Starting phenix.real_space_refine on Thu Feb 22 18:19:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oid_12926/02_2024/7oid_12926_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oid_12926/02_2024/7oid_12926.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oid_12926/02_2024/7oid_12926_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oid_12926/02_2024/7oid_12926_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oid_12926/02_2024/7oid_12926_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oid_12926/02_2024/7oid_12926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oid_12926/02_2024/7oid_12926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oid_12926/02_2024/7oid_12926_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oid_12926/02_2024/7oid_12926_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1601 5.49 5 Mg 2 5.21 5 S 285 5.16 5 C 58066 2.51 5 N 18410 2.21 5 O 22759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E ASP 69": "OD1" <-> "OD2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ASP 205": "OD1" <-> "OD2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 331": "OD1" <-> "OD2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 137": "OD1" <-> "OD2" Residue "I PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ASP 55": "OD1" <-> "OD2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K GLU 143": "OE1" <-> "OE2" Residue "K GLU 144": "OE1" <-> "OE2" Residue "K TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "L ARG 37": "NH1" <-> "NH2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "L TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M GLU 143": "OE1" <-> "OE2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M GLU 208": "OE1" <-> "OE2" Residue "M TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M GLU 235": "OE1" <-> "OE2" Residue "M TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 259": "NH1" <-> "NH2" Residue "M ASP 279": "OD1" <-> "OD2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N GLU 171": "OE1" <-> "OE2" Residue "N PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 201": "OD1" <-> "OD2" Residue "N TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 61": "OD1" <-> "OD2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "P GLU 42": "OE1" <-> "OE2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "P ARG 75": "NH1" <-> "NH2" Residue "P GLU 76": "OE1" <-> "OE2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "P GLU 152": "OE1" <-> "OE2" Residue "P GLU 174": "OE1" <-> "OE2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "P TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 74": "NH1" <-> "NH2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q GLU 101": "OE1" <-> "OE2" Residue "Q TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q GLU 161": "OE1" <-> "OE2" Residue "Q GLU 173": "OE1" <-> "OE2" Residue "Q GLU 180": "OE1" <-> "OE2" Residue "Q ASP 185": "OD1" <-> "OD2" Residue "Q TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 191": "NH1" <-> "NH2" Residue "Q TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q ASP 246": "OD1" <-> "OD2" Residue "Q ARG 271": "NH1" <-> "NH2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "Q TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 274": "OD1" <-> "OD2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 109": "OE1" <-> "OE2" Residue "R PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "S GLU 71": "OE1" <-> "OE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 111": "OE1" <-> "OE2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T GLU 66": "OE1" <-> "OE2" Residue "T ASP 100": "OD1" <-> "OD2" Residue "T PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T GLU 135": "OE1" <-> "OE2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "T GLU 168": "OE1" <-> "OE2" Residue "T GLU 180": "OE1" <-> "OE2" Residue "T TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "U TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 109": "OD1" <-> "OD2" Residue "U PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 143": "NH1" <-> "NH2" Residue "V ARG 20": "NH1" <-> "NH2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V ASP 53": "OD1" <-> "OD2" Residue "V TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "V TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "V GLU 134": "OE1" <-> "OE2" Residue "V ARG 143": "NH1" <-> "NH2" Residue "V ARG 145": "NH1" <-> "NH2" Residue "V ASP 172": "OD1" <-> "OD2" Residue "V ASP 176": "OD1" <-> "OD2" Residue "V GLU 184": "OE1" <-> "OE2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "V GLU 206": "OE1" <-> "OE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 18": "OE1" <-> "OE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 120": "OD1" <-> "OD2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 151": "OE1" <-> "OE2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 210": "OE1" <-> "OE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 220": "OE1" <-> "OE2" Residue "X TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y GLU 130": "OE1" <-> "OE2" Residue "Y ASP 143": "OD1" <-> "OD2" Residue "Y GLU 148": "OE1" <-> "OE2" Residue "Y ARG 162": "NH1" <-> "NH2" Residue "Y ASP 171": "OD1" <-> "OD2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Z GLU 43": "OE1" <-> "OE2" Residue "Z ASP 84": "OD1" <-> "OD2" Residue "0 GLU 88": "OE1" <-> "OE2" Residue "0 GLU 128": "OE1" <-> "OE2" Residue "0 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "1 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 ASP 112": "OD1" <-> "OD2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "4 TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 32": "OE1" <-> "OE2" Residue "5 ARG 80": "NH1" <-> "NH2" Residue "5 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 151": "OD1" <-> "OD2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 GLU 168": "OE1" <-> "OE2" Residue "5 GLU 174": "OE1" <-> "OE2" Residue "5 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "5 PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 276": "OD1" <-> "OD2" Residue "5 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "5 PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 409": "OE1" <-> "OE2" Residue "6 ARG 27": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 58": "NH1" <-> "NH2" Residue "6 ARG 60": "NH1" <-> "NH2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "6 GLU 64": "OE1" <-> "OE2" Residue "6 ARG 72": "NH1" <-> "NH2" Residue "6 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 124": "NH1" <-> "NH2" Residue "6 ARG 136": "NH1" <-> "NH2" Residue "6 TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 182": "OD1" <-> "OD2" Residue "6 GLU 192": "OE1" <-> "OE2" Residue "6 GLU 203": "OE1" <-> "OE2" Residue "6 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 343": "OE1" <-> "OE2" Residue "6 ARG 364": "NH1" <-> "NH2" Residue "6 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 371": "OD1" <-> "OD2" Residue "7 PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 51": "OE1" <-> "OE2" Residue "7 GLU 63": "OE1" <-> "OE2" Residue "7 ASP 114": "OD1" <-> "OD2" Residue "7 TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 137": "OE1" <-> "OE2" Residue "7 GLU 155": "OE1" <-> "OE2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 GLU 171": "OE1" <-> "OE2" Residue "7 PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 191": "OE1" <-> "OE2" Residue "7 ASP 205": "OD1" <-> "OD2" Residue "7 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 213": "OD1" <-> "OD2" Residue "7 GLU 220": "OE1" <-> "OE2" Residue "7 GLU 249": "OE1" <-> "OE2" Residue "7 ARG 250": "NH1" <-> "NH2" Residue "7 GLU 265": "OE1" <-> "OE2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "7 GLU 318": "OE1" <-> "OE2" Residue "8 GLU 105": "OE1" <-> "OE2" Residue "8 ARG 137": "NH1" <-> "NH2" Residue "8 GLU 174": "OE1" <-> "OE2" Residue "9 ARG 25": "NH1" <-> "NH2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 49": "NH1" <-> "NH2" Residue "9 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 82": "OE1" <-> "OE2" Residue "9 PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 103": "OD1" <-> "OD2" Residue "9 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 115": "OE1" <-> "OE2" Residue "9 GLU 120": "OE1" <-> "OE2" Residue "9 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 70": "OE1" <-> "OE2" Residue "a GLU 105": "OE1" <-> "OE2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a ARG 131": "NH1" <-> "NH2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a ASP 141": "OD1" <-> "OD2" Residue "a ARG 142": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b GLU 48": "OE1" <-> "OE2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c GLU 62": "OE1" <-> "OE2" Residue "c ASP 67": "OD1" <-> "OD2" Residue "c ASP 86": "OD1" <-> "OD2" Residue "c TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 101": "OE1" <-> "OE2" Residue "c GLU 127": "OE1" <-> "OE2" Residue "c ASP 147": "OD1" <-> "OD2" Residue "c GLU 151": "OE1" <-> "OE2" Residue "c GLU 163": "OE1" <-> "OE2" Residue "c GLU 164": "OE1" <-> "OE2" Residue "c PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "c GLU 254": "OE1" <-> "OE2" Residue "c TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 283": "OE1" <-> "OE2" Residue "c TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 309": "OE1" <-> "OE2" Residue "d ARG 74": "NH1" <-> "NH2" Residue "d PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 143": "OD1" <-> "OD2" Residue "d PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 158": "OD1" <-> "OD2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "d ASP 237": "OD1" <-> "OD2" Residue "d TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 290": "OE1" <-> "OE2" Residue "e PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 44": "OE1" <-> "OE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ASP 99": "OD1" <-> "OD2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "h ARG 69": "NH1" <-> "NH2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "h ASP 125": "OD1" <-> "OD2" Residue "i ASP 45": "OD1" <-> "OD2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 67": "OE1" <-> "OE2" Residue "i GLU 72": "OE1" <-> "OE2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i GLU 87": "OE1" <-> "OE2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 