start: 0.8092 (mm) cc_final: 0.7696 (mp) REVERT: W 137 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8745 (mtpt) REVERT: X 5 LYS cc_start: 0.8862 (tptm) cc_final: 0.8632 (tppt) REVERT: X 21 CYS cc_start: 0.8575 (p) cc_final: 0.8188 (p) REVERT: X 71 PHE cc_start: 0.9123 (m-80) cc_final: 0.8798 (m-80) REVERT: X 80 TRP cc_start: 0.8547 (m-10) cc_final: 0.8115 (m-10) REVERT: X 90 ILE cc_start: 0.9423 (tp) cc_final: 0.9152 (tt) REVERT: X 142 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: X 189 ASP cc_start: 0.8113 (p0) cc_final: 0.7899 (t0) REVERT: X 192 LYS cc_start: 0.8314 (pttm) cc_final: 0.7832 (ptmt) REVERT: Y 111 MET cc_start: 0.8544 (tmm) cc_final: 0.8142 (tmm) REVERT: Y 160 GLN cc_start: 0.9092 (mp-120) cc_final: 0.8558 (mp10) REVERT: Y 176 ILE cc_start: 0.9478 (tt) cc_final: 0.9263 (tt) REVERT: Z 136 ASN cc_start: 0.8129 (p0) cc_final: 0.7740 (p0) REVERT: b 14 VAL cc_start: 0.8592 (t) cc_final: 0.8352 (t) REVERT: b 25 GLN cc_start: 0.9288 (tp-100) cc_final: 0.9038 (mm-40) REVERT: b 32 SER cc_start: 0.8840 (m) cc_final: 0.8569 (t) REVERT: b 66 ASN cc_start: 0.7893 (t0) cc_final: 0.7652 (t0) REVERT: b 103 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.9028 (pttt) REVERT: b 110 LEU cc_start: 0.8990 (pt) cc_final: 0.8317 (mt) REVERT: c 257 LEU cc_start: 0.8894 (pt) cc_final: 0.8669 (tp) REVERT: d 158 ASP cc_start: 0.8638 (t0) cc_final: 0.8277 (t70) REVERT: d 172 MET cc_start: 0.8674 (ttm) cc_final: 0.8239 (ttp) REVERT: d 202 MET cc_start: 0.2736 (tpt) cc_final: 0.1816 (ptt) REVERT: e 63 LEU cc_start: 0.8018 (mp) cc_final: 0.7697 (mt) REVERT: e 124 TRP cc_start: 0.7430 (m-10) cc_final: 0.7192 (m-10) REVERT: e 189 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7811 (tp30) REVERT: e 205 LEU cc_start: 0.8519 (pp) cc_final: 0.8161 (mt) REVERT: f 109 TYR cc_start: 0.9038 (t80) cc_final: 0.8783 (t80) REVERT: f 120 LYS cc_start: 0.8902 (tttp) cc_final: 0.8549 (tmtt) REVERT: f 122 GLU cc_start: 0.7317 (mp0) cc_final: 0.6619 (mp0) REVERT: g 68 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8050 (p) REVERT: h 139 LYS cc_start: 0.7571 (tppt) cc_final: 0.7338 (tppt) REVERT: i 32 ILE cc_start: 0.7237 (mm) cc_final: 0.6968 (mm) REVERT: i 63 LEU cc_start: 0.9282 (pt) cc_final: 0.8844 (pp) REVERT: i 79 TRP cc_start: 0.8995 (p90) cc_final: 0.8676 (p90) REVERT: i 122 ASN cc_start: 0.9175 (m-40) cc_final: 0.8776 (m-40) REVERT: j 75 ARG cc_start: 0.8762 (mmt90) cc_final: 0.8546 (tpp80) REVERT: j 97 LYS cc_start: 0.8435 (mtpp) cc_final: 0.8010 (mtmm) REVERT: k 8 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6203 (tp) REVERT: k 43 ARG cc_start: 0.7655 (mtp180) cc_final: 0.7268 (mtp180) REVERT: l 99 MET cc_start: 0.2939 (ttm) cc_final: 0.2330 (ptm) REVERT: l 124 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: m 48 TYR cc_start: 0.7239 (p90) cc_final: 0.6584 (p90) REVERT: m 52 TYR cc_start: 0.7284 (m-80) cc_final: 0.6709 (m-80) REVERT: m 74 MET cc_start: 0.8328 (ppp) cc_final: 0.7848 (tpp) REVERT: m 79 ILE cc_start: 0.7854 (mp) cc_final: 0.7556 (mm) REVERT: p 115 VAL cc_start: 0.8149 (m) cc_final: 0.7922 (t) REVERT: p 142 TYR cc_start: 0.8011 (m-10) cc_final: 0.7788 (m-10) REVERT: p 152 GLN cc_start: 0.8957 (tp40) cc_final: 0.8702 (tp40) REVERT: p 157 MET cc_start: 0.8208 (mtp) cc_final: 0.7886 (mtp) REVERT: p 190 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: q 92 TRP cc_start: 0.8808 (m100) cc_final: 0.8410 (m100) REVERT: q 136 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: q 140 ARG cc_start: 0.7212 (mmp-170) cc_final: 0.6274 (mtm110) REVERT: r 117 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7790 (tm-30) REVERT: r 190 THR cc_start: 0.7128 (OUTLIER) cc_final: 0.6900 (m) REVERT: s 214 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8242 (mt-10) REVERT: s 241 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.8960 (mt) REVERT: s 269 ASP cc_start: 0.8329 (m-30) cc_final: 0.7914 (t0) REVERT: s 296 HIS cc_start: 0.8779 (t-90) cc_final: 0.8561 (t-170) REVERT: s 419 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8124 (mt) REVERT: s 425 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8896 (mt) outliers start: 423 outliers final: 233 residues processed: 2072 average time/residue: 1.0273 time to fit residues: 3616.7615 Evaluate side-chains 1790 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1531 time to evaluate : 6.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 141 ILE Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 1 residue 35 ASN Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 155 SER Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 4 residue 102 GLN Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 396 VAL Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 6 residue 92 LEU Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 249 GLN Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 356 ARG Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 46 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 186 ASP Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 53 ILE Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain 9 residue 64 ASP Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 126 LYS Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 294 ASN Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 280 TYR Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 188 CYS Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 98 HIS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 63 LYS Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 175 GLN Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 254 MET Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 38 CYS Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 203 CYS Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 153 LEU Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 56 ASN Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 135 VAL Chi-restraints excluded: chain Y residue 143 ASP Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 146 VAL Chi-restraints excluded: chain Z residue 152 LYS Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 103 LYS Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 140 PHE Chi-restraints excluded: chain c residue 228 LEU Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 140 LYS Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 207 ASN Chi-restraints excluded: chain d residue 237 ASP Chi-restraints excluded: chain d residue 277 LEU Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 146 ARG Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 272 VAL Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 151 THR Chi-restraints excluded: chain f residue 156 VAL Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 87 ARG Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 117 ILE Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 142 GLU Chi-restraints excluded: chain h residue 154 ILE Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain k residue 8 LEU Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 64 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 49 LEU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 98 THR Chi-restraints excluded: chain p residue 119 ILE Chi-restraints excluded: chain p residue 134 ILE Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 188 LEU Chi-restraints excluded: chain p residue 190 GLN Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 119 GLN Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 136 GLN Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain r residue 128 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 214 GLU Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 270 LYS Chi-restraints excluded: chain s residue 312 LEU Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain s residue 424 PHE Chi-restraints excluded: chain s residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 859 optimal weight: 9.9990 chunk 653 optimal weight: 0.0870 chunk 451 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 415 optimal weight: 5.9990 chunk 584 optimal weight: 0.8980 chunk 872 optimal weight: 1.9990 chunk 924 optimal weight: 2.9990 chunk 456 optimal weight: 0.7980 chunk 827 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN ** 0 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 77 GLN ** 5 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 380 GLN 6 266 HIS ** 6 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 320 GLN 7 49 ASN ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN E 115 GLN ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN I 128 ASN K 89 GLN M 58 GLN M 114 GLN M 153 ASN N 237 HIS ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 HIS R 12 ASN R 89 ASN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN V 18 HIS X 177 HIS Y 240 HIS Z 62 ASN ** Z 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 154 ASN ** d 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 158 GLN i 122 ASN k 46 ASN k 80 HIS ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 105693 Z= 0.194 Angle : 0.630 13.616 150386 Z= 0.315 Chirality : 0.038 0.331 17680 Planarity : 0.005 0.116 13535 Dihedral : 19.821 178.249 32483 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 4.41 % Allowed : 22.00 % Favored : 73.59 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % 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: -0.78 (0.09), residues: 8037 helix: 0.39 (0.10), residues: 2734 sheet: -1.06 (0.15), residues: 1015 loop : -0.94 (0.09), residues: 4288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP 5 78 HIS 0.011 0.001 HIS F 97 PHE 0.031 0.002 PHE 7 179 TYR 0.031 0.002 TYR F 280 ARG 0.009 0.001 ARG b 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2014 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1695 time to evaluate : 7.056 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: 2 66 TRP cc_start: 0.8958 (t-100) cc_final: 0.8587 (t-100) REVERT: 3 164 SER cc_start: 0.9548 (m) cc_final: 0.9233 (t) REVERT: 4 85 ARG cc_start: 0.9235 (ptp90) cc_final: 0.8847 (ptp90) REVERT: 4 93 LYS cc_start: 0.8654 (mmtp) cc_final: 0.8103 (mtpp) REVERT: 4 102 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: 5 336 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8049 (pp) REVERT: 6 44 ASN cc_start: 0.7958 (t0) cc_final: 0.7267 (p0) REVERT: 6 105 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7600 (tm-30) REVERT: 6 120 GLU cc_start: 0.7613 (tp30) cc_final: 0.7223 (tp30) REVERT: 6 337 MET cc_start: 0.7629 (mtm) cc_final: 0.6932 (ttm) REVERT: 6 356 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7836 (ttp80) REVERT: 7 46 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8890 (m-30) REVERT: 7 51 GLU cc_start: 0.7829 (tp30) cc_final: 0.7399 (tp30) REVERT: 7 97 GLU cc_start: 0.8276 (pp20) cc_final: 0.7809 (pp20) REVERT: 9 18 MET cc_start: 0.8755 (mmm) cc_final: 0.8520 (mpp) REVERT: 9 44 LEU cc_start: 0.8895 (tp) cc_final: 0.8485 (tt) REVERT: 9 69 LYS cc_start: 0.7488 (pttm) cc_final: 0.7222 (tppt) REVERT: D 123 GLU cc_start: 0.8362 (tt0) cc_final: 0.8064 (tt0) REVERT: D 132 ASP cc_start: 0.8649 (t0) cc_final: 0.8267 (t0) REVERT: D 177 ARG cc_start: 0.7643 (mtm180) cc_final: 0.7428 (ttp-110) REVERT: D 178 GLU cc_start: 0.8022 (tt0) cc_final: 0.7818 (tt0) REVERT: D 197 GLU cc_start: 0.8183 (pt0) cc_final: 0.7712 (pt0) REVERT: D 227 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8433 (tm-30) REVERT: D 235 GLN cc_start: 0.8787 (tp40) cc_final: 0.8236 (tp-100) REVERT: D 265 TRP cc_start: 0.8348 (m-10) cc_final: 0.7352 (m-10) REVERT: E 227 GLN cc_start: 0.8743 (mp10) cc_final: 0.8291 (mp10) REVERT: E 239 ARG cc_start: 0.9549 (mmm-85) cc_final: 0.9264 (tpp80) REVERT: F 101 MET cc_start: 0.8055 (mtm) cc_final: 0.7760 (mmm) REVERT: F 103 GLN cc_start: 0.9263 (pt0) cc_final: 0.8986 (pt0) REVERT: F 190 MET cc_start: 0.8390 (mpp) cc_final: 0.7736 (mtp) REVERT: F 192 SER cc_start: 0.8762 (m) cc_final: 0.8148 (p) REVERT: F 194 GLU cc_start: 0.8101 (mp0) cc_final: 0.7306 (mp0) REVERT: F 280 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.6905 (t80) REVERT: H 80 TYR cc_start: 0.9294 (m-80) cc_final: 0.9069 (m-80) REVERT: H 91 LYS cc_start: 0.7630 (mmmt) cc_final: 0.7258 (ptpt) REVERT: H 115 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8259 (mtpt) REVERT: I 112 MET cc_start: 0.8344 (ttp) cc_final: 0.7987 (tmm) REVERT: I 144 LEU cc_start: 0.7153 (mt) cc_final: 0.6881 (mt) REVERT: J 51 LYS cc_start: 0.8925 (pptt) cc_final: 0.8568 (pptt) REVERT: J 142 ARG cc_start: 0.7313 (mtm180) cc_final: 0.6944 (mtm180) REVERT: J 177 LYS cc_start: 0.4480 (ptpp) cc_final: 0.4034 (tptt) REVERT: K 99 ASP cc_start: 0.7931 (t0) cc_final: 0.7537 (t0) REVERT: K 122 MET cc_start: 0.8881 (tpp) cc_final: 0.8540 (tpp) REVERT: K 147 GLN cc_start: 0.8333 (mt0) cc_final: 0.8110 (mt0) REVERT: K 150 LYS cc_start: 0.8785 (mppt) cc_final: 0.8548 (mtpp) REVERT: L 33 GLN cc_start: 0.7935 (pt0) cc_final: 0.7628 (pt0) REVERT: L 111 ASN cc_start: 0.8888 (p0) cc_final: 0.8471 (p0) REVERT: L 117 THR cc_start: 0.8890 (p) cc_final: 0.8298 (t) REVERT: L 118 ARG cc_start: 0.8137 (mpp-170) cc_final: 0.7473 (mpp-170) REVERT: M 91 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6304 (tpp-160) REVERT: M 99 ASN cc_start: 0.8962 (m110) cc_final: 0.8063 (m110) REVERT: M 111 ASP cc_start: 0.7679 (t0) cc_final: 0.7012 (t70) REVERT: M 143 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7039 (tm-30) REVERT: M 204 MET cc_start: 0.8226 (mmm) cc_final: 0.7896 (mmt) REVERT: N 118 MET cc_start: 0.9036 (ptp) cc_final: 0.8128 (ptp) REVERT: N 247 MET cc_start: 0.8583 (mpp) cc_final: 0.8191 (mtt) REVERT: O 84 ASP cc_start: 0.8953 (p0) cc_final: 0.8633 (p0) REVERT: P 56 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8708 (tm-30) REVERT: P 96 GLN cc_start: 0.8693 (tp40) cc_final: 0.8301 (tp40) REVERT: P 99 LYS cc_start: 0.9236 (ttpt) cc_final: 0.8976 (ttpp) REVERT: P 109 TRP cc_start: 0.8277 (t-100) cc_final: 0.8072 (t-100) REVERT: P 131 LEU cc_start: 0.9307 (tp) cc_final: 0.9055 (tt) REVERT: P 140 ILE cc_start: 0.9095 (mm) cc_final: 0.8333 (mm) REVERT: Q 259 LYS cc_start: 0.8233 (pptt) cc_final: 0.7839 (mtmt) REVERT: Q 276 SER cc_start: 0.8345 (p) cc_final: 0.7979 (t) REVERT: R 76 SER cc_start: 0.9390 (m) cc_final: 0.8690 (t) REVERT: S 81 LYS cc_start: 0.8544 (tmmt) cc_final: 0.7915 (tppt) REVERT: S 85 GLU cc_start: 0.8209 (pp20) cc_final: 0.7659 (pp20) REVERT: S 152 ASP cc_start: 0.7789 (p0) cc_final: 0.7413 (t0) REVERT: T 173 HIS cc_start: 0.8484 (m-70) cc_final: 0.7937 (m-70) REVERT: U 12 LEU cc_start: 0.8250 (mm) cc_final: 0.7775 (tp) REVERT: U 16 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7586 (tm-30) REVERT: U 17 LEU cc_start: 0.9353 (tp) cc_final: 0.8952 (tp) REVERT: U 78 LYS cc_start: 0.9260 (tttp) cc_final: 0.8571 (ttpt) REVERT: V 51 ASP cc_start: 0.7763 (m-30) cc_final: 0.7017 (p0) REVERT: V 92 ASN cc_start: 0.8834 (t0) cc_final: 0.8605 (t0) REVERT: V 115 LEU cc_start: 0.8040 (mm) cc_final: 0.7835 (mp) REVERT: V 122 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6945 (mm) REVERT: V 127 ASP cc_start: 0.6264 (t0) cc_final: 0.6000 (t0) REVERT: W 53 ILE cc_start: 0.9137 (pt) cc_final: 0.8440 (pt) REVERT: W 74 ARG cc_start: 0.9029 (ttt180) cc_final: 0.8614 (ttt180) REVERT: W 102 GLU cc_start: 0.8222 (mp0) cc_final: 0.7537 (mp0) REVERT: W 137 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8718 (mtpt) REVERT: X 21 CYS cc_start: 0.8576 (p) cc_final: 0.7553 (p) REVERT: X 71 PHE cc_start: 0.9092 (m-80) cc_final: 0.8776 (m-80) REVERT: X 80 TRP cc_start: 0.8454 (m-10) cc_final: 0.7983 (m-10) REVERT: X 90 ILE cc_start: 0.9438 (tp) cc_final: 0.9134 (tt) REVERT: X 100 ARG cc_start: 0.8894 (ttp-110) cc_final: 0.8671 (ttp-110) REVERT: X 189 ASP cc_start: 0.8138 (p0) cc_final: 0.7767 (t0) REVERT: Y 111 MET cc_start: 0.8563 (tmm) cc_final: 0.8115 (tmm) REVERT: Y 160 GLN cc_start: 0.9053 (mp-120) cc_final: 0.8517 (mp10) REVERT: Y 176 ILE cc_start: 0.9481 (tt) cc_final: 0.9258 (tt) REVERT: Z 136 ASN cc_start: 0.8168 (p0) cc_final: 0.7653 (p0) REVERT: a 70 GLU cc_start: 0.6334 (tm-30) cc_final: 0.5947 (tm-30) REVERT: b 25 GLN cc_start: 0.9318 (tp-100) cc_final: 0.9077 (mm-40) REVERT: b 32 SER cc_start: 0.8861 (m) cc_final: 0.8306 (t) REVERT: b 103 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8981 (pttt) REVERT: b 110 LEU cc_start: 0.8997 (pt) cc_final: 0.8332 (mt) REVERT: c 82 ASN cc_start: 0.8031 (p0) cc_final: 0.7671 (p0) REVERT: c 243 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: d 158 ASP cc_start: 0.8551 (t0) cc_final: 0.8241 (t70) REVERT: d 172 MET cc_start: 0.8554 (ttm) cc_final: 0.8294 (ttp) REVERT: d 202 MET cc_start: 0.2750 (tpt) cc_final: 0.1833 (ptt) REVERT: e 63 LEU cc_start: 0.7923 (mp) cc_final: 0.7560 (mt) REVERT: e 124 TRP cc_start: 0.7510 (m-10) cc_final: 0.7180 (m-10) REVERT: e 205 LEU cc_start: 0.8522 (pp) cc_final: 0.8041 (mt) REVERT: f 99 ASP cc_start: 0.7517 (t0) cc_final: 0.7265 (t0) REVERT: f 109 TYR cc_start: 0.9003 (t80) cc_final: 0.8741 (t80) REVERT: f 120 LYS cc_start: 0.8781 (tttp) cc_final: 0.8473 (tptp) REVERT: f 122 GLU cc_start: 0.7456 (mp0) cc_final: 0.6734 (mp0) REVERT: g 68 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8180 (p) REVERT: g 112 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8342 (mtpt) REVERT: h 71 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7571 (mm-30) REVERT: i 63 LEU cc_start: 0.9199 (pt) cc_final: 0.8694 (pp) REVERT: i 79 TRP cc_start: 0.8866 (p90) cc_final: 0.8644 (p90) REVERT: i 122 ASN cc_start: 0.9146 (m110) cc_final: 0.8727 (m-40) REVERT: j 75 ARG cc_start: 0.8663 (mmt90) cc_final: 0.8295 (mtt-85) REVERT: j 91 TRP cc_start: 0.8621 (t60) cc_final: 0.8080 (t60) REVERT: j 97 LYS cc_start: 0.8395 (mtpp) cc_final: 0.7957 (mtmm) REVERT: k 14 LYS cc_start: 0.6997 (pttm) cc_final: 0.6691 (pttm) REVERT: l 99 MET cc_start: 0.3064 (ttm) cc_final: 0.2503 (ptm) REVERT: l 124 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: m 46 GLN cc_start: 0.7443 (tp-100) cc_final: 0.7151 (mm-40) REVERT: m 48 TYR cc_start: 0.7261 (p90) cc_final: 0.6692 (p90) REVERT: m 52 TYR cc_start: 0.7242 (m-80) cc_final: 0.6661 (m-80) REVERT: m 68 TYR cc_start: 0.6699 (t80) cc_final: 0.6371 (t80) REVERT: m 74 MET cc_start: 0.8242 (ppp) cc_final: 0.7698 (tpp) REVERT: m 79 ILE cc_start: 0.7769 (mp) cc_final: 0.7476 (mm) REVERT: o 26 PHE cc_start: 0.7831 (m-80) cc_final: 0.7599 (m-80) REVERT: o 47 TYR cc_start: 0.8947 (t80) cc_final: 0.7977 (t80) REVERT: p 181 GLU cc_start: 0.8326 (tp30) cc_final: 0.7990 (tm-30) REVERT: p 190 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7176 (mp10) REVERT: q 80 GLU cc_start: 0.8214 (tp30) cc_final: 0.7993 (tp30) REVERT: q 92 TRP cc_start: 0.8798 (m100) cc_final: 0.8430 (m100) REVERT: q 136 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8158 (mm110) REVERT: q 140 ARG cc_start: 0.7049 (mmp-170) cc_final: 0.6148 (mtm-85) REVERT: r 117 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7626 (tm-30) REVERT: s 66 TRP cc_start: 0.8210 (p-90) cc_final: 0.7889 (p-90) REVERT: s 152 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7567 (pp30) REVERT: s 241 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8884 (mt) REVERT: s 269 ASP cc_start: 0.8322 (m-30) cc_final: 0.7856 (t0) REVERT: s 309 GLU cc_start: 0.7828 (pp20) cc_final: 0.7606 (pp20) outliers start: 319 outliers final: 190 residues processed: 1875 average time/residue: 0.9198 time to fit residues: 2983.1699 Evaluate side-chains 1745 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1538 time to evaluate : 6.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 123 CYS Chi-restraints excluded: chain 0 residue 156 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 1 residue 35 ASN Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 4 residue 102 GLN Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 396 VAL Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 140 GLU Chi-restraints excluded: chain 6 residue 153 GLU Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 356 ARG Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 46 ASP Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 85 ILE Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 186 ASP Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain 7 residue 306 LEU Chi-restraints excluded: chain 8 residue 127 GLN Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 141 GLU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 53 ILE Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain 9 residue 64 ASP Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 280 TYR Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain M residue 139 GLN Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 260 TRP Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 147 SER Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 194 LEU Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 154 CYS Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 135 VAL Chi-restraints excluded: chain Y residue 143 ASP Chi-restraints excluded: chain Y residue 145 VAL Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 93 SER Chi-restraints excluded: chain b residue 103 LYS Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 140 PHE Chi-restraints excluded: chain c residue 228 LEU Chi-restraints excluded: chain c residue 243 GLU Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 237 ASP Chi-restraints excluded: chain d residue 238 VAL Chi-restraints excluded: chain d residue 249 GLU Chi-restraints excluded: chain d residue 277 LEU Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 272 VAL Chi-restraints excluded: chain f residue 62 LEU Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 117 ILE Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 142 GLU Chi-restraints excluded: chain h residue 154 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain k residue 80 HIS Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 49 LEU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain p residue 134 ILE Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 150 CYS Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain p residue 190 GLN Chi-restraints excluded: chain q residue 119 GLN Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 136 GLN Chi-restraints excluded: chain r residue 91 GLN Chi-restraints excluded: chain r residue 128 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 260 GLU Chi-restraints excluded: chain s residue 360 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 769 optimal weight: 5.9990 chunk 524 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 688 optimal weight: 5.9990 chunk 381 optimal weight: 6.9990 chunk 788 optimal weight: 9.9990 chunk 638 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 471 optimal weight: 2.9990 chunk 829 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN ** 0 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 181 HIS 5 109 HIS 6 102 GLN 6 249 GLN ** 6 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN 7 277 GLN 9 52 GLN D 158 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN F 103 GLN ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN I 101 ASN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 GLN I 151 ASN ** K 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN M 102 GLN M 170 ASN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN Q 107 HIS R 89 ASN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS ** V 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 240 HIS Z 62 ASN ** Z 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 HIS d 153 ASN f 158 GLN f 189 HIS h 119 GLN m 44 HIS ** o 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 104 HIS ** p 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN q 130 GLN q 142 ASN r 76 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 296 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 105693 Z= 0.413 Angle : 0.753 16.902 150386 Z= 0.381 Chirality : 0.043 0.323 17680 Planarity : 0.006 0.115 13535 Dihedral : 19.891 179.458 32483 Min Nonbonded Distance : 0.982 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.29 % Favored : 94.69 % Rotamer: Outliers : 6.69 % Allowed : 21.79 % Favored : 71.52 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % 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: -0.80 (0.09), residues: 8037 helix: 0.32 (0.10), residues: 2735 sheet: -1.02 (0.15), residues: 1027 loop : -0.92 (0.09), residues: 4275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP 5 78 HIS 0.048 0.002 HIS k 80 PHE 0.043 0.003 PHE U 25 TYR 0.038 0.003 TYR F 280 ARG 0.013 0.001 ARG M 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2127 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 484 poor density : 1643 time to evaluate : 7.061 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: 1 20 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7773 (mtm) REVERT: 2 59 LYS cc_start: 0.9307 (mtpp) cc_final: 0.8979 (mttt) REVERT: 2 66 TRP cc_start: 0.8959 (t-100) cc_final: 0.8614 (t-100) REVERT: 3 115 LEU cc_start: 0.9243 (tt) cc_final: 0.8999 (tp) REVERT: 4 93 LYS cc_start: 0.8816 (mmtp) cc_final: 0.8389 (mtpp) REVERT: 5 241 SER cc_start: 0.6528 (p) cc_final: 0.5794 (m) REVERT: 6 44 ASN cc_start: 0.8155 (t0) cc_final: 0.7414 (p0) REVERT: 6 96 LYS cc_start: 0.5158 (tttp) cc_final: 0.4847 (tptt) REVERT: 6 103 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8696 (tt) REVERT: 6 105 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7627 (tm-30) REVERT: 6 337 MET cc_start: 0.8154 (mtm) cc_final: 0.7635 (mtm) REVERT: 6 356 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7730 (ttp80) REVERT: 7 51 GLU cc_start: 0.7931 (tp30) cc_final: 0.7671 (mm-30) REVERT: 7 115 MET cc_start: 0.8840 (mmm) cc_final: 0.8507 (tpp) REVERT: 9 102 LYS cc_start: 0.6095 (mmtp) cc_final: 0.5777 (mmpt) REVERT: 9 126 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8153 (ttpt) REVERT: D 111 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7932 (mmm-85) REVERT: D 128 GLN cc_start: 0.8385 (tt0) cc_final: 0.7846 (tt0) REVERT: D 134 CYS cc_start: 0.8439 (m) cc_final: 0.7784 (m) REVERT: D 177 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7658 (ttp-110) REVERT: D 197 GLU cc_start: 0.8346 (pt0) cc_final: 0.8041 (pt0) REVERT: D 199 GLU cc_start: 0.8365 (pm20) cc_final: 0.8068 (pm20) REVERT: D 208 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8256 (mtt180) REVERT: D 227 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8472 (tm-30) REVERT: D 235 GLN cc_start: 0.8883 (tp40) cc_final: 0.8465 (tt0) REVERT: D 265 TRP cc_start: 0.8563 (m-10) cc_final: 0.7420 (m-10) REVERT: E 227 GLN cc_start: 0.8941 (mp10) cc_final: 0.8593 (mp10) REVERT: F 98 GLN cc_start: 0.8852 (mt0) cc_final: 0.8627 (mt0) REVERT: F 108 ARG cc_start: 0.8925 (ttt180) cc_final: 0.8507 (ttt180) REVERT: F 182 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9312 (tp) REVERT: F 190 MET cc_start: 0.8302 (mpp) cc_final: 0.7641 (mtp) REVERT: F 194 GLU cc_start: 0.8352 (mp0) cc_final: 0.8102 (mp0) REVERT: F 280 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7551 (t80) REVERT: H 70 LYS cc_start: 0.8449 (mtmm) cc_final: 0.7706 (mmmt) REVERT: H 115 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8217 (mtpt) REVERT: I 48 MET cc_start: 0.8753 (mmm) cc_final: 0.8543 (mtt) REVERT: I 112 MET cc_start: 0.8380 (ttp) cc_final: 0.8026 (tmm) REVERT: J 142 ARG cc_start: 0.7285 (mtm180) cc_final: 0.6956 (mtm180) REVERT: J 165 PHE cc_start: 0.8154 (m-80) cc_final: 0.7854 (m-80) REVERT: J 177 LYS cc_start: 0.4204 (ptpp) cc_final: 0.3881 (tptt) REVERT: K 80 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8153 (t70) REVERT: K 99 ASP cc_start: 0.8166 (t0) cc_final: 0.7783 (t0) REVERT: K 116 LEU cc_start: 0.9085 (mt) cc_final: 0.8835 (mm) REVERT: K 122 MET cc_start: 0.9169 (tpp) cc_final: 0.8528 (tpp) REVERT: K 150 LYS cc_start: 0.8845 (mppt) cc_final: 0.8589 (mtpp) REVERT: K 174 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6719 (mm-30) REVERT: L 33 GLN cc_start: 0.8206 (pt0) cc_final: 0.7890 (pt0) REVERT: L 111 ASN cc_start: 0.8935 (p0) cc_final: 0.8516 (p0) REVERT: L 117 THR cc_start: 0.8871 (p) cc_final: 0.8534 (t) REVERT: M 91 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6898 (tpp80) REVERT: M 99 ASN cc_start: 0.9080 (m110) cc_final: 0.8662 (m110) REVERT: M 111 ASP cc_start: 0.7802 (t0) cc_final: 0.7279 (t70) REVERT: M 170 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8053 (t0) REVERT: M 281 LYS cc_start: 0.7051 (mtmm) cc_final: 0.6696 (mttm) REVERT: N 118 MET cc_start: 0.8981 (ptp) cc_final: 0.8132 (ptp) REVERT: N 247 MET cc_start: 0.8697 (mpp) cc_final: 0.8401 (mtt) REVERT: P 56 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8705 (tm-30) REVERT: P 57 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8760 (mm) REVERT: P 96 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8661 (tp40) REVERT: P 99 LYS cc_start: 0.9296 (ttpt) cc_final: 0.8997 (mtmm) REVERT: P 140 ILE cc_start: 0.9301 (mm) cc_final: 0.8503 (mm) REVERT: Q 259 LYS cc_start: 0.8640 (pptt) cc_final: 0.8337 (mtmt) REVERT: R 20 ARG cc_start: 0.8950 (ptp-170) cc_final: 0.8724 (ptp-170) REVERT: R 64 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8386 (mmm) REVERT: R 76 SER cc_start: 0.9515 (m) cc_final: 0.8791 (t) REVERT: R 89 ASN cc_start: 0.8906 (m-40) cc_final: 0.8677 (m110) REVERT: S 81 LYS cc_start: 0.8706 (tmmt) cc_final: 0.8106 (tppt) REVERT: S 85 GLU cc_start: 0.8354 (pp20) cc_final: 0.7795 (pp20) REVERT: S 95 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8376 (mp) REVERT: S 105 GLN cc_start: 0.9413 (mm-40) cc_final: 0.8666 (mt0) REVERT: S 152 ASP cc_start: 0.7951 (p0) cc_final: 0.7518 (t0) REVERT: S 165 GLU cc_start: 0.8153 (pt0) cc_final: 0.7612 (pt0) REVERT: T 87 MET cc_start: 0.8322 (ptm) cc_final: 0.8063 (ptm) REVERT: T 101 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8760 (tp40) REVERT: U 37 GLU cc_start: 0.8348 (pm20) cc_final: 0.8000 (pt0) REVERT: U 104 THR cc_start: 0.8131 (m) cc_final: 0.7690 (t) REVERT: V 115 LEU cc_start: 0.7954 (mm) cc_final: 0.7741 (mp) REVERT: W 56 MET cc_start: 0.8639 (mmm) cc_final: 0.8383 (mmt) REVERT: W 74 ARG cc_start: 0.9125 (ttt180) cc_final: 0.8795 (ttt180) REVERT: W 137 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8800 (mtpt) REVERT: X 80 TRP cc_start: 0.8596 (m-10) cc_final: 0.8311 (m-10) REVERT: X 90 ILE cc_start: 0.9500 (tp) cc_final: 0.9255 (tt) REVERT: X 100 ARG cc_start: 0.9057 (ttp-110) cc_final: 0.8847 (ttp-110) REVERT: X 120 ASP cc_start: 0.8468 (t70) cc_final: 0.7766 (t0) REVERT: X 189 ASP cc_start: 0.8282 (p0) cc_final: 0.7893 (t0) REVERT: X 192 LYS cc_start: 0.8436 (pttm) cc_final: 0.7969 (ptmt) REVERT: Y 111 MET cc_start: 0.8644 (tmm) cc_final: 0.8133 (tmm) REVERT: Y 176 ILE cc_start: 0.9561 (OUTLIER) cc_final: 0.9275 (tt) REVERT: Y 185 VAL cc_start: 0.9077 (t) cc_final: 0.8825 (t) REVERT: Z 136 ASN