53": "OD1" <-> "OD2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j ARG 94": "NH1" <-> "NH2" Residue "j ARG 103": "NH1" <-> "NH2" Residue "k ARG 31": "NH1" <-> "NH2" Residue "k ARG 77": "NH1" <-> "NH2" Residue "k GLU 85": "OE1" <-> "OE2" Residue "l ARG 115": "NH1" <-> "NH2" Residue "l ARG 120": "NH1" <-> "NH2" Residue "l ARG 128": "NH1" <-> "NH2" Residue "l ARG 131": "NH1" <-> "NH2" Residue "m TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 11": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o GLU 72": "OE1" <-> "OE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "p GLU 51": "OE1" <-> "OE2" Residue "p GLU 113": "OE1" <-> "OE2" Residue "p GLU 138": "OE1" <-> "OE2" Residue "p GLU 181": "OE1" <-> "OE2" Residue "q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q GLU 43": "OE1" <-> "OE2" Residue "q ASP 44": "OD1" <-> "OD2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 84": "OE1" <-> "OE2" Residue "q GLU 91": "OE1" <-> "OE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "q ARG 140": "NH1" <-> "NH2" Residue "q GLU 141": "OE1" <-> "OE2" Residue "r TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 117": "OE1" <-> "OE2" Residue "r ARG 132": "NH1" <-> "NH2" Residue "r TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 153": "NH1" <-> "NH2" Residue "r TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 168": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "r TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 103": "OD1" <-> "OD2" Residue "s TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 158": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s ARG 162": "NH1" <-> "NH2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 212": "NH1" <-> "NH2" Residue "s GLU 215": "OE1" <-> "OE2" Residue "s ARG 219": "NH1" <-> "NH2" Residue "s ARG 222": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 242": "NH1" <-> "NH2" Residue "s PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 269": "OD1" <-> "OD2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s ASP 290": "OD1" <-> "OD2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s GLU 309": "OE1" <-> "OE2" Residue "s GLU 348": "OE1" <-> "OE2" Residue "s ASP 384": "OD1" <-> "OD2" Residue "s ARG 389": "NH1" <-> "NH2" Residue "s ASP 415": "OD1" <-> "OD2" Residue "s ASP 416": "OD1" <-> "OD2" Residue "u ASP 95": "OD1" <-> "OD2" Residue "u GLU 160": "OE1" <-> "OE2" Residue "u ASP 165": "OD1" <-> "OD2" Residue "u TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 200": "OD1" <-> "OD2" Residue "v ARG 6": "NH1" <-> "NH2" Residue "v ARG 14": "NH1" <-> "NH2" Residue "v ARG 24": "NH1" <-> "NH2" Residue "v TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 28": "NH1" <-> "NH2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 49": "OE1" <-> "OE2" Residue "w ASP 91": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 101125 Number of models: 1 Model: "" Number of chains: 61 Chain: "D" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1842 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 12, 'TRANS': 223} Chain: "E" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2396 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 24, 'TRANS': 279} Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} Chain breaks: 1 Chain: "J" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1061 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "P" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1148 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain: "Q" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1805 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1305 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 12, 'TRANS': 146} Chain breaks: 1 Chain: "U" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain breaks: 1 Chain: "V" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1575 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 16, 'TRANS': 175} Chain breaks: 1 Chain: "W" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2035 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 322 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "5" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3156 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 354} Chain breaks: 1 Chain: "6" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2640 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "8" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 836 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 9, 'TRANS': 89} Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Chain: "a" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 611 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 8, 'TRANS': 64} Chain breaks: 1 Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} Chain breaks: 1 Chain: "d" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1741 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain breaks: 3 Chain: "e" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1762 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "f" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 915 