cc_start: 0.8290 (p0) cc_final: 0.7793 (p0) REVERT: a 70 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6363 (tm-30) REVERT: a 111 GLN cc_start: 0.8854 (pp30) cc_final: 0.8582 (tt0) REVERT: a 137 ASN cc_start: 0.8140 (p0) cc_final: 0.7453 (p0) REVERT: b 32 SER cc_start: 0.8702 (m) cc_final: 0.8476 (t) REVERT: b 103 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8985 (pttt) REVERT: b 110 LEU cc_start: 0.9127 (pt) cc_final: 0.8497 (mt) REVERT: c 97 TYR cc_start: 0.7908 (t80) cc_final: 0.7442 (t80) REVERT: c 199 ILE cc_start: 0.9550 (mm) cc_final: 0.9295 (tp) REVERT: c 240 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8393 (tt) REVERT: d 158 ASP cc_start: 0.8530 (t0) cc_final: 0.8244 (t70) REVERT: d 172 MET cc_start: 0.8774 (ttm) cc_final: 0.8300 (ttp) REVERT: d 281 MET cc_start: 0.9125 (ppp) cc_final: 0.8833 (ppp) REVERT: e 63 LEU cc_start: 0.8385 (mp) cc_final: 0.8137 (mt) REVERT: e 124 TRP cc_start: 0.7674 (m-10) cc_final: 0.7305 (m-10) REVERT: e 173 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6532 (tt) REVERT: e 205 LEU cc_start: 0.8665 (pp) cc_final: 0.8061 (mt) REVERT: f 120 LYS cc_start: 0.8878 (tttp) cc_final: 0.8656 (tptp) REVERT: f 122 GLU cc_start: 0.7372 (mp0) cc_final: 0.6642 (mp0) REVERT: g 45 TYR cc_start: 0.7963 (t80) cc_final: 0.7548 (t80) REVERT: g 68 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8316 (p) REVERT: g 152 TYR cc_start: 0.8608 (m-80) cc_final: 0.8371 (m-10) REVERT: i 42 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7457 (ptpt) REVERT: i 63 LEU cc_start: 0.9379 (pt) cc_final: 0.8973 (pp) REVERT: i 122 ASN cc_start: 0.9180 (m110) cc_final: 0.8800 (m-40) REVERT: j 91 TRP cc_start: 0.8768 (t60) cc_final: 0.8112 (t60) REVERT: j 97 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8017 (mtmm) REVERT: k 8 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7005 (tp) REVERT: k 43 ARG cc_start: 0.7609 (mtp180) cc_final: 0.7335 (mtp180) REVERT: l 67 GLN cc_start: 0.5800 (tm-30) cc_final: 0.5491 (tm-30) REVERT: l 73 MET cc_start: 0.8172 (mmt) cc_final: 0.7945 (mmt) REVERT: l 82 GLN cc_start: 0.4706 (mp-120) cc_final: 0.4478 (mp10) REVERT: l 121 LEU cc_start: 0.8298 (tt) cc_final: 0.7920 (tp) REVERT: l 124 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: m 46 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7248 (mm-40) REVERT: m 48 TYR cc_start: 0.7310 (p90) cc_final: 0.6796 (p90) REVERT: m 52 TYR cc_start: 0.7241 (m-80) cc_final: 0.6695 (m-80) REVERT: m 74 MET cc_start: 0.8271 (ppp) cc_final: 0.7754 (tpp) REVERT: o 40 GLU cc_start: 0.8227 (pp20) cc_final: 0.7694 (tm-30) REVERT: p 141 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7916 (ptt180) REVERT: q 51 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: q 56 TYR cc_start: 0.8752 (t80) cc_final: 0.8361 (t80) REVERT: q 136 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: q 140 ARG cc_start: 0.7113 (mmp-170) cc_final: 0.6229 (mtm110) REVERT: r 40 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6526 (tm-30) REVERT: r 76 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8670 (t0) REVERT: r 81 TYR cc_start: 0.8884 (p90) cc_final: 0.8591 (p90) REVERT: r 117 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7774 (tm-30) REVERT: s 152 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7521 (pp30) REVERT: s 241 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9165 (mt) REVERT: s 269 ASP cc_start: 0.8392 (m-30) cc_final: 0.7912 (t0) REVERT: s 298 GLN cc_start: 0.8555 (mt0) cc_final: 0.7999 (mt0) REVERT: s 335 TRP cc_start: 0.9185 (t60) cc_final: 0.8538 (t60) REVERT: s 419 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8291 (mt) outliers start: 484 outliers final: 322 residues processed: 1923 average time/residue: 1.0010 time to fit residues: 3365.5697 Evaluate side-chains 1875 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 1520 time to evaluate : 8.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 123 CYS Chi-restraints excluded: chain 0 residue 137 ILE Chi-restraints excluded: chain 0 residue 141 ILE Chi-restraints excluded: chain 0 residue 153 THR Chi-restraints excluded: chain 0 residue 156 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 175 ILE Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 1 residue 35 ASN Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 2 residue 79 ILE Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 119 CYS Chi-restraints excluded: chain 3 residue 155 SER Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 93 LEU Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 198 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 210 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 331 ASN Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 396 VAL Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 6 residue 41 ASP Chi-restraints excluded: chain 6 residue 47 ARG Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 140 GLU Chi-restraints excluded: chain 6 residue 153 GLU Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 249 GLN Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 284 ASP Chi-restraints excluded: chain 6 residue 290 CYS Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 356 ARG Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 46 ASP Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 85 ILE Chi-restraints excluded: chain 7 residue 97 GLU Chi-restraints excluded: chain 7 residue 150 MET Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 186 ASP Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 300 VAL Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain 8 residue 127 GLN Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 52 GLN Chi-restraints excluded: chain 9 residue 53 ILE Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain 9 residue 64 ASP Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 126 LYS Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 294 ASN Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 280 TYR Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 80 HIS Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 57 CYS Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 58 GLN Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 170 ASN Chi-restraints excluded: chain M residue 188 CYS Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 98 HIS Chi-restraints excluded: chain N residue 172 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 130 LEU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 161 GLU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 260 TRP Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 203 CYS Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 101 GLN Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 147 SER Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 205 SER Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 57 LEU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 60 ASP Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 194 LEU Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 135 VAL Chi-restraints excluded: chain Y residue 137 ASP Chi-restraints excluded: chain Y residue 143 ASP Chi-restraints excluded: chain Y residue 145 VAL Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 108 MET Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 93 SER Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 103 LYS Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 35 PHE Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 228 LEU Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 243 GLU Chi-restraints excluded: chain c residue 301 LEU Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 95 TYR Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 140 LYS Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 207 ASN Chi-restraints excluded: chain d residue 237 ASP Chi-restraints excluded: chain d residue 249 GLU Chi-restraints excluded: chain d residue 277 LEU Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 146 ARG Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 173 LEU Chi-restraints excluded: chain e residue 192 LEU Chi-restraints excluded: chain e residue 272 VAL Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 151 THR Chi-restraints excluded: chain f residue 156 VAL Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain g residue 39 VAL Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 117 ILE Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 142 GLU Chi-restraints excluded: chain h residue 154 ILE Chi-restraints excluded: chain i residue 42 LYS Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain k residue 8 LEU Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 46 GLN Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 49 LEU Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain p residue 45 LEU Chi-restraints excluded: chain p residue 76 LEU Chi-restraints excluded: chain p residue 119 ILE Chi-restraints excluded: chain p residue 134 ILE Chi-restraints excluded: chain p residue 141 ARG Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 150 CYS Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 119 GLN Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain q residue 136 GLN Chi-restraints excluded: chain r residue 76 ASN Chi-restraints excluded: chain r residue 77 LEU Chi-restraints excluded: chain r residue 115 ILE Chi-restraints excluded: chain r residue 128 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 181 LEU Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 145 VAL Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 260 GLU Chi-restraints excluded: chain s residue 270 LYS Chi-restraints excluded: chain s residue 307 ARG Chi-restraints excluded: chain s residue 312 LEU Chi-restraints excluded: chain s residue 415 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain s residue 424 PHE Chi-restraints excluded: chain s residue 426 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 310 optimal weight: 9.9990 chunk 832 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 542 optimal weight: 0.7980 chunk 228 optimal weight: 7.9990 chunk 924 optimal weight: 1.9990 chunk 767 optimal weight: 0.7980 chunk 428 optimal weight: 0.9990 chunk 76 optimal weight: 0.0010 chunk 305 optimal weight: 4.9990 chunk 485 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN ** 0 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 77 GLN ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 249 GLN 6 266 HIS ** 6 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 126 GLN 8 177 HIS D 158 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 ASN ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN M 99 ASN ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN M 170 ASN ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 GLN S 190 GLN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS Y 240 HIS ** Z 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 HIS d 154 ASN d 207 ASN f 158 GLN h 119 GLN i 109 ASN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 146 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 105693 Z= 0.182 Angle : 0.641 13.784 150386 Z= 0.320 Chirality : 0.038 0.332 17680 Planarity : 0.005 0.116 13535 Dihedral : 19.879 179.813 32483 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.47 % Favored : 96.52 % Rotamer: Outliers : 4.96 % Allowed : 24.05 % Favored : 70.99 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % 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: 8037 helix: 0.62 (0.10), residues: 2724 sheet: -0.95 (0.16), residues: 1003 loop : -0.76 (0.09), residues: 4310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP 5 78 HIS 0.010 0.001 HIS F 97 PHE 0.028 0.002 PHE J 172 TYR 0.035 0.002 TYR R 83 ARG 0.009 0.001 ARG X 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2043 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 1684 time to evaluate : 7.148 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: 1 20 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7675 (mtm) REVERT: 2 66 TRP cc_start: 0.9001 (t-100) cc_final: 0.8605 (t-100) REVERT: 4 93 LYS cc_start: 0.8648 (mmtp) cc_final: 0.8194 (mtpp) REVERT: 5 64 MET cc_start: 0.8879 (mtm) cc_final: 0.7985 (mtp) REVERT: 5 270 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8408 (mm) REVERT: 5 381 LEU cc_start: 0.8747 (mt) cc_final: 0.8544 (tp) REVERT: 6 44 ASN cc_start: 0.8204 (t0) cc_final: 0.7371 (p0) REVERT: 6 96 LYS cc_start: 0.5034 (tttp) cc_final: 0.4784 (tptt) REVERT: 6 103 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8679 (tt) REVERT: 6 105 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7611 (tm-30) REVERT: 6 247 GLU cc_start: 0.6631 (pt0) cc_final: 0.6380 (mp0) REVERT: 6 249 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7585 (pp30) REVERT: 6 356 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7895 (ttp80) REVERT: 7 44 ARG cc_start: 0.8339 (ttm170) cc_final: 0.7309 (tpp80) REVERT: 7 46 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8865 (m-30) REVERT: 7 51 GLU cc_start: 0.7819 (tp30) cc_final: 0.7409 (tp30) REVERT: 7 115 MET cc_start: 0.8615 (mmm) cc_final: 0.8295 (tpp) REVERT: 7 148 MET cc_start: 0.8893 (tmm) cc_final: 0.8627 (tmm) REVERT: 7 200 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8186 (tpp80) REVERT: 7 246 GLN cc_start: 0.6447 (tm-30) cc_final: 0.6177 (tm-30) REVERT: 9 48 TRP cc_start: 0.9054 (m-90) cc_final: 0.8844 (m-90) REVERT: D 111 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7810 (mmm-85) REVERT: D 124 GLU cc_start: 0.8374 (tp30) cc_final: 0.7794 (tp30) REVERT: D 132 ASP cc_start: 0.8676 (t0) cc_final: 0.8017 (t0) REVERT: D 177 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7496 (ttp-110) REVERT: D 227 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8629 (tm-30) REVERT: D 265 TRP cc_start: 0.8375 (m-10) cc_final: 0.7399 (m-10) REVERT: E 225 LYS cc_start: 0.8267 (tmtt) cc_final: 0.8000 (tmtt) REVERT: F 98 GLN cc_start: 0.8620 (mt0) cc_final: 0.8323 (mt0) REVERT: F 101 MET cc_start: 0.8663 (mmm) cc_final: 0.8256 (mmm) REVERT: F 103 GLN cc_start: 0.9274 (pt0) cc_final: 0.8891 (pt0) REVERT: F 108 ARG cc_start: 0.8945 (ttt180) cc_final: 0.7950 (ttt90) REVERT: F 190 MET cc_start: 0.8205 (mpp) cc_final: 0.7455 (mtp) REVERT: F 257 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8002 (mm-40) REVERT: F 280 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7379 (t80) REVERT: H 70 LYS cc_start: 0.8437 (mtmm) cc_final: 0.7721 (mmmt) REVERT: H 72 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7757 (mtp180) REVERT: H 91 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7255 (ptpt) REVERT: H 115 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8214 (mtpt) REVERT: I 44 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.7797 (ttm170) REVERT: I 48 MET cc_start: 0.8660 (mmm) cc_final: 0.8337 (mtt) REVERT: I 95 MET cc_start: 0.4584 (ttp) cc_final: 0.4358 (tmm) REVERT: I 112 MET cc_start: 0.8391 (ttp) cc_final: 0.7966 (tmm) REVERT: I 144 LEU cc_start: 0.7616 (mt) cc_final: 0.7170 (tp) REVERT: J 51 LYS cc_start: 0.8828 (pptt) cc_final: 0.8509 (pptt) REVERT: J 142 ARG cc_start: 0.7293 (mtm180) cc_final: 0.6947 (mtm180) REVERT: J 177 LYS cc_start: 0.4290 (ptpp) cc_final: 0.3988 (tptt) REVERT: K 22 ASP cc_start: 0.8511 (t0) cc_final: 0.8072 (t0) REVERT: K 99 ASP cc_start: 0.8069 (t0) cc_final: 0.7703 (t0) REVERT: K 147 GLN cc_start: 0.8607 (mt0) cc_final: 0.7959 (mt0) REVERT: K 150 