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} Chain: "h" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "l" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 221 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "m" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "o" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 786 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 Chain: "q" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1379 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 15, 'TRANS': 148} Chain: "r" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1203 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 16, 'TRANS': 129} Chain breaks: 2 Chain: "s" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3036 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 1 Chain: "u" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 927 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 31265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 31265 Classifications: {'RNA': 1472} Modifications used: {'rna2p_pur': 156, 'rna2p_pyr': 111, 'rna3p_pur': 623, 'rna3p_pyr': 582} Link IDs: {'rna2p': 266, 'rna3p': 1205} Chain breaks: 13 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 54} Chain breaks: 4 Chain: "z" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Inner-chain residues flagged as termini: ['pdbres=" G z 1 "'] Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 25} Link IDs: {'rna2p': 16, 'rna3p': 56} Chain breaks: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7322 SG CYS I 64 142.201 99.263 62.935 1.00 47.71 S ATOM 60940 SG CYS r 70 146.181 98.796 61.932 1.00 39.42 S ATOM 60961 SG CYS r 73 144.561 96.928 62.125 1.00 39.33 S ATOM 61255 SG CYS r 108 144.550 101.181 62.126 1.00 36.70 S ATOM 31967 SG CYS 0 110 164.367 85.160 174.930 1.00 31.59 S ATOM 31989 SG CYS 0 113 162.696 83.050 177.682 1.00 30.89 S ATOM 32069 SG CYS 0 123 160.789 86.078 175.636 1.00 22.15 S ATOM 32092 SG CYS 0 126 162.873 86.359 178.479 1.00 24.97 S Time building chain proxies: 37.41, per 1000 atoms: 0.37 Number of scatterers: 101125 At special positions: 0 Unit cell: (220.052, 223.304, 253.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 285 16.00 P 1601 15.00 Mg 2 11.99 O 22759 8.00 N 18410 7.00 C 58066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.90 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 64 " pdb="ZN ZN I 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN I 301 " - pdb=" SG CYS r 108 " pdb="ZN ZN I 301 " - pdb=" SG CYS r 73 " Number of angles added : 12 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15506 Finding SS restraints... 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: 271 helices and 74 sheets defined 41.9% alpha, 13.4% beta 423 base pairs and 837 stacking pairs defined. Time for finding SS restraints: 56.00 Creating SS restraints... 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 Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 4.629A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 304 through 309 removed outlier: 4.965A pdb=" N ASP E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 109 removed outlier: 4.656A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 Processing helix chain 'F' and resid 199 through 211 Processing helix chain 'F' and resid 227 through 238 removed outlier: 5.323A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 3.812A pdb=" N HIS F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 4.916A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'H' and resid 74 through 79 removed outlier: 4.722A pdb=" N VAL H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 90 Proline residue: H 90 - end of helix Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'H' and resid 133 through 147 removed outlier: 5.593A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 52 Processing helix chain 'I' and resid 61 through 66 Proline residue: I 66 - end of helix Processing helix chain 'I' and resid 77 through 94 removed outlier: 5.434A pdb=" N ARG I 94 " --> pdb=" O PHE I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 4.884A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 139 Proline residue: I 133 - end of helix Processing helix chain 'I' and resid 140 through 145 Proline residue: I 145 - end of helix Processing helix chain 'I' and resid 160 through 172 Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'J' and resid 36 through 43 removed outlier: 4.781A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.733A pdb=" N LYS J 61 " --> pdb=" O THR J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 Processing helix chain 'J' and resid 113 through 125 Processing helix chain 'J' and resid 136 through 152 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 41 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 Proline residue: K 113 - end of helix Processing helix chain 'K' and resid 115 through 126 removed outlier: 4.373A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 4.321A pdb=" N ASN K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 167 Proline residue: K 167 - end of helix Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.785A pdb=" N SER L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 131 removed outlier: 4.913A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 142 removed outlier: 4.719A pdb=" N VAL L 137 " --> pdb=" O GLU L 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLN L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 20 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 Processing helix chain 'M' and resid 86 through 91 removed outlier: 5.883A pdb=" N ARG M 91 " --> pdb=" O HIS M 87 " (cutoff:3.500A) 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 Proline residue: M 190 - end of helix Processing helix chain 'M' and resid 191 through 197 Processing helix chain 'M' and resid 207 through 216 Proline residue: M 212 - end of helix Processing helix chain 'M' and resid 225 through 241 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 Processing helix chain 'N' and resid 68 through 74 removed outlier: 5.293A pdb=" N ILE N 72 " --> pdb=" O ASN N 68 " (cutoff:3.500A) removed outlier: 5.935A 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 168 through 183 removed outlier: 5.407A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 209 Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 225 through 231 removed outlier: 4.904A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.693A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 66 removed outlier: 3.958A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 5.436A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 98 removed outlier: 4.225A pdb=" N LYS O 88 " --> pdb=" O ASP O 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 4.546A 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 Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 109 through 116 removed outlier: 3.885A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 140 Processing helix chain 'P' and resid 149 through 156 removed outlier: 5.640A pdb=" N ASP P 156 " --> pdb=" O GLU P 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 169 Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.430A pdb=" N ILE Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Proline residue: Q 82 - end of helix No H-bonds generated for 'chain 'Q' and resid 77 through 82' Processing helix chain 'Q' and resid 88 through 107 removed outlier: 4.342A pdb=" N HIS Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 193 removed outlier: 4.246A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 4.442A pdb=" N SER Q 198 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 Processing helix chain 'Q' and resid 250 through 262 removed outlier: 5.635A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.608A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 290 Processing helix chain 'R' and resid 16 through 29 removed outlier: 4.480A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 38 Processing helix chain 'R' and resid 46 through 80 removed outlier: 5.227A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 109 through 134 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'S' and resid 150 through 155 removed outlier: 5.925A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 57 removed outlier: 3.565A pdb=" N LYS T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 95 Processing helix chain 'T' and resid 98 through 109 Processing helix chain 'T' and resid 111 through 131 Processing helix chain 'T' and resid 191 through 206 Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'V' and resid 28 through 35 Processing helix chain 'V' and resid 178 through 184 Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'W' and resid 110 through 121 Proline residue: W 121 - end of helix Processing helix chain 'X' and resid 8 through 18 removed outlier: 4.647A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 25 Proline residue: X 25 - end of helix Processing helix chain 'X' and resid 26 through 34 Processing helix chain 'X' and resid 72 through 79 removed outlier: 5.002A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 192 Processing helix chain 'X' and resid 197 through 204 removed outlier: 4.899A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 244 Processing helix chain 'Y' and resid 63 through 69 removed outlier: 5.262A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 94 removed outlier: 5.444A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.226A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 3.684A pdb=" N ASN Y 191 " --> pdb=" O PRO Y 187 " (cutoff:3.500A) removed outlier: 5.479A 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: 5.666A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 238 removed outlier: 4.810A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.513A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA Z 48 " --> pdb=" O LYS Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 57 removed outlier: 4.901A pdb=" N GLY Z 57 " --> pdb=" O HIS Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 114 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 Processing helix chain '3' and resid 107 through 114 Processing helix chain '3' and resid 132 through 137 removed