LYS cc_start: 0.8794 (mppt) cc_final: 0.8571 (mtpp) REVERT: L 33 GLN cc_start: 0.7974 (pt0) cc_final: 0.7622 (pt0) REVERT: L 96 MET cc_start: 0.8634 (mmm) cc_final: 0.8226 (mmt) REVERT: L 111 ASN cc_start: 0.8916 (p0) cc_final: 0.8484 (p0) REVERT: L 117 THR cc_start: 0.8894 (p) cc_final: 0.8681 (m) REVERT: M 91 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6933 (tpp80) REVERT: M 99 ASN cc_start: 0.9117 (m-40) cc_final: 0.7890 (m110) REVERT: M 111 ASP cc_start: 0.7766 (t0) cc_final: 0.7172 (t70) REVERT: M 143 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7194 (tm-30) REVERT: M 281 LYS cc_start: 0.6959 (mtmm) cc_final: 0.6663 (mttm) REVERT: M 289 ASN cc_start: 0.8877 (t0) cc_final: 0.8404 (t0) REVERT: N 118 MET cc_start: 0.8972 (ptp) cc_final: 0.8239 (ptp) REVERT: N 223 MET cc_start: 0.8592 (mmm) cc_final: 0.8233 (mmm) REVERT: N 242 TRP cc_start: 0.9253 (t-100) cc_final: 0.8689 (t-100) REVERT: N 247 MET cc_start: 0.8641 (mpp) cc_final: 0.8269 (mtt) REVERT: O 73 MET cc_start: 0.9363 (tpp) cc_final: 0.9110 (tpp) REVERT: P 56 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: P 96 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8539 (tp-100) REVERT: P 99 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8932 (mtmm) REVERT: P 131 LEU cc_start: 0.9478 (tp) cc_final: 0.9237 (tt) REVERT: P 140 ILE cc_start: 0.9075 (mm) cc_final: 0.8425 (mm) REVERT: Q 259 LYS cc_start: 0.8605 (pptt) cc_final: 0.8294 (mtmt) REVERT: R 76 SER cc_start: 0.9359 (m) cc_final: 0.8789 (t) REVERT: R 89 ASN cc_start: 0.8701 (m-40) cc_final: 0.8477 (m110) REVERT: S 81 LYS cc_start: 0.8577 (tmmt) cc_final: 0.7985 (tppt) REVERT: S 95 LEU cc_start: 0.8741 (pt) cc_final: 0.8349 (mp) REVERT: S 152 ASP cc_start: 0.7835 (p0) cc_final: 0.7414 (t0) REVERT: S 165 GLU cc_start: 0.8156 (pt0) cc_final: 0.7656 (pt0) REVERT: T 87 MET cc_start: 0.8023 (ptm) cc_final: 0.7665 (ptm) REVERT: T 101 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8715 (tp40) REVERT: U 12 LEU cc_start: 0.8508 (mm) cc_final: 0.8073 (tp) REVERT: U 77 ASN cc_start: 0.8914 (t0) cc_final: 0.8433 (t0) REVERT: U 104 THR cc_start: 0.8146 (m) cc_final: 0.7698 (t) REVERT: V 115 LEU cc_start: 0.7901 (mm) cc_final: 0.7620 (mp) REVERT: V 188 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8518 (m) REVERT: W 53 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8531 (pt) REVERT: W 74 ARG cc_start: 0.9114 (ttt180) cc_final: 0.8876 (ttt180) REVERT: W 102 GLU cc_start: 0.8201 (mp0) cc_final: 0.7559 (mp0) REVERT: W 137 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8688 (mtpt) REVERT: W 147 MET cc_start: 0.8270 (tpt) cc_final: 0.7976 (tpt) REVERT: X 15 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7672 (tm-30) REVERT: X 36 ARG cc_start: 0.7679 (mtp-110) cc_final: 0.7460 (mtp-110) REVERT: X 71 PHE cc_start: 0.9255 (m-80) cc_final: 0.8894 (m-80) REVERT: X 80 TRP cc_start: 0.8499 (m-10) cc_final: 0.8210 (m-10) REVERT: X 90 ILE cc_start: 0.9477 (tp) cc_final: 0.9214 (tt) REVERT: X 189 ASP cc_start: 0.8194 (p0) cc_final: 0.7905 (t0) REVERT: X 192 LYS cc_start: 0.8299 (pttm) cc_final: 0.7876 (ptmt) REVERT: Y 111 MET cc_start: 0.8557 (tmm) cc_final: 0.8147 (tmm) REVERT: Y 176 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9240 (tt) REVERT: Y 188 TRP cc_start: 0.9030 (p-90) cc_final: 0.8208 (p-90) REVERT: Z 88 MET cc_start: 0.8939 (mtm) cc_final: 0.8627 (mtm) REVERT: Z 136 ASN cc_start: 0.8271 (p0) cc_final: 0.7784 (p0) REVERT: a 41 ASP cc_start: 0.7870 (t0) cc_final: 0.7542 (t0) REVERT: a 53 SER cc_start: 0.9004 (t) cc_final: 0.8691 (p) REVERT: a 70 GLU cc_start: 0.6635 (tm-30) cc_final: 0.6216 (tm-30) REVERT: a 137 ASN cc_start: 0.8176 (p0) cc_final: 0.7480 (p0) REVERT: b 26 LEU cc_start: 0.9475 (tt) cc_final: 0.9263 (tt) REVERT: b 32 SER cc_start: 0.8673 (m) cc_final: 0.8386 (t) REVERT: b 110 LEU cc_start: 0.9026 (pt) cc_final: 0.8396 (mt) REVERT: c 82 ASN cc_start: 0.8336 (p0) cc_final: 0.8031 (p0) REVERT: d 158 ASP cc_start: 0.8509 (t0) cc_final: 0.8211 (t70) REVERT: d 172 MET cc_start: 0.8505 (ttm) cc_final: 0.8179 (ttp) REVERT: d 281 MET cc_start: 0.9126 (ppp) cc_final: 0.8819 (ppp) REVERT: e 63 LEU cc_start: 0.8270 (mp) cc_final: 0.8028 (mt) REVERT: e 124 TRP cc_start: 0.7636 (m-10) cc_final: 0.7325 (m-10) REVERT: e 173 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6483 (tt) REVERT: e 187 THR cc_start: 0.6598 (p) cc_final: 0.6261 (p) REVERT: e 205 LEU cc_start: 0.8637 (pp) cc_final: 0.8047 (mt) REVERT: f 120 LYS cc_start: 0.8893 (tttp) cc_final: 0.8685 (tptp) REVERT: f 122 GLU cc_start: 0.7467 (mp0) cc_final: 0.6739 (mp0) REVERT: f 130 LYS cc_start: 0.3942 (tptt) cc_final: 0.3656 (tmtt) REVERT: g 45 TYR cc_start: 0.8003 (t80) cc_final: 0.7687 (t80) REVERT: g 152 TYR cc_start: 0.8439 (m-80) cc_final: 0.8059 (m-10) REVERT: h 71 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7603 (mm-30) REVERT: i 63 LEU cc_start: 0.9283 (pt) cc_final: 0.8862 (pp) REVERT: i 122 ASN cc_start: 0.9192 (m110) cc_final: 0.8796 (m-40) REVERT: j 71 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7537 (tm-30) REVERT: j 97 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8073 (mmtm) REVERT: l 67 GLN cc_start: 0.5763 (tm-30) cc_final: 0.5380 (tm-30) REVERT: l 73 MET cc_start: 0.8054 (mmt) cc_final: 0.7845 (mmt) REVERT: l 82 GLN cc_start: 0.4670 (mp-120) cc_final: 0.4465 (mp10) REVERT: l 99 MET cc_start: 0.3354 (ttm) cc_final: 0.2815 (ptm) REVERT: l 119 ARG cc_start: 0.7512 (ttt90) cc_final: 0.7306 (mtt180) REVERT: l 121 LEU cc_start: 0.8286 (tt) cc_final: 0.7900 (tp) REVERT: l 122 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7462 (ttp80) REVERT: l 124 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: m 46 GLN cc_start: 0.7368 (tp-100) cc_final: 0.7150 (mm-40) REVERT: m 48 TYR cc_start: 0.7314 (p90) cc_final: 0.6876 (p90) REVERT: m 52 TYR cc_start: 0.7234 (m-80) cc_final: 0.6696 (m-80) REVERT: m 55 LEU cc_start: 0.8730 (tp) cc_final: 0.8357 (tp) REVERT: m 74 MET cc_start: 0.8268 (ppp) cc_final: 0.7856 (tpp) REVERT: m 79 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7578 (mm) REVERT: o 40 GLU cc_start: 0.7974 (pp20) cc_final: 0.7363 (tm-30) REVERT: o 47 TYR cc_start: 0.9072 (t80) cc_final: 0.8105 (t80) REVERT: o 88 ILE cc_start: 0.9061 (mm) cc_final: 0.8723 (mm) REVERT: p 109 GLU cc_start: 0.8219 (pm20) cc_final: 0.8015 (tp30) REVERT: p 146 ASN cc_start: 0.8791 (m110) cc_final: 0.8584 (m-40) REVERT: p 181 GLU cc_start: 0.8234 (tp30) cc_final: 0.7888 (tm-30) REVERT: q 56 TYR cc_start: 0.8596 (t80) cc_final: 0.7906 (t80) REVERT: q 92 TRP cc_start: 0.8868 (m100) cc_final: 0.8584 (m100) REVERT: q 99 MET cc_start: 0.8488 (mmt) cc_final: 0.7737 (mmt) REVERT: q 108 LEU cc_start: 0.9012 (pp) cc_final: 0.8706 (tp) REVERT: q 136 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7630 (mp10) REVERT: q 140 ARG cc_start: 0.7135 (mmp-170) cc_final: 0.6212 (mtm-85) REVERT: r 40 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6590 (tm-30) REVERT: r 81 TYR cc_start: 0.8846 (p90) cc_final: 0.8492 (p90) REVERT: r 117 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7355 (tm-30) REVERT: s 152 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7662 (pp30) REVERT: s 222 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8027 (ptt180) REVERT: s 241 ILE cc_start: 0.9515 (OUTLIER) cc_final: 0.9181 (mt) REVERT: s 269 ASP cc_start: 0.8452 (m-30) cc_final: 0.7971 (t0) REVERT: s 296 HIS cc_start: 0.9144 (t-90) cc_final: 0.8942 (t-90) REVERT: s 298 GLN cc_start: 0.8616 (mt0) cc_final: 0.8008 (mt0) REVERT: s 335 TRP cc_start: 0.9190 (t60) cc_final: 0.8460 (t60) REVERT: s 425 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9024 (mt) outliers start: 359 outliers final: 245 residues processed: 1875 average time/residue: 0.9104 time to fit residues: 2953.6178 Evaluate side-chains 1818 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1549 time to evaluate : 6.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 123 CYS Chi-restraints excluded: chain 0 residue 156 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 35 ASN Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 155 SER Chi-restraints excluded: chain 3 residue 178 GLN Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 255 THR Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 396 VAL Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 153 GLU Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 249 GLN Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 290 CYS Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 6 residue 356 ARG Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 46 ASP Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 85 ILE Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 186 ASP Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 127 GLN Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 53 ILE Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain 9 residue 64 ASP Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 280 TYR Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 58 GLN Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 161 GLU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 260 TRP Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 101 GLN Chi-restraints excluded: chain T residue 103 LEU Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 147 SER Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 84 ASN Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 180 GLU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 194 LEU Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 135 VAL Chi-restraints excluded: chain Y residue 143 ASP Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain a residue 108 MET Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 35 PHE Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 140 PHE Chi-restraints excluded: chain c residue 228 LEU Chi-restraints excluded: chain c residue 243 GLU Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 95 TYR Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 276 ILE Chi-restraints excluded: chain d residue 277 LEU Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 146 ARG Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 173 LEU Chi-restraints excluded: chain e residue 272 VAL Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 156 VAL Chi-restraints excluded: chain g residue 39 VAL Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 117 ILE Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 142 GLU Chi-restraints excluded: chain h residue 154 ILE Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 49 LEU Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain p residue 76 LEU Chi-restraints excluded: chain p residue 117 GLN Chi-restraints excluded: chain p residue 134 ILE Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 150 CYS Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 136 GLN Chi-restraints excluded: chain r residue 77 LEU Chi-restraints excluded: chain r residue 115 ILE Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 181 LEU Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 145 VAL Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 222 ARG Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 260 GLU Chi-restraints excluded: chain s residue 312 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 424 PHE Chi-restraints excluded: chain s residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 891 optimal weight: 0.0270 chunk 104 optimal weight: 4.9990 chunk 527 optimal weight: 0.7980 chunk 675 optimal weight: 4.9990 chunk 523 optimal weight: 4.9990 chunk 778 optimal weight: 6.9990 chunk 516 optimal weight: 3.9990 chunk 921 optimal weight: 0.8980 chunk 576 optimal weight: 0.9980 chunk 561 optimal weight: 0.6980 chunk 425 optimal weight: 5.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN ** 0 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 62 ASN 2 77 GLN ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 116 ASN 6 249 GLN ** 6 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 320 GLN ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 144 GLN D 235 GLN ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN J 54 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN M 114 GLN M 170 ASN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 GLN T 55 ASN ** T 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 177 HIS Y 240 HIS ** Z 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 111 GLN b 66 ASN ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 HIS d 153 ASN e 67 GLN ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 122 ASN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 GLN p 104 HIS ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 105693 Z= 0.176 Angle : 0.621 12.983 150386 Z= 0.310 Chirality : 0.037 0.294 17680 Planarity : 0.005 0.115 13535 Dihedral : 19.798 179.318 32483 Min Nonbonded Distance : 1.133 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.11 % Favored : 95.88 % Rotamer: Outliers : 4.60 % Allowed : 25.06 % Favored : 70.34 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % 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: -0.33 (0.09), residues: 8037 helix: 0.76 (0.10), residues: 2739 sheet: -0.88 (0.16), residues: 1004 loop : -0.64 (0.10), residues: 4294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP 5 78 HIS 0.008 0.001 HIS F 97 PHE 0.034 0.002 PHE M 253 TYR 0.031 0.002 TYR K 47 ARG 0.011 0.000 ARG W 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1998 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1665 time to evaluate : 7.084 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: 1 20 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7590 (mtm) REVERT: 2 66 TRP cc_start: 0.8973 (t-100) cc_final: 0.8564 (t-100) REVERT: 3 100 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7373 (mmm160) REVERT: 3 161 MET cc_start: 0.8762 (ttm) cc_final: 0.8536 (mtp) REVERT: 4 93 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8178 (mtpp) REVERT: 5 64 MET cc_start: 0.8918 (mtm) cc_final: 0.8023 (mtp) REVERT: 5 98 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7964 (pp) REVERT: 5 304 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7692 (tt) REVERT: 6 44 ASN cc_start: 0.8214 (t0) cc_final: 0.7372 (p0) REVERT: 6 96 LYS cc_start: 0.5233 (tttp) cc_final: 0.5010 (tptt) REVERT: 6 103 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8610 (tt) REVERT: 6 105 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7672 (tm-30) REVERT: 6 249 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7684 (pp30) REVERT: 6 356 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7828 (ttp80) REVERT: 7 46 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8860 (m-30) REVERT: 7 51 GLU cc_start: 0.7836 (tp30) cc_final: 0.7461 (tp30) REVERT: 7 115 MET cc_start: 0.8637 (mmm) cc_final: 0.7411 (tpp) REVERT: 7 148 MET cc_start: 0.8922 (tmm) cc_final: 0.8629 (tmm) REVERT: 7 200 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.8156 (tpp80) REVERT: 8 126 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8669 (mm-40) REVERT: 9 102 LYS cc_start: 0.6109 (mmtp) cc_final: 0.5739 (mmpt) REVERT: D 177 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7465 (ttp-110) REVERT: D 227 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8535 (tm-30) REVERT: D 265 TRP cc_start: 0.8403 (m-10) cc_final: 0.7458 (m-10) REVERT: E 121 LEU cc_start: 0.9477 (mt) cc_final: 0.9101 (mt) REVERT: F 103 GLN cc_start: 0.9250 (pt0) cc_final: 0.8900 (pt0) REVERT: F 108 ARG cc_start: 0.8858 (ttt180) cc_final: 0.8577 (ptm-80) REVERT: F 190 MET cc_start: 0.8121 (mpp) cc_final: 0.7397 (mtp) REVERT: F 257 GLN cc_start: 0.8687 (mm-40) cc_final: 0.7902 (mm-40) REVERT: F 280 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7241 (t80) REVERT: H 70 LYS cc_start: 0.8436 (mtmm) cc_final: 0.7675 (mmmt) REVERT: H 72 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7653 (mtp180) REVERT: H 115 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8231 (mtpt) REVERT: I 48 MET cc_start: 0.8647 (mmm) cc_final: 0.8359 (mtt) REVERT: I 144 LEU cc_start: 0.7578 (mt) cc_final: 0.7040 (tp) REVERT: J 51 LYS cc_start: 0.8830 (pptt) cc_final: 0.8517 (pptt) REVERT: J 142 ARG cc_start: 0.7296 (mtm180) cc_final: 0.6956 (mtm180) REVERT: J 177 LYS cc_start: 0.4239 (ptpp) cc_final: 0.3984 (tptt) REVERT: K 22 ASP cc_start: 0.8533 (t0) cc_final: 0.8152 (t0) REVERT: K 99 ASP cc_start: 0.7994 (t0) cc_final: 0.7672 (t0) REVERT: K 147 GLN cc_start: 0.8705 (mt0) cc_final: 0.8096 (mt0) REVERT: K 150 LYS cc_start: 0.8803 (mppt) cc_final: 0.8564 (mtpp) REVERT: L 33 GLN cc_start: 0.7920 (pt0) cc_final: 0.7576 (pt0) REVERT: L 111 ASN cc_start: 0.8894 (p0) cc_final: 0.8543 (p0) REVERT: M 99 ASN cc_start: 0.9172 (m-40) cc_final: 0.8752 (m110) REVERT: M 111 ASP cc_start: 0.7756 (t0) cc_final: 0.7158 (t70) REVERT: M 281 LYS cc_start: 0.6918 (mtmm) cc_final: 0.6648 (mttm) REVERT: N 118 MET cc_start: 0.8903 (ptp) cc_final: 0.8085 (ptp) REVERT: N 223 MET cc_start: 0.8764 (mmm) cc_final: 0.8524 (mmm) REVERT: N 242 TRP cc_start: 0.9245 (t-100) cc_final: 0.8683 (t-100) REVERT: N 247 MET cc_start: 0.8592 (mpp) cc_final: 0.8206 (mtt) REVERT: O 130 LEU cc_start: 0.9157 (mp) cc_final: 0.8940 (mt) REVERT: P 56 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: P 99 LYS cc_start: 0.9169 (ttpt) cc_final: 0.8910 (mtmm) REVERT: P 131 LEU cc_start: 0.9521 (tp) cc_final: 0.9210 (tt) REVERT: P 140 ILE cc_start: 0.9002 (mm) cc_final: 0.7984 (mm) REVERT: Q 259 LYS cc_start: 0.8595 (pptt) cc_final: 0.8334 (mtmt) REVERT: R 68 TRP cc_start: 0.9095 (m-10) cc_final: 0.8865 (m-10) REVERT: R 76 SER cc_start: 0.9350 (m) cc_final: 0.8769 (t) REVERT: S 81 LYS cc_start: 0.8594 (tmmt) cc_final: 0.7990 (tppt) REVERT: S 95 LEU cc_start: 0.8761 (pt) cc_final: 0.8362 (mp) REVERT: S 105 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8949 (mt0) REVERT: S 152 ASP cc_start: 0.7871 (p0) cc_final: 0.7456 (t0) REVERT: T 57 ILE cc_start: 0.9153 (pt) cc_final: 0.8939 (tp) REVERT: T 82 TYR cc_start: 0.8984 (t80) cc_final: 0.8192 (t80) REVERT: T 97 MET cc_start: 0.6753 (ptt) cc_final: 0.6187 (ptt) REVERT: U 12 LEU cc_start: 0.8361 (mm) cc_final: 0.7877 (tp) REVERT: U 37 GLU cc_start: 0.8127 (pm20) cc_final: 0.7883 (pt0) REVERT: U 77 ASN cc_start: 0.8828 (t0) cc_final: 0.8406 (t0) REVERT: U 104 THR cc_start: 0.8047 (m) cc_final: 0.7527 (t) REVERT: V 188 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8512 (m) REVERT: W 137 LYS cc_start: 0.8914 (ptpp) cc_final: 0.8649 (mtpt) REVERT: X 15 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7679 (tm-30) REVERT: X 36 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7498 (mtp-110) REVERT: X 71 PHE cc_start: 0.9277 (m-80) cc_final: 0.8889 (m-80) REVERT: X 90 ILE cc_start: 0.9468 (tp) cc_final: 0.9171 (tt) REVERT: X 189 ASP cc_start: 0.8256 (p0) cc_final: 0.7895 (t0) REVERT: Y 111 MET cc_start: 0.8531 (tmm) cc_final: 0.8046 (tmm) REVERT: Y 161 GLU cc_start: 0.8238 (mp0) cc_final: 0.8018 (mp0) REVERT: Y 176 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9184 (tt) REVERT: Y 188 TRP cc_start: 0.8909 (p-90) cc_final: 0.8077 (p-90) REVERT: Z 88 MET cc_start: 0.8928 (mtm) cc_final: 0.8583 (mtm) REVERT: Z 136 ASN cc_start: 0.8308 (p0) cc_final: 0.7896 (p0) REVERT: a 41 ASP cc_start: 0.7918 (t0) cc_final: 0.7632 (t0) REVERT: a 53 SER cc_start: 0.8962 (t) cc_final: 0.8680 (p) REVERT: a 70 GLU cc_start: 0.6568 (tm-30) cc_final: 0.6172 (tm-30) REVERT: a 137 ASN cc_start: 0.8181 (p0) cc_final: 0.7471 (p0) REVERT: b 26 LEU cc_start: 0.9440 (tt) cc_final: 0.9165 (tt) REVERT: b 32 SER cc_start: 0.8654 (m) cc_final: 0.8387 (t) REVERT: b 110 LEU cc_start: 0.8876 (pt) cc_final: 0.8290 (mt) REVERT: c 82 ASN cc_start: 0.8306 (p0) cc_final: 0.8016 (p0) REVERT: d 158 ASP cc_start: 0.8529 (t0) cc_final: 0.8228 (t70) REVERT: d 172 MET cc_start: 0.8324 (ttm) cc_final: 0.8026 (ttp) REVERT: d 202 MET cc_start: 0.2648 (tpt) cc_final: 0.1470 (ptt) REVERT: d 281 MET cc_start: 0.9136 (ppp) cc_final: 0.8810 (ppp) REVERT: e 63 LEU cc_start: 0.8423 (mp) cc_final: 0.8190 (mt) REVERT: e 78 GLU cc_start: 0.7314 (tm-30) cc_final: 0.7020 (tm-30) REVERT: e 124 TRP cc_start: 0.7598 (m-10) cc_final: 0.7267 (m-10) REVERT: e 205 LEU cc_start: 0.8734 (pp) cc_final: 0.8051 (mt) REVERT: f 120 LYS cc_start: 0.8904 (tttp) cc_final: 0.8693 (tptp) REVERT: f 122 GLU cc_start: 0.7465 (mp0) cc_final: 0.6737 (mp0) REVERT: f 130 LYS cc_start: 0.4002 (tptt) cc_final: 0.3648 (tmtt) REVERT: f 183 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7476 (mtp85) REVERT: g 45 TYR cc_start: 0.8003 (t80) cc_final: 0.7737 (t80) REVERT: g 152 TYR cc_start: 0.8343 (m-80) cc_final: 0.8036 (m-10) REVERT: i 42 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7378 (ptpt) REVERT: i 63 LEU cc_start: 0.9147 (pt) cc_final: 0.8850 (pp) REVERT: i 122 ASN cc_start: 0.9234 (m-40) cc_final: 0.8808 (m-40) REVERT: j 71 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7793 (tm-30) REVERT: j 97 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8061 (mmtm) REVERT: l 67 GLN cc_start: 0.5707 (tm-30) cc_final: 0.5302 (tm-30) REVERT: l 99 MET cc_start: 0.3853 (ttm) cc_final: 0.3250 (ptm) REVERT: l 119 ARG cc_start: 0.7441 (ttt90) cc_final: 0.7122 (ttt180) REVERT: l 122 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7475 (ttp80) REVERT: l 124 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: m 48 TYR cc_start: 0.7353 (p90) cc_final: 0.6888 (p90) REVERT: m 52 TYR cc_start: 0.7124 (m-80) cc_final: 0.6562 (m-80) REVERT: m 55 LEU cc_start: 0.8736 (tp) cc_final: 0.8511 (tp) REVERT: m 74 MET cc_start: 0.8186 (ppp) cc_final: 0.7621 (tpp) REVERT: m 79 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7599 (mm) REVERT: o 40 GLU cc_start: 0.7968 (pp20) cc_final: 0.7381 (tm-30) REVERT: o 47 TYR cc_start: 0.9022 (t80) cc_final: 0.8234 (t80) REVERT: p 146 ASN cc_start: 0.8514 (m110) cc_final: 0.8279 (m-40) REVERT: q 56 TYR cc_start: 0.8616 (t80) cc_final: 0.8357 (t80) REVERT: q 92 TRP cc_start: 0.8863 (m100) cc_final: 0.8574 (m100) REVERT: q 99 MET cc_start: 0.8482 (mmt) cc_final: 0.7855 (mmt) REVERT: q 108 LEU cc_start: 0.8998 (pp) cc_final: 0.8684 (tp) REVERT: q 136 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: q 140 ARG cc_start: 0.7078 (mmp-170) cc_final: 0.6179 (mtm-85) REVERT: r 40 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6673 (tm-30) REVERT: r 81 TYR cc_start: 0.8815 (p90) cc_final: 0.8466 (p90) REVERT: r 84 ASP cc_start: 0.7601 (p0) cc_final: 0.7341 (p0) REVERT: r 117 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7429 (tm-30) REVERT: s 152 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7793 (pp30) REVERT: s 222 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8078 (ptt180) REVERT: s 241 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9124 (mt) REVERT: s 269 ASP cc_start: 0.8437 (m-30) cc_final: 0.7965 (t0) REVERT: s 274 PHE cc_start: 0.9009 (m-80) cc_final: 0.8524 (m-80) REVERT: s 298 GLN cc_start: 0.8526 (mt0) cc_final: 0.7891 (mt0) REVERT: s 335 TRP cc_start: 0.9191 (t60) cc_final: 0.8440 (t60) REVERT: s 425 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9019 (mt) outliers start: 333 outliers final: 236 residues processed: 1845 average time/residue: 0.9119 time to fit residues: 2920.3703 Evaluate side-chains 1826 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1571 time to evaluate : 6.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 123 CYS Chi-restraints excluded: chain 0 residue 156 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 35 ASN Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 2 residue 89 SER Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 154 GLN Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 3 residue 178 GLN Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 396 VAL Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 249 GLN Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 290 CYS Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 356 ARG Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 46 ASP Chi-restraints excluded: chain 7 residue 63 GLU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 85 ILE Chi-restraints excluded: chain 7 residue 97 GLU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 186 ASP Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain 8 residue 127 GLN Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 53 ILE Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 280 TYR Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 58 GLN Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain P residue 171 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 161 GLU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 260 TRP Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 103 LEU Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain T residue 147 SER Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 84 ASN Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain V residue 180 GLU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 135 VAL Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain a residue 108 MET Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 143 ASP Chi-restraints excluded: chain c residue 228 LEU Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 95 TYR Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 177 LYS Chi-restraints excluded: chain d residue 276 ILE Chi-restraints excluded: chain d residue 277 LEU Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 146 ARG Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 272 VAL Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 151 THR Chi-restraints excluded: chain f residue 156 VAL Chi-restraints excluded: chain f residue 169 ILE Chi-restraints excluded: chain f residue 186 VAL Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 117 ILE Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 142 GLU Chi-restraints excluded: chain h residue 154 ILE Chi-restraints excluded: chain i residue 42 LYS Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 49 LEU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain p residue 59 TRP Chi-restraints excluded: chain p residue 134 ILE Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 136 GLN Chi-restraints excluded: chain r residue 77 LEU Chi-restraints excluded: chain r residue 115 ILE Chi-restraints excluded: chain r residue 128 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 181 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 145 VAL Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 222 ARG Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 260 GLU Chi-restraints excluded: chain s residue 304 ASP Chi-restraints excluded: chain s residue 312 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 424 PHE Chi-restraints excluded: chain s residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 570 optimal weight: 0.8980 chunk 367 optimal weight: 0.9980 chunk 550 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 585 optimal weight: 3.9990 chunk 627 optimal weight: 7.9990 chunk 455 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 724 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN ** 0 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 62 ASN 6 249 GLN ** 6 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN 8 144 GLN 8 177 HIS ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 GLN O 100 GLN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN ** T 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS V 119 GLN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 GLN W 107 HIS X 177 HIS Y 240 HIS ** Z 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 153 ASN d 154 ASN ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 158 GLN ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 82 GLN p 104 HIS q 51 GLN ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 130 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 105693 Z= 0.274 Angle : 0.664 14.915 150386 Z= 0.333 Chirality : 0.039 0.319 17680 Planarity : 0.005 0.115 13535 Dihedral : 19.790 178.567 32483 Min Nonbonded Distance : 1.035 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.72 % Favored : 95.27 % Rotamer: Outliers : 5.03 % Allowed : 25.17 % Favored : 69.80 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % 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: -0.34 (0.09), residues: 8037 helix: 0.71 (0.10), residues: 2742 sheet: -0.83 (0.15), residues: 1033 loop : -0.63 (0.10), residues: 4262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP 5 78 HIS 0.007 0.001 HIS b 90 PHE 0.042 0.002 PHE M 253 TYR 0.031 0.002 TYR h 73 ARG 0.009 0.001 ARG j 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1953 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1589 time to evaluate : 7.119 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: 1 20 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7583 (mtm) REVERT: 1 52 GLN cc_start: 0.9115 (pm20) cc_final: 0.8747 (pm20) REVERT: 2 66 TRP cc_start: 0.8965 (t-100) cc_final: 0.8600 (t-100) REVERT: 3 133 LEU cc_start: 0.9519 (mm) cc_final: 0.9310 (mm) REVERT: 3 161 MET cc_start: 0.8811 (ttm) cc_final: 0.8595 (mtp) REVERT: 4 93 LYS cc_start: 0.8756 (mmtp) cc_final: 0.8297 (mtpp) REVERT: 5 270 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8413 (mm) REVERT: 5 304 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7725 (tt) REVERT: 5 322 LEU cc_start: 0.9066 (tt) cc_final: 0.8850 (tt) REVERT: 5 365 ASP cc_start: 0.7314 (m-30) cc_final: 0.7062 (m-30) REVERT: 6 44 ASN cc_start: 0.8233 (t0) cc_final: 0.7286 (p0) REVERT: 6 96 LYS cc_start: 0.5322 (tttp) cc_final: 0.5094 (tptt) REVERT: 6 103 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8663 (tt) REVERT: 6 105 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7650 (tm-30) REVERT: 6 337 MET cc_start: 0.6532 (mtp) cc_final: 0.6208 (ttm) REVERT: 6 356 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7606 (ttp80) REVERT: 7 46 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8864 (m-30) REVERT: 7 51 GLU cc_start: 0.7895 (tp30) cc_final: 0.7534 (tp30) REVERT: 7 115 MET cc_start: 0.8793 (mmm) cc_final: 0.7838 (tpp) REVERT: 7 148 MET cc_start: 0.8976 (tmm) cc_final: 0.8680 (tmm) REVERT: 7 200 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8238 (tpp80) REVERT: 7 259 ASP cc_start: 0.8402 (p0) cc_final: 0.7766 (p0) REVERT: 7 298 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6439 (mt0) REVERT: 8 126 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8651 (mm-40) REVERT: 9 102 LYS cc_start: 0.6023 (mmtp) cc_final: 0.5645 (mmpt) REVERT: D 132 ASP cc_start: 0.8642 (t0) cc_final: 0.8156 (m-30) REVERT: D 177 ARG cc_start: 0.7650 (mtm180) cc_final: 0.7383 (ttp-110) REVERT: D 227 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8543 (tm-30) REVERT: D 233 GLN cc_start: 0.9037 (mt0) cc_final: 0.8816 (mt0) REVERT: F 103 GLN cc_start: 