outlier: 5.722A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 138 through 146 removed outlier: 4.464A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 5.192A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 5.897A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 53 removed outlier: 4.574A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) Proline residue: 5 53 - end of helix Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 142 removed outlier: 3.824A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP 5 142 " --> pdb=" O SER 5 138 " (cutoff:3.500A) Processing helix chain '5' and resid 149 through 163 Processing helix chain '5' and resid 172 through 196 Proline residue: 5 178 - end of helix removed outlier: 5.951A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.118A 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: 4.621A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 329 Processing helix chain '5' and resid 408 through 420 Processing helix chain '6' and resid 44 through 49 removed outlier: 4.857A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 removed outlier: 5.111A 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 78 Processing helix chain '6' and resid 99 through 117 removed outlier: 5.399A pdb=" N VAL 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) Processing helix chain '6' and resid 118 through 126 Processing helix chain '6' and resid 131 through 143 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: 5.949A pdb=" N PHE 6 298 " --> pdb=" O ALA 6 294 " (cutoff:3.500A) Processing helix chain '6' and resid 299 through 308 Processing helix chain '6' and resid 324 through 333 Processing helix chain '6' and resid 362 through 371 removed outlier: 4.805A pdb=" N LEU 6 366 " --> pdb=" O PRO 6 362 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP 6 367 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 59 removed outlier: 4.203A pdb=" N THR 7 59 " --> pdb=" O GLN 7 55 " (cutoff:3.500A) 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 Processing helix chain '7' and resid 186 through 191 removed outlier: 3.674A pdb=" N ASP 7 190 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 5.439A 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 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: 4.550A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 5.354A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 91 through 97 removed outlier: 4.380A pdb=" N LEU 8 95 " --> pdb=" O PRO 8 91 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP 8 96 " --> pdb=" O LEU 8 92 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS 8 97 " --> pdb=" O LYS 8 93 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 91 through 97' Processing helix chain '8' and resid 107 through 154 Processing helix chain '8' and resid 156 through 164 removed outlier: 5.099A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 165 through 171 removed outlier: 4.782A 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 35 removed outlier: 6.034A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 removed outlier: 3.658A pdb=" N VAL 9 57 " --> pdb=" O ILE 9 53 " (cutoff:3.500A) Proline residue: 9 58 - end of helix No H-bonds generated for 'chain '9' and resid 53 through 58' Processing helix chain '9' and resid 87 through 95 Processing helix chain '9' and resid 96 through 106 Processing helix chain '9' and resid 113 through 118 removed outlier: 4.116A pdb=" N LYS 9 116 " --> pdb=" O ASN 9 113 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY 9 118 " --> pdb=" O GLU 9 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 119 through 125 removed outlier: 4.405A pdb=" N TRP a 123 " --> pdb=" O THR a 119 " (cutoff:3.500A) Proline residue: a 125 - end of helix Processing helix chain 'a' and resid 127 through 135 removed outlier: 5.874A pdb=" N ASN a 135 " --> pdb=" O ARG a 131 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 7 removed outlier: 4.356A pdb=" N THR b 6 " --> pdb=" O THR b 2 " (cutoff:3.500A) Proline residue: b 7 - end of helix No H-bonds generated for 'chain 'b' and resid 2 through 7' Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.684A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 37 through 50 removed outlier: 4.981A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 59 Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 107 Processing helix chain 'c' and resid 34 through 54 removed outlier: 5.111A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) Proline residue: c 54 - end of helix 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 removed outlier: 4.666A pdb=" N GLN c 107 " --> pdb=" O ALA c 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 145 Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 163 through 174 Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 225 removed outlier: 5.027A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLY c 225 " --> pdb=" O THR c 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 4.649A pdb=" N LYS c 233 " --> pdb=" O PHE c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 52 through 64 Processing helix chain 'd' and resid 118 through 130 removed outlier: 4.777A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 155 Proline residue: d 138 - end of helix Processing helix chain 'd' and resid 156 through 164 Processing helix chain 'd' and resid 165 through 174 Proline residue: d 170 - end of helix Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 85 through 104 removed outlier: 5.232A pdb=" N GLU e 94 " --> pdb=" O ARG e 90 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 132 removed outlier: 5.001A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 137 through 143 removed outlier: 5.436A pdb=" N ASP e 141 " --> pdb=" O ILE e 137 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 195 Processing helix chain 'e' and resid 257 through 265 removed outlier: 4.499A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYS e 265 " --> pdb=" O GLY e 261 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 4.911A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ARG e 273 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 4.576A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 118 Processing helix chain 'f' and resid 163 through 178 Processing helix chain 'g' and resid 45 through 53 removed outlier: 4.152A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) Proline residue: g 53 - end of helix Processing helix chain 'g' and resid 116 through 132 Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 Processing helix chain 'h' and resid 65 through 78 Processing helix chain 'h' and resid 93 through 108 Processing helix chain 'h' and resid 113 through 121 removed outlier: 4.276A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 133 Proline residue: h 133 - end of helix Processing helix chain 'h' and resid 138 through 146 removed outlier: 4.377A pdb=" N SER h 146 " --> pdb=" O GLU h 142 " (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 75 removed outlier: 6.552A pdb=" N ARG i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) 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 Processing helix chain 'j' and resid 60 through 108 removed outlier: 4.995A pdb=" N ALA j 108 " --> pdb=" O LYS j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 41 through 46 removed outlier: 4.733A pdb=" N LEU j 46 " --> pdb=" O GLY j 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 41 through 46' Processing helix chain 'k' and resid 27 through 37 Processing helix chain 'k' and resid 39 through 47 Processing helix chain 'k' and resid 82 through 96 Processing helix chain 'l' and resid 114 through 136 removed outlier: 3.856A pdb=" N ASN l 135 " --> pdb=" O ARG l 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 51 removed outlier: 4.357A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 63 through 81 removed outlier: 4.751A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 97 removed outlier: 4.706A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 50 Proline residue: p 50 - end of helix Processing helix chain 'p' and resid 54 through 60 Processing helix chain 'p' and resid 72 through 77 removed outlier: 4.991A pdb=" N THR p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) Processing helix chain 'p' and resid 112 through 123 Processing helix chain 'p' and resid 142 through 163 Processing helix chain 'p' and resid 174 through 190 Processing helix chain 'q' and resid 48 through 53 removed outlier: 4.128A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 54 through 65 Processing helix chain 'q' and resid 71 through 76 removed outlier: 3.803A pdb=" N TRP q 76 " --> pdb=" O PRO q 72 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 93 Processing helix chain 'q' and resid 95 through 156 Proline residue: q 129 - end of helix Processing helix chain 'q' and resid 167 through 188 removed outlier: 3.704A pdb=" N SER q 172 " --> pdb=" O VAL q 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 76 Processing helix chain 'r' and resid 85 through 93 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: 4.079A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.265A 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 74 removed outlier: 5.642A pdb=" N GLU s 74 " --> pdb=" O VAL s 70 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 Processing helix chain 's' and resid 140 through 155 Processing helix chain 's' and resid 164 through 169 removed outlier: 4.871A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (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 267 through 272 Proline residue: s 272 - end of helix Processing helix chain 's' and resid 307 through 315 removed outlier: 4.875A pdb=" N GLN s 314 " --> pdb=" O ARG s 310 " (cutoff:3.500A) Processing helix chain 's' and resid 316 through 344 Processing helix chain 's' and resid 380 through 385 Processing helix chain 's' and resid 414 through 427 removed outlier: 5.176A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 105 Processing helix chain 'u' and resid 131 through 150 Processing helix chain 'u' and resid 181 through 189 Processing helix chain 'u' and resid 190 through 196 Processing helix chain 'v' and resid 5 through 23 Processing helix chain 'v' and resid 27 