0.9318 (pt0) cc_final: 0.8914 (pt0) REVERT: F 108 ARG cc_start: 0.8972 (ttt180) cc_final: 0.8007 (ttt90) REVERT: F 190 MET cc_start: 0.8102 (mpp) cc_final: 0.7366 (mtp) REVERT: F 257 GLN cc_start: 0.8590 (mm-40) cc_final: 0.7761 (mm-40) REVERT: F 280 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7528 (t80) REVERT: H 70 LYS cc_start: 0.8452 (mtmm) cc_final: 0.7717 (mmmt) REVERT: H 91 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7184 (ptpt) REVERT: H 115 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8253 (mtpt) REVERT: I 44 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7958 (ttm170) REVERT: I 48 MET cc_start: 0.8727 (mmm) cc_final: 0.8468 (mtt) REVERT: I 84 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7236 (ptt180) REVERT: I 144 LEU cc_start: 0.7562 (mt) cc_final: 0.7031 (tp) REVERT: J 177 LYS cc_start: 0.4359 (ptpp) cc_final: 0.4015 (tptt) REVERT: K 99 ASP cc_start: 0.8066 (t0) cc_final: 0.7725 (t0) REVERT: K 147 GLN cc_start: 0.8784 (mt0) cc_final: 0.8330 (mt0) REVERT: K 150 LYS cc_start: 0.8801 (mppt) cc_final: 0.8570 (mtpp) REVERT: L 33 GLN cc_start: 0.8078 (pt0) cc_final: 0.7732 (pt0) REVERT: L 111 ASN cc_start: 0.8900 (p0) cc_final: 0.8507 (p0) REVERT: L 117 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8288 (t) REVERT: M 91 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7092 (tpp80) REVERT: M 99 ASN cc_start: 0.9178 (m-40) cc_final: 0.8664 (m110) REVERT: M 111 ASP cc_start: 0.7847 (t0) cc_final: 0.7258 (t70) REVERT: M 253 PHE cc_start: 0.8661 (t80) cc_final: 0.8388 (t80) REVERT: M 281 LYS cc_start: 0.7055 (mtmm) cc_final: 0.6709 (mttm) REVERT: N 118 MET cc_start: 0.8893 (ptp) cc_final: 0.8155 (ptp) REVERT: N 223 MET cc_start: 0.8871 (mmm) cc_final: 0.8425 (mmm) REVERT: N 242 TRP cc_start: 0.9288 (t-100) cc_final: 0.9029 (t-100) REVERT: N 247 MET cc_start: 0.8665 (mpp) cc_final: 0.8309 (mtt) REVERT: P 56 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: P 87 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7194 (m170) REVERT: P 99 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8994 (mtmm) REVERT: P 140 ILE cc_start: 0.9237 (mm) cc_final: 0.8546 (mm) REVERT: Q 259 LYS cc_start: 0.8632 (pptt) cc_final: 0.8335 (mtpt) REVERT: R 64 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8004 (mmm) REVERT: R 68 TRP cc_start: 0.9124 (m-10) cc_final: 0.8877 (m-10) REVERT: R 76 SER cc_start: 0.9385 (m) cc_final: 0.8754 (t) REVERT: R 89 ASN cc_start: 0.8741 (m-40) cc_final: 0.8476 (m110) REVERT: S 81 LYS cc_start: 0.8674 (tmmt) cc_final: 0.8045 (tppt) REVERT: S 95 LEU cc_start: 0.8862 (pt) cc_final: 0.8449 (mp) REVERT: S 105 GLN cc_start: 0.9337 (mm-40) cc_final: 0.9068 (mt0) REVERT: S 152 ASP cc_start: 0.7956 (p0) cc_final: 0.7508 (t0) REVERT: T 82 TYR cc_start: 0.9067 (t80) cc_final: 0.8482 (t80) REVERT: T 87 MET cc_start: 0.8164 (ptm) cc_final: 0.7579 (ptm) REVERT: U 12 LEU cc_start: 0.8365 (mm) cc_final: 0.7900 (tp) REVERT: U 37 GLU cc_start: 0.8188 (pm20) cc_final: 0.7924 (pt0) REVERT: U 77 ASN cc_start: 0.8872 (t0) cc_final: 0.8403 (t0) REVERT: U 78 LYS cc_start: 0.9278 (tttm) cc_final: 0.8763 (ttpt) REVERT: U 104 THR cc_start: 0.8173 (m) cc_final: 0.7696 (t) REVERT: V 188 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8475 (m) REVERT: W 137 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8708 (mtpt) REVERT: X 15 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7747 (tm-30) REVERT: X 36 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.7427 (mtp-110) REVERT: X 71 PHE cc_start: 0.9254 (m-80) cc_final: 0.8964 (m-80) REVERT: X 90 ILE cc_start: 0.9494 (tp) cc_final: 0.9219 (tt) REVERT: X 189 ASP cc_start: 0.8290 (p0) cc_final: 0.7909 (t0) REVERT: Y 111 MET cc_start: 0.8552 (tmm) cc_final: 0.8075 (tmm) REVERT: Y 126 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7400 (ptt) REVERT: Y 176 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9216 (tt) REVERT: Y 188 TRP cc_start: 0.9046 (p-90) cc_final: 0.8228 (p-90) REVERT: Z 88 MET cc_start: 0.9016 (mtm) cc_final: 0.8668 (mtm) REVERT: Z 136 ASN cc_start: 0.8512 (p0) cc_final: 0.8011 (p0) REVERT: a 41 ASP cc_start: 0.7968 (t0) cc_final: 0.7650 (t0) REVERT: a 53 SER cc_start: 0.8986 (t) cc_final: 0.8689 (p) REVERT: a 70 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6371 (tm-30) REVERT: a 137 ASN cc_start: 0.8157 (p0) cc_final: 0.7477 (p0) REVERT: b 26 LEU cc_start: 0.9441 (tt) cc_final: 0.9168 (tt) REVERT: b 32 SER cc_start: 0.8786 (m) cc_final: 0.8486 (t) REVERT: b 110 LEU cc_start: 0.8764 (pt) cc_final: 0.8418 (mt) REVERT: c 82 ASN cc_start: 0.8561 (p0) cc_final: 0.8240 (p0) REVERT: d 158 ASP cc_start: 0.8544 (t0) cc_final: 0.8267 (t70) REVERT: d 172 MET cc_start: 0.8426 (ttm) cc_final: 0.7999 (ttp) REVERT: d 202 MET cc_start: 0.2896 (tpt) cc_final: 0.1423 (ptt) REVERT: d 281 MET cc_start: 0.9133 (ppp) cc_final: 0.8800 (ppp) REVERT: e 124 TRP cc_start: 0.7636 (m-10) cc_final: 0.7285 (m-10) REVERT: e 187 THR cc_start: 0.6394 (p) cc_final: 0.6051 (p) REVERT: f 120 LYS cc_start: 0.8937 (tttp) cc_final: 0.8698 (tptp) REVERT: f 122 GLU cc_start: 0.7476 (mp0) cc_final: 0.6745 (mp0) REVERT: f 130 LYS cc_start: 0.4032 (tptt) cc_final: 0.3674 (tmtt) REVERT: f 183 ARG cc_start: 0.7862 (mtp-110) cc_final: 0.7552 (mtp85) REVERT: g 45 TYR cc_start: 0.8138 (t80) cc_final: 0.7816 (t80) REVERT: g 152 TYR cc_start: 0.8511 (m-80) cc_final: 0.8157 (m-10) REVERT: h 86 TRP cc_start: 0.7563 (p-90) cc_final: 0.7222 (p-90) REVERT: i 63 LEU cc_start: 0.9267 (pt) cc_final: 0.8980 (pp) REVERT: i 122 ASN cc_start: 0.9273 (m-40) cc_final: 0.8872 (m-40) REVERT: j 71 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7515 (tp30) REVERT: j 75 ARG cc_start: 0.8839 (mtt-85) cc_final: 0.8109 (tpp80) REVERT: j 97 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8140 (mmtm) REVERT: j 100 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7798 (tm-30) REVERT: l 67 GLN cc_start: 0.5746 (tm-30) cc_final: 0.5355 (tm-30) REVERT: l 99 MET cc_start: 0.3678 (ttm) cc_final: 0.3102 (ptm) REVERT: l 119 ARG cc_start: 0.7482 (ttt90) cc_final: 0.7194 (mtt180) REVERT: l 122 ARG cc_start: 0.8137 (ttm170) cc_final: 0.7504 (ttp80) REVERT: l 124 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: m 48 TYR cc_start: 0.7399 (p90) cc_final: 0.7015 (p90) REVERT: m 52 TYR cc_start: 0.7255 (m-80) cc_final: 0.6736 (m-80) REVERT: m 55 LEU cc_start: 0.8731 (tp) cc_final: 0.8506 (tp) REVERT: m 70 GLU cc_start: 0.7347 (mp0) cc_final: 0.7127 (mp0) REVERT: m 74 MET cc_start: 0.8153 (ppp) cc_final: 0.7566 (tpp) REVERT: m 79 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7673 (mm) REVERT: o 40 GLU cc_start: 0.8033 (pp20) cc_final: 0.7500 (tm-30) REVERT: o 51 MET cc_start: 0.9486 (ptp) cc_final: 0.9228 (ptt) REVERT: p 146 ASN cc_start: 0.8629 (m110) cc_final: 0.8428 (m-40) REVERT: q 56 TYR cc_start: 0.8674 (t80) cc_final: 0.8376 (t80) REVERT: q 92 TRP cc_start: 0.8920 (m100) cc_final: 0.8604 (m100) REVERT: q 99 MET cc_start: 0.8533 (mmt) cc_final: 0.7874 (mmt) REVERT: q 108 LEU cc_start: 0.9040 (pp) cc_final: 0.8802 (tp) REVERT: q 125 MET cc_start: 0.8981 (mmt) cc_final: 0.8670 (mmt) REVERT: q 136 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7641 (mp10) REVERT: q 140 ARG cc_start: 0.7137 (mmp-170) cc_final: 0.6196 (mtm-85) REVERT: r 81 TYR cc_start: 0.8876 (p90) cc_final: 0.8540 (p90) REVERT: r 84 ASP cc_start: 0.7757 (p0) cc_final: 0.7473 (p0) REVERT: r 117 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7611 (tm-30) REVERT: s 61 ARG cc_start: 0.8660 (tpp80) cc_final: 0.8326 (tpp80) REVERT: s 152 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7566 (pp30) REVERT: s 222 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8113 (ptt180) REVERT: s 241 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9193 (mt) REVERT: s 269 ASP cc_start: 0.8440 (m-30) cc_final: 0.8012 (t0) REVERT: s 298 GLN cc_start: 0.8588 (mt0) cc_final: 0.7970 (mt0) REVERT: s 335 TRP cc_start: 0.9233 (t60) cc_final: 0.8540 (t60) REVERT: s 425 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9074 (mt) outliers start: 364 outliers final: 286 residues processed: 1797 average time/residue: 0.9172 time to fit residues: 2861.3056 Evaluate side-chains 1843 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1532 time to evaluate : 7.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 123 CYS Chi-restraints excluded: chain 0 residue 141 ILE Chi-restraints excluded: chain 0 residue 156 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 35 ASN Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 123 VAL Chi-restraints excluded: chain 3 residue 154 GLN Chi-restraints excluded: chain 3 residue 155 SER Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 3 residue 178 GLN Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 130 GLU Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 255 THR Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 356 VAL Chi-restraints excluded: chain 5 residue 396 VAL Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 243 ASN Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 249 GLN Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 290 CYS Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 356 ARG Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 46 ASP Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 85 ILE Chi-restraints excluded: chain 7 residue 149 MET Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 186 ASP Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 298 GLN Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain 8 residue 127 GLN Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 53 ILE Chi-restraints excluded: chain 9 residue 64 ASP Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 280 TYR Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 58 GLN Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 87 HIS Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 161 GLU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 260 TRP Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 103 LEU Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 147 SER Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 119 GLN Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain V residue 180 GLU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 194 LEU Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 56 ASN Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 135 VAL Chi-restraints excluded: chain Y residue 156 LEU Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain a residue 108 MET Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 35 PHE Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 143 ASP Chi-restraints excluded: chain c residue 228 LEU Chi-restraints excluded: chain c residue 245 LEU Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 95 TYR Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 140 LYS Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 177 LYS Chi-restraints excluded: chain d residue 237 ASP Chi-restraints excluded: chain d residue 276 ILE Chi-restraints excluded: chain d residue 277 LEU Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 146 ARG Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 272 VAL Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 151 THR Chi-restraints excluded: chain f residue 156 VAL Chi-restraints excluded: chain f residue 169 ILE Chi-restraints excluded: chain f residue 186 VAL Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 117 ILE Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 142 GLU Chi-restraints excluded: chain h residue 154 ILE Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 49 LEU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain p residue 45 LEU Chi-restraints excluded: chain p residue 76 LEU Chi-restraints excluded: chain p residue 134 ILE Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 150 CYS Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 119 GLN Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain q residue 136 GLN Chi-restraints excluded: chain r residue 77 LEU Chi-restraints excluded: chain r residue 128 LEU Chi-restraints excluded: chain r residue 130 ASN Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 181 LEU Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 145 VAL Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 222 ARG Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 260 GLU Chi-restraints excluded: chain s residue 304 ASP Chi-restraints excluded: chain s residue 312 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 415 ASP Chi-restraints excluded: chain s residue 424 PHE Chi-restraints excluded: chain s residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 838 optimal weight: 0.9980 chunk 882 optimal weight: 0.9980 chunk 805 optimal weight: 0.7980 chunk 858 optimal weight: 0.1980 chunk 516 optimal weight: 3.9990 chunk 374 optimal weight: 5.9990 chunk 674 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 775 optimal weight: 2.9990 chunk 812 optimal weight: 1.9990 chunk 855 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN ** 0 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN 8 144 GLN 8 177 HIS 8 184 ASN D 233 GLN ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 ASN I 151 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 125 HIS ** T 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 240 HIS ** Z 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 HIS d 153 ASN ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN r 130 ASN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 105693 Z= 0.185 Angle : 0.638 13.961 150386 Z= 0.318 Chirality : 0.038 0.431 17680 Planarity : 0.005 0.172 13535 Dihedral : 19.806 179.445 32483 Min Nonbonded Distance : 1.125 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.92 % Favored : 96.07 % Rotamer: Outliers : 4.37 % Allowed : 25.93 % Favored : 69.70 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % 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: -0.26 (0.09), residues: 8037 helix: 0.77 (0.10), residues: 2742 sheet: -0.81 (0.15), residues: 1036 loop : -0.57 (0.10), residues: 4259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP X 80 HIS 0.007 0.001 HIS b 90 PHE 0.033 0.002 PHE Q 75 TYR 0.035 0.002 TYR h 73 ARG 0.014 0.001 ARG U 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1947 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1631 time to evaluate : 7.346 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: 1 52 GLN cc_start: 0.8994 (pm20) cc_final: 0.8774 (pm20) REVERT: 1 58 GLU cc_start: 0.7779 (pm20) cc_final: 0.7327 (mp0) REVERT: 2 66 TRP cc_start: 0.8985 (t-100) cc_final: 0.8557 (t-100) REVERT: 3 161 MET cc_start: 0.8757 (ttm) cc_final: 0.8531 (mtp) REVERT: 4 93 LYS cc_start: 0.8735 (mmtp) cc_final: 0.8254 (mtpp) REVERT: 5 64 MET cc_start: 0.8959 (mtm) cc_final: 0.8084 (mtp) REVERT: 5 98 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7960 (pp) REVERT: 5 270 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8368 (mm) REVERT: 5 304 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7703 (tt) REVERT: 6 44 ASN cc_start: 0.8267 (t0) cc_final: 0.7392 (p0) REVERT: 6 96 LYS cc_start: 0.5654 (tttp) cc_final: 0.5410 (tptt) REVERT: 6 103 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8622 (tt) REVERT: 6 105 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7615 (tm-30) REVERT: 6 337 MET cc_start: 0.6468 (mtp) cc_final: 0.6257 (ttm) REVERT: 6 356 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7651 (ttp80) REVERT: 7 51 GLU cc_start: 0.7879 (tp30) cc_final: 0.7496 (tp30) REVERT: 7 115 MET cc_start: 0.8707 (mmm) cc_final: 0.7773 (tpp) REVERT: 7 148 MET cc_start: 0.8955 (tmm) cc_final: 0.8579 (tmm) REVERT: 7 200 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8222 (tpp80) REVERT: 7 259 ASP cc_start: 0.8385 (p0) cc_final: 0.7754 (p0) REVERT: 7 298 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6419 (mt0) REVERT: 8 126 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8630 (mm-40) REVERT: 9 102 LYS cc_start: 0.6018 (mmtp) cc_final: 0.5638 (mmpt) REVERT: D 132 ASP cc_start: 0.8565 (t0) cc_final: 0.8167 (m-30) REVERT: D 227 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8564 (tm-30) REVERT: D 233 GLN cc_start: 0.8976 (mt0) cc_final: 0.8758 (mt0) REVERT: D 265 TRP cc_start: 0.8426 (m-10) cc_final: 0.7451 (m-10) REVERT: F 101 MET cc_start: 0.8447 (mmm) cc_final: 0.8231 (mmm) REVERT: F 103 GLN cc_start: 0.9126 (pt0) cc_final: 0.8781 (pt0) REVERT: F 108 ARG cc_start: 0.8917 (ttt180) cc_final: 0.7927 (ttt90) REVERT: F 190 MET cc_start: 0.8087 (mpp) cc_final: 0.7271 (mtp) REVERT: F 257 GLN cc_start: 0.8577 (mm-40) cc_final: 0.7699 (mm-40) REVERT: F 280 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7706 (t80) REVERT: H 70 LYS cc_start: 0.8475 (mtmm) cc_final: 0.7718 (mmmt) REVERT: H 91 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7276 (ptpt) REVERT: H 115 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8233 (mtpt) REVERT: I 44 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8202 (ttm170) REVERT: I 48 MET cc_start: 0.8683 (mmm) cc_final: 0.8409 (mtt) REVERT: I 84 ARG cc_start: 0.8078 (ttp-170) cc_final: 0.7546 (ptm160) REVERT: I 144 LEU cc_start: 0.7505 (mt) cc_final: 0.7024 (tp) REVERT: J 177 LYS cc_start: 0.4339 (ptpp) cc_final: 0.4013 (tptt) REVERT: K 99 ASP cc_start: 0.8013 (t0) cc_final: 0.7676 (t0) REVERT: K 150 LYS cc_start: 0.8789 (mppt) cc_final: 0.8551 (mtpp) REVERT: L 96 MET cc_start: 0.8562 (mmm) cc_final: 0.8278 (mmt) REVERT: L 111 ASN cc_start: 0.8857 (p0) cc_final: 0.8519 (p0) REVERT: M 30 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7713 (m-40) REVERT: M 91 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7024 (tpp80) REVERT: M 99 ASN cc_start: 0.9216 (m-40) cc_final: 0.8712 (m110) REVERT: M 111 ASP cc_start: 0.7824 (t0) cc_final: 0.7196 (t70) REVERT: M 253 PHE cc_start: 0.8664 (t80) cc_final: 0.8375 (t80) REVERT: N 92 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8455 (mt) REVERT: N 118 MET cc_start: 0.8853 (ptp) cc_final: 0.8104 (ptp) REVERT: N 223 MET cc_start: 0.8780 (mmm) cc_final: 0.8457 (mmm) REVERT: N 242 TRP cc_start: 0.9272 (t-100) cc_final: 0.8811 (t-100) REVERT: N 247 MET cc_start: 0.8638 (mpp) cc_final: 0.8274 (mtt) REVERT: P 56 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: P 87 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7070 (m170) REVERT: P 140 ILE cc_start: 0.9134 (mm) cc_final: 0.8629 (mm) REVERT: Q 259 LYS cc_start: 0.8558 (pptt) cc_final: 0.8324 (mtpt) REVERT: R 64 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7927 (mmm) REVERT: R 68 TRP cc_start: 0.9103 (m-10) cc_final: 0.8846 (m-10) REVERT: R 76 SER cc_start: 0.9329 (m) cc_final: 0.8722 (t) REVERT: R 89 ASN cc_start: 0.8676 (m-40) cc_final: 0.8445 (m110) REVERT: S 81 LYS cc_start: 0.8666 (tmmt) cc_final: 0.8031 (tppt) REVERT: S 95 LEU cc_start: 0.8848 (pt) cc_final: 0.8453 (mp) REVERT: S 105 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8868 (mt0) REVERT: S 152 ASP cc_start: 0.7900 (p0) cc_final: 0.7440 (t0) REVERT: S 203 CYS cc_start: 0.8272 (p) cc_final: 0.7977 (t) REVERT: T 82 TYR cc_start: 0.9064 (t80) cc_final: 0.8496 (t80) REVERT: T 87 MET cc_start: 0.8044 (ptm) cc_final: 0.7395 (ptm) REVERT: T 134 VAL cc_start: 0.9376 (t) cc_final: 0.8984 (p) REVERT: U 12 LEU cc_start: 0.8028 (mm) cc_final: 0.7520 (tp) REVERT: U 37 GLU cc_start: 0.8140 (pm20) cc_final: 0.7912 (pt0) REVERT: U 77 ASN cc_start: 0.8736 (t0) cc_final: 0.8364 (t0) REVERT: U 104 THR cc_start: 0.8121 (m) cc_final: 0.7627 (t) REVERT: V 118 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.7060 (mmt-90) REVERT: V 122 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6727 (mm) REVERT: V 124 ASP cc_start: 0.6607 (p0) cc_final: 0.6098 (p0) REVERT: V 134 GLU cc_start: 0.5098 (mp0) cc_final: 0.4818 (mp0) REVERT: V 188 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8504 (m) REVERT: W 137 LYS cc_start: 0.8923 (ptpp) cc_final: 0.8654 (mtpt) REVERT: X 15 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7730 (tm-30) REVERT: X 36 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7417 (mtp-110) REVERT: X 71 PHE cc_start: 0.9231 (m-80) cc_final: 0.8917 (m-80) REVERT: X 80 TRP cc_start: 0.8268 (m-10) cc_final: 0.7782 (m-90) REVERT: X 90 ILE cc_start: 0.9479 (tp) cc_final: 0.9189 (tt) REVERT: X 189 ASP cc_start: 0.8277 (p0) cc_final: 0.7896 (t0) REVERT: Y 111 MET cc_start: 0.8528 (tmm) cc_final: 0.8130 (tmm) REVERT: Y 126 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7388 (ptt) REVERT: Y 188 TRP cc_start: 0.8938 (p-90) cc_final: 0.8150 (p-90) REVERT: Z 59 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7908 (p0) REVERT: Z 88 MET cc_start: 0.8939 (mtm) cc_final: 0.8588 (mtm) REVERT: Z 136 ASN cc_start: 0.8473 (p0) cc_final: 0.7986 (p0) REVERT: a 41 ASP cc_start: 0.7949 (t0) cc_final: 0.7608 (t0) REVERT: a 48 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7177 (mt-10) REVERT: a 53 SER cc_start: 0.8963 (t) cc_final: 0.8683 (p) REVERT: a 70 GLU cc_start: 0.6611 (tm-30) cc_final: 0.6264 (tm-30) REVERT: a 137 ASN cc_start: 0.8114 (p0) cc_final: 0.7503 (p0) REVERT: b 26 LEU cc_start: 0.9434 (tt) cc_final: 0.9161 (tt) REVERT: b 32 SER cc_start: 0.8733 (m) cc_final: 0.8406 (t) REVERT: b 110 LEU cc_start: 0.8677 (pt) cc_final: 0.8448 (mt) REVERT: c 82 ASN cc_start: 0.8484 (p0) cc_final: 0.8225 (p0) REVERT: d 122 ILE cc_start: 0.8199 (mt) cc_final: 0.7985 (mt) REVERT: d 156 ASP cc_start: 0.8207 (t70) cc_final: 0.7787 (t0) REVERT: d 158 ASP cc_start: 0.8540 (t0) cc_final: 0.8337 (t70) REVERT: d 172 MET cc_start: 0.8361 (ttm) cc_final: 0.7977 (ttp) REVERT: d 202 MET cc_start: 0.2813 (tpt) cc_final: 0.1354 (ptt) REVERT: d 281 MET cc_start: 0.9137 (ppp) cc_final: 0.8833 (ppp) REVERT: e 78 GLU cc_start: 0.7339 (tm-30) cc_final: 0.7075 (tm-30) REVERT: e 124 TRP cc_start: 0.7627 (m-10) cc_final: 0.7318 (m-10) REVERT: e 187 THR cc_start: 0.6255 (p) cc_final: 0.4817 (p) REVERT: f 120 LYS cc_start: 0.8966 (tttp) cc_final: 0.8596 (tptm) REVERT: f 122 GLU cc_start: 0.7395 (mp0) cc_final: 0.6744 (mp0) REVERT: f 130 LYS cc_start: 0.4248 (tptt) cc_final: 0.3869 (tmtt) REVERT: f 183 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.7438 (mtp85) REVERT: g 40 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6187 (tm-30) REVERT: g 45 TYR cc_start: 0.8106 (t80) cc_final: 0.7720 (t80) REVERT: g 152 TYR cc_start: 0.8427 (m-80) cc_final: 0.8034 (m-10) REVERT: h 71 GLU cc_start: 0.7722 (mm-30) cc_final: 0.6696 (mm-30) REVERT: i 63 LEU cc_start: 0.9167 (pt) cc_final: 0.8902 (pp) REVERT: i 79 TRP cc_start: 0.9006 (p90) cc_final: 0.8721 (p90) REVERT: i 94 LYS cc_start: 0.8754 (tttp) cc_final: 0.8514 (tttp) REVERT: i 122 ASN cc_start: 0.9256 (m-40) cc_final: 0.8870 (m-40) REVERT: j 97 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8093 (mmtm) REVERT: j 100 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7785 (tm-30) REVERT: l 67 GLN cc_start: 0.5748 (tm-30) cc_final: 0.5134 (tm-30) REVERT: l 99 MET cc_start: 0.3753 (ttm) cc_final: 0.3250 (ptm) REVERT: l 119 ARG cc_start: 0.7426 (ttt90) cc_final: 0.7132 (mtt180) REVERT: l 122 ARG cc_start: 0.8088 (ttm170) cc_final: 0.7473 (ttp80) REVERT: l 124 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7054 (mp10) REVERT: m 48 TYR cc_start: 0.7349 (p90) cc_final: 0.6866 (p90) REVERT: m 52 TYR cc_start: 0.7164 (m-80) cc_final: 0.6644 (m-80) REVERT: m 55 LEU cc_start: 0.8722 (tp) cc_final: 0.8436 (tp) REVERT: m 70 GLU cc_start: 0.7324 (mp0) cc_final: 0.7101 (mp0) REVERT: m 74 MET cc_start: 0.8181 (ppp) cc_final: 0.7652 (tpp) REVERT: m 79 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7649 (mm) REVERT: o 40 GLU cc_start: 0.7965 (pp20) cc_final: 0.7440 (tm-30) REVERT: o 51 MET cc_start: 0.9433 (ptp) cc_final: 0.8932 (ptp) REVERT: p 146 ASN cc_start: 0.8490 (m110) cc_final: 0.8253 (m-40) REVERT: q 51 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: q 56 TYR cc_start: 0.8611 (t80) cc_final: 0.8368 (t80) REVERT: q 92 TRP cc_start: 0.8879 (m100) cc_final: 0.8574 (m100) REVERT: q 99 MET cc_start: 0.8564 (mmt) cc_final: 0.7848 (mmt) REVERT: q 108 LEU cc_start: 0.9008 (pp) cc_final: 0.8743 (tp) REVERT: q 136 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: q 140 ARG cc_start: 0.7111 (mmp-170) cc_final: 0.6158 (mtm-85) REVERT: r 81 TYR cc_start: 0.8830 (p90) cc_final: 0.8468 (p90) REVERT: r 84 ASP cc_start: 0.7771 (p0) cc_final: 0.7484 (p0) REVERT: r 117 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7593 (tm-30) REVERT: s 61 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8376 (tpp80) REVERT: s 78 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: s 89 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: s 152 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7745 (pp30) REVERT: s 222 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8111 (ptt180) REVERT: s 241 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9156 (mt) REVERT: s 269 ASP cc_start: 0.8412 (m-30) cc_final: 0.8003 (t0) REVERT: s 274 PHE cc_start: 0.8981 (m-80) cc_final: 0.8510 (m-80) REVERT: s 298 GLN cc_start: 0.8553 (mt0) cc_final: 0.8166 (mt0) REVERT: s 335 TRP cc_start: 0.9208 (t60) cc_final: 0.8606 (t60) REVERT: s 379 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9020 (mm) REVERT: s 425 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9064 (mt) outliers start: 316 outliers final: 246 residues processed: 1807 average time/residue: 0.9119 time to fit residues: 2857.8693 Evaluate side-chains 1853 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1577 time to evaluate : 7.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 123 CYS Chi-restraints excluded: chain 0 residue 156 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 35 ASN Chi-restraints excluded: chain 2 residue 89 SER Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 154 GLN Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 3 residue 178 GLN Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 396 VAL Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 290 CYS Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 356 ARG Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 85 ILE Chi-restraints excluded: chain 7 residue 149 MET Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 186 ASP Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 298 GLN Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain 8 residue 127 GLN Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 184 ASN Chi-restraints excluded: chain 9 residue 53 ILE Chi-restraints excluded: chain 9 residue 64 ASP Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 280 TYR Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 58 GLN Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 172 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 87 HIS Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 161 GLU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 260 TRP Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 147 SER Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 118 ARG Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain V residue 180 GLU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 56 ASN Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 156 LEU Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain a residue 108 MET Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 143 ASP Chi-restraints excluded: chain c residue 228 LEU Chi-restraints excluded: chain c residue 245 LEU Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 95 TYR Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 177 LYS Chi-restraints excluded: chain d residue 237 ASP Chi-restraints excluded: chain d residue 238 VAL Chi-restraints excluded: chain d residue 277 LEU Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 146 ARG Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 272 VAL Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 156 VAL Chi-restraints excluded: chain f residue 169 ILE Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain f residue 186 VAL Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 117 ILE Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 142 GLU Chi-restraints excluded: chain h residue 154 ILE Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 49 LEU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain p residue 76 LEU Chi-restraints excluded: chain p residue 134 ILE Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 119 GLN Chi-restraints excluded: chain q residue 136 GLN Chi-restraints excluded: chain r residue 77 LEU Chi-restraints excluded: chain r residue 128 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 181 LEU Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 89 MET Chi-restraints excluded: chain s residue 145 VAL Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 222 ARG Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 260 GLU Chi-restraints excluded: chain s residue 312 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 379 LEU Chi-restraints excluded: chain s residue 424 PHE Chi-restraints excluded: chain s residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 563 optimal weight: 2.9990 chunk 907 optimal weight: 0.1980 chunk 554 optimal weight: 0.9990 chunk 430 optimal weight: 0.9980 chunk 631 optimal weight: 3.9990 chunk 952 optimal weight: 0.9980 chunk 876 optimal weight: 1.9990 chunk 758 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 585 optimal weight: 4.9990 chunk 465 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN ** 0 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 144 GLN 8 177 HIS 8 184 ASN ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN Y 240 HIS ** Z 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 236 ASN d 154 ASN ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 104 HIS q 51 GLN ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 130 ASN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 105693 Z= 0.247 Angle : 0.730 59.193 150386 Z= 0.384 Chirality : 0.038 0.532 17680 Planarity : 0.005 0.159 13535 Dihedral : 19.803 179.435 32483 Min Nonbonded Distance : 1.124 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.04 % Favored : 95.94 % Rotamer: Outliers : 4.18 % Allowed : 26.47 % Favored : 69.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % 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: -0.26 (0.09), residues: 8037 helix: 0.76 (0.10), residues: 2742 sheet: -0.79 (0.15), residues: 1034 loop : -0.57 (0.10), residues: 4261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP X 80 HIS 0.007 0.001 HIS b 90 PHE 0.066 0.002 PHE c 159 TYR 0.035 0.002 TYR s 108 ARG 0.013 0.000 ARG l 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16074 Ramachandran restraints generated. 8037 Oldfield, 0 Emsley, 8037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1877 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1575 time to evaluate : 7.108 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: 1 52 GLN cc_start: 0.8945 (pm20) cc_final: 0.8737 (pm20) REVERT: 2 66 TRP cc_start: 0.8985 (t-100) cc_final: 0.8559 (t-100) REVERT: 3 161 MET cc_start: 0.8761 (ttm) cc_final: 0.8538 (mtp) REVERT: 4 93 LYS cc_start: 0.8737 (mmtp) cc_final: 0.8254 (mtpp) REVERT: 5 64 MET cc_start: 0.8957 (mtm) cc_final: 0.8089 (mtp) REVERT: 5 98 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7960 (pp) REVERT: 5 270 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8370 (mm) REVERT: 5 304 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7699 (tt) REVERT: 6 44 ASN cc_start: 0.8269 (t0) cc_final: 0.7390 (p0) REVERT: 6 96 LYS cc_start: 0.5662 (tttp) cc_final: 0.5412 (tptt) REVERT: 6 103 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8624 (tt) REVERT: 6 105 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7617 (tm-30) REVERT: 6 337 MET cc_start: 0.6461 (mtp) cc_final: 0.6215 (ttm) REVERT: 6 356 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7650 (ttp80) REVERT: 7 51 GLU cc_start: 0.7877 (tp30) cc_final: 0.7501 (tp30) REVERT: 7 115 MET cc_start: 0.8707 (mmm) cc_final: 0.7791 (tpp) REVERT: 7 148 MET cc_start: 0.8952 (tmm) cc_final: 0.8556 (tmm) REVERT: 7 200 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8225 (tpp80) REVERT: 7 259 ASP cc_start: 0.8388 (p0) cc_final: 0.7768 (p0) REVERT: 8 126 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8614 (mm-40) REVERT: 9 102 LYS cc_start: 0.6013 (mmtp) cc_final: 0.5635 (mmpt) REVERT: D 106 MET cc_start: 0.8610 (mtp) cc_final: 0.8328 (mtt) REVERT: D 132 ASP cc_start: 0.8571 (t0) cc_final: 0.8185 (m-30) REVERT: D 227 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8582 (tm-30) REVERT: D 233 GLN cc_start: 0.8972 (mt0) cc_final: 0.8770 (mt0) REVERT: D 265 TRP cc_start: 0.8434 (m-10) cc_final: 0.7453 (m-10) REVERT: F 103 GLN cc_start: 0.9128 (pt0) cc_final: 0.8778 (pt0) REVERT: F 108 ARG cc_start: 0.8921 (ttt180) cc_final: 0.7934 (ttt90) REVERT: F 190 MET cc_start: 0.8064 (mpp) cc_final: 0.7252 (mtp) REVERT: F 257 GLN cc_start: 0.8585 (mm-40) cc_final: 0.7697 (mm-40) REVERT: F 280 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7707 (t80) REVERT: H 70 LYS cc_start: 0.8485 (mtmm) cc_final: 0.7720 (mmmt) REVERT: H 91 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7268 (ptpt) REVERT: H 115 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8233 (mtpt) REVERT: I 44 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.7598 (ttm170) REVERT: I 48 MET cc_start: 0.8684 (mmm) cc_final: 0.8431 (mtt) REVERT: I 84 ARG cc_start: 0.8080 (ttp-170) cc_final: 0.7548 (ptm160) REVERT: I 144 LEU cc_start: 0.7509 (mt) cc_final: 0.7027 (tp) REVERT: J 177 LYS cc_start: 0.4337 (ptpp) cc_final: 0.4011 (tptt) REVERT: K 99 ASP cc_start: 0.8009 (t0) cc_final: 0.7672 (t0) REVERT: K 150 LYS cc_start: 0.8786 (mppt) cc_final: 0.8554 (mtpp) REVERT: L 96 MET cc_start: 0.8568 (mmm) cc_final: 0.8281 (mmt) REVERT: L 111 ASN cc_start: 0.8862 (p0) cc_final: 0.8520 (p0) REVERT: M 30 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7709 (m-40) REVERT: M 99 ASN cc_start: 0.9217 (m-40) cc_final: 0.8708 (m110) REVERT: M 111 ASP cc_start: 0.7828 (t0) cc_final: 0.7200 (t70) REVERT: M 253 PHE cc_start: 0.8675 (t80) cc_final: 0.8362 (t80) REVERT: N 92 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8453 (mt) REVERT: N 118 MET cc_start: 0.8849 (ptp) cc_final: 0.8105 (ptp) REVERT: N 223 MET cc_start: 0.8841 (mmm) cc_final: 0.8438 (mmm) REVERT: N 242 TRP cc_start: 0.9278 (t-100) cc_final: 0.9027 (t-100) REVERT: N 247 MET cc_start: 0.8643 (mpp) cc_final: 0.8257 (mtt) REVERT: O 120 MET cc_start: 0.8183 (mmm) cc_final: 0.7710 (mpp) REVERT: P 56 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: P 87 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.7071 (m170) REVERT: P 140 ILE cc_start: 0.9194 (mm) cc_final: 0.8632 (mm) REVERT: Q 259 LYS cc_start: 0.8585 (pptt) cc_final: 0.8326 (mtpt) REVERT: R 64 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7934 (mmm) REVERT: R 68 TRP cc_start: 0.9113 (m-10) cc_final: 0.8841 (m-10) REVERT: R 76 SER cc_start: 0.9331 (m) cc_final: 0.8721 (t) REVERT: R 89 ASN cc_start: 0.8681 (m-40) cc_final: 0.8431 (m110) REVERT: S 81 LYS cc_start: 0.8668 (tmmt) cc_final: 0.8034 (tppt) REVERT: S 95 LEU cc_start: 0.8854 (pt) cc_final: 0.8460 (mp) REVERT: S 105 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8871 (mt0) REVERT: S 152 ASP cc_start: 0.7898 (p0) cc_final: 0.7441 (t0) REVERT: S 203 CYS cc_start: 0.8298 (p) cc_final: 0.7974 (t) REVERT: T 82 TYR cc_start: 0.9066 (t80) cc_final: 0.8498 (t80) REVERT: T 87 MET cc_start: 0.8054 (ptm) cc_final: 0.7470 (ptm) REVERT: T 134 VAL cc_start: 0.9371 (t) cc_final: 0.8988 (p) REVERT: U 12 LEU cc_start: 0.8025 (mm) cc_final: 0.7522 (tp) REVERT: U 37 GLU cc_start: 0.8142 (pm20) cc_final: 0.7914 (pt0) REVERT: U 77 ASN cc_start: 0.8737 (t0) cc_final: 0.8360 (t0) REVERT: U 104 THR cc_start: 0.8124 (m) cc_final: 0.7626 (t) REVERT: V 124 ASP cc_start: 0.6604 (p0) cc_final: 0.6112 (p0) REVERT: V 134 GLU cc_start: 0.5083 (mp0) cc_final: 0.4812 (mp0) REVERT: W 137 LYS cc_start: 0.8923 (ptpp) cc_final: 0.8654 (mtpt) REVERT: X 15 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7735 (tm-30) REVERT: X 36 ARG cc_start: 0.7623 (mtp-110) cc_final: 0.7414 (mtp-110) REVERT: X 71 PHE cc_start: 0.9227 (m-80) cc_final: 0.8917 (m-80) REVERT: X 80 TRP cc_start: 0.8246 (m-10) cc_final: 0.7740 (m-90) REVERT: X 90 ILE cc_start: 0.9479 (tp) cc_final: 0.9189 (tt) REVERT: X 189 ASP cc_start: 0.8282 (p0) cc_final: 0.7897 (t0) REVERT: Y 111 MET cc_start: 0.8533 (tmm) cc_final: 0.8132 (tmm) REVERT: Y 126 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7388 (ptt) REVERT: Y 188 TRP cc_start: 0.8940 (p-90) cc_final: 0.8160 (p-90) REVERT: Z 59 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7914 (p0) REVERT: Z 88 MET cc_start: 0.8966 (mtm) cc_final: 0.8614 (mtm) REVERT: Z 136 ASN cc_start: 0.8490 (p0) cc_final: 0.7976 (p0) REVERT: a 41 ASP cc_start: 0.7959 (t0) cc_final: 0.7609 (t0) REVERT: a 48 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7193 (mt-10) REVERT: a 53 SER cc_start: 0.8967 (t) cc_final: 0.8683 (p) REVERT: a 70 GLU cc_start: 0.6615 (tm-30) cc_final: 0.6270 (tm-30) REVERT: a 137 ASN cc_start: 0.8114 (p0) cc_final: 0.7499 (p0) REVERT: b 26 LEU cc_start: 0.9435 (tt) cc_final: 0.9158 (tt) REVERT: b 32 SER cc_start: 0.8723 (m) cc_final: 0.8409 (t) REVERT: b 110 LEU cc_start: 0.8682 (pt) cc_final: 0.8450 (mt) REVERT: c 82 ASN cc_start: 0.8505 (p0) cc_final: 0.8225 (p0) REVERT: d 122 ILE cc_start: 0.8193 (mt) cc_final: 0.7985 (mt) REVERT: d 158 ASP cc_start: 0.8535 (t0) cc_final: 0.8284 (t70) REVERT: d 172 MET cc_start: 0.8332 (ttm) cc_final: 0.7985 (ttp) REVERT: d 202 MET cc_start: 0.2809 (tpt) cc_final: 0.1354 (ptt) REVERT: d 281 MET cc_start: 0.9120 (ppp) cc_final: 0.8823 (ppp) REVERT: e 124 TRP cc_start: 0.7629 (m-10) cc_final: 0.7315 (m-10) REVERT: e 187 THR cc_start: 0.5381 (p) cc_final: 0.4994 (p) REVERT: f 120 LYS cc_start: 0.8965 (tttp) cc_final: 0.8597 (tptm) REVERT: f 122 GLU cc_start: 0.7390 (mp0) cc_final: 0.6746 (mp0) REVERT: f 130 LYS cc_start: 0.4243 (tptt) cc_final: 0.3866 (tmtt) REVERT: f 183 ARG cc_start: 0.7722 (mtp-110) cc_final: 0.7441 (mtp85) REVERT: g 45 TYR cc_start: 0.8104 (t80) cc_final: 0.7721 (t80) REVERT: g 152 TYR cc_start: 0.8427 (m-80) cc_final: 0.8021 (m-10) REVERT: i 63 LEU cc_start: 0.9158 (pt) cc_final: 0.8883 (pp) REVERT: i 122 ASN cc_start: 0.9258 (m-40) cc_final: 0.8878 (m-40) REVERT: j 97 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8095 (mmtm) REVERT: j 100 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7784 (tm-30) REVERT: l 99 MET cc_start: 0.3758 (ttm) cc_final: 0.3251 (ptm) REVERT: l 119 ARG cc_start: 0.7429 (ttt90) cc_final: 0.7133 (mtt180) REVERT: l 122 ARG cc_start: 0.8093 (ttm170) cc_final: 0.7475 (ttp80) REVERT: l 124 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: m 48 TYR cc_start: 0.7348 (p90) cc_final: 0.6976 (p90) REVERT: m 52 TYR cc_start: 0.7156 (m-80) cc_final: 0.6657 (m-80) REVERT: m 55 LEU cc_start: 0.8723 (tp) cc_final: 0.8435 (tp) REVERT: m 70 GLU cc_start: 0.7322 (mp0) cc_final: 0.7110 (mp0) REVERT: m 74 MET cc_start: 0.8179 (ppp) cc_final: 0.7649 (tpp) REVERT: m 79 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7648 (mm) REVERT: o 40 GLU cc_start: 0.7964 (pp20) cc_final: 0.7443 (tm-30) REVERT: o 51 MET cc_start: 0.9429 (ptp) cc_final: 0.8932 (ptp) REVERT: p 146 ASN cc_start: 0.8492 (m110) cc_final: 0.8255 (m-40) REVERT: q 92 TRP cc_start: 0.8896 (m100) cc_final: 0.8584 (m100) REVERT: q 99 MET cc_start: 0.8568 (mmt) cc_final: 0.7849 (mmt) REVERT: q 108 LEU cc_start: 0.9004 (pp) cc_final: 0.8742 (tp) REVERT: q 136 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7608 (mp10) REVERT: q 140 ARG cc_start: 0.7116 (mmp-170) cc_final: 0.6157 (mtm-85) REVERT: r 81 TYR cc_start: 0.8843 (p90) cc_final: 0.8458 (p90) REVERT: r 84 ASP cc_start: 0.7764 (p0) cc_final: 0.7469 (p0) REVERT: r 117 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7597 (tm-30) REVERT: s 78 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: s 89 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7945 (mmm) REVERT: s 152 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7748 (pp30) REVERT: s 222 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8113 (ptt180) REVERT: s 241 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9156 (mt) REVERT: s 269 ASP cc_start: 0.8411 (m-30) cc_final: 0.8004 (t0) REVERT: s 274 PHE cc_start: 0.8985 (m-80) cc_final: 0.8513 (m-80) REVERT: s 298 GLN cc_start: 0.8542 (mt0) cc_final: 0.8163 (mt0) REVERT: s 335 TRP cc_start: 0.9218 (t60) cc_final: 0.8605 (t60) REVERT: s 379 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9022 (mm) REVERT: s 425 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9064 (mt) outliers start: 302 outliers final: 258 residues processed: 1738 average time/residue: 0.9001 time to fit residues: 2719.2690 Evaluate side-chains 1848 residues out of total 7232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1566 time to evaluate : 6.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 123 CYS Chi-restraints excluded: chain 0 residue 156 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 35 ASN Chi-restraints excluded: chain 2 residue 89 SER Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 154 GLN Chi-restraints excluded: chain 3 residue 155 SER Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 3 residue 178 GLN Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 396 VAL Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 290 CYS Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 335 LEU Chi-restraints excluded: chain 6 residue 356 ARG Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 85 ILE Chi-restraints excluded: chain 7 residue 149 MET Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 186 ASP Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain 8 residue 127 GLN Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 53 ILE Chi-restraints excluded: chain 9 residue 64 ASP Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 280 TYR Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 58 GLN Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 172 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 87 HIS Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 161 GLU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 260 TRP Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 103 LEU Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 147 SER Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain V residue 180 GLU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 56 ASN Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 156 LEU Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain a residue 108 MET Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 143 ASP Chi-restraints excluded: chain c residue 228 LEU Chi-restraints excluded: chain c residue 245 LEU Chi-restraints excluded: chain c residue 283 GLU Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 95 TYR Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 177 LYS Chi-restraints excluded: chain d residue 237 ASP Chi-restraints excluded: chain d residue 238 VAL Chi-restraints excluded: chain d residue 277 LEU Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 146 ARG Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 272 VAL Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 156 VAL Chi-restraints excluded: chain f residue 169 ILE Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain f residue 186 VAL Chi-restraints excluded: chain g residue 39 VAL Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 117 ILE Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 142 GLU Chi-restraints excluded: chain h residue 154 ILE Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 49 LEU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain p residue 76 LEU Chi-restraints excluded: chain p residue 134 ILE Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 119 GLN Chi-restraints excluded: chain q residue 136 GLN Chi-restraints excluded: chain r residue 77 LEU Chi-restraints excluded: chain r residue 128 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 181 LEU Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 89 MET Chi-restraints excluded: chain s residue 145 VAL Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 222 ARG Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 260 GLU Chi-restraints excluded: chain s residue 312 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 379 LEU Chi-restraints excluded: chain s residue 424 PHE Chi-restraints excluded: chain s residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 602 optimal weight: 0.7980 chunk 807 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 699 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 759 optimal weight: 3.9990 chunk 317 optimal weight: 0.0050 chunk 780 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN ** 0 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN 8 144 GLN 8 177 HIS ** 8 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN Y 240 HIS ** Z 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 130 ASN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.085848 restraints weight = 225637.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.088449 restraints weight = 94000.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.089965 restraints weight = 52693.171| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 105693 Z= 0.247 Angle : 0.730 59.193 150386 Z= 0.384 Chirality : 0.038 0.532 17680 Planarity : 0.005 0.159 13535 Dihedral : 19.803 179.435 32483 Min Nonbonded Distance : 1.124 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.04 % Favored : 95.94 % Rotamer: Outliers : 3.94 % Allowed : 26.60 % Favored : 69.46 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % 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: -0.26 (0.09), residues: 8037 helix: 0.76 (0.10), residues: 2742 sheet: -0.79 (0.15), residues: 1034 loop : -0.57 (0.10), residues: 4261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP X 80 HIS 0.007 0.001 HIS b 90 PHE 0.066 0.002 PHE c 159 TYR 0.035 0.002 TYR s 108 ARG 0.013 0.000 ARG l 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39256.29 seconds wall clock time: 684 minutes 0.97 seconds (41040.97 seconds total)