through 43 removed outlier: 4.998A pdb=" N LYS v 41 " --> pdb=" O ARG v 37 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASN v 42 " --> pdb=" O GLU v 38 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLN v 43 " --> pdb=" O PHE v 39 " (cutoff:3.500A) Processing helix chain 'v' and resid 47 through 64 Processing helix chain 'w' and resid 75 through 91 removed outlier: 5.894A pdb=" N ASP w 91 " --> pdb=" O LEU w 87 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 5.397A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 4.330A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N MET w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 152 Processing helix chain 'w' and resid 103 through 108 Processing sheet with id= 1, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.596A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 179 through 182 removed outlier: 5.027A pdb=" N ASP D 180 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 214 through 217 removed outlier: 6.802A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU D 237 " --> pdb=" O TYR D 295 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 138 through 144 removed outlier: 5.265A pdb=" N ASP D 138 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 98 through 101 Processing sheet with id= 6, first strand: chain 'E' and resid 105 through 110 removed outlier: 4.005A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS E 117 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 131 through 134 removed outlier: 6.415A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 265 through 269 Processing sheet with id= 9, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= 10, first strand: chain 'F' and resid 46 through 51 removed outlier: 7.787A pdb=" N HIS F 83 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 12, first strand: chain 'H' and resid 94 through 97 Processing sheet with id= 13, first strand: chain 'I' and resid 96 through 100 Processing sheet with id= 14, first strand: chain 'J' and resid 18 through 24 Processing sheet with id= 15, first strand: chain 'K' and resid 55 through 60 removed outlier: 5.257A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'K' and resid 77 through 81 Processing sheet with id= 17, first strand: chain 'L' and resid 38 through 41 removed outlier: 6.163A pdb=" N LEU L 107 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLN L 72 " --> pdb=" O TYR L 61 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS L 59 " --> pdb=" O LEU L 74 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'M' and resid 273 through 276 Processing sheet with id= 19, first strand: chain 'N' and resid 119 through 123 removed outlier: 6.272A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'N' and resid 129 through 132 Processing sheet with id= 21, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.756A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'P' and resid 79 through 85 removed outlier: 6.319A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Q' and resid 129 through 135 removed outlier: 4.291A pdb=" N LYS Q 129 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Q' and resid 139 through 142 removed outlier: 7.439A pdb=" N ALA Q 147 " --> pdb=" O LEU Q 166 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'S' and resid 105 through 109 Processing sheet with id= 26, first strand: chain 'S' and resid 112 through 117 removed outlier: 6.402A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'S' and resid 162 through 165 Processing sheet with id= 28, first strand: chain 'S' and resid 168 through 175 Processing sheet with id= 29, first strand: chain 'T' and resid 71 through 78 removed outlier: 5.258A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN T 139 " --> pdb=" O GLY T 181 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 144 through 150 removed outlier: 3.587A pdb=" N GLU T 144 " --> pdb=" O LYS T 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE T 175 " --> pdb=" O THR T 146 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR T 171 " --> pdb=" O GLY T 150 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'T' and resid 152 through 156 Processing sheet with id= 32, first strand: chain 'U' and resid 26 through 29 removed outlier: 7.332A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'V' and resid 60 through 63 Processing sheet with id= 34, first strand: chain 'V' and resid 78 through 81 Processing sheet with id= 35, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.642A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'W' and resid 80 through 84 removed outlier: 7.959A pdb=" N HIS W 80 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 96 through 102 Processing sheet with id= 38, first strand: chain 'X' and resid 49 through 52 removed outlier: 5.315A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'X' and resid 85 through 91 Processing sheet with id= 40, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 41, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.107A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '0' and resid 107 through 111 Processing sheet with id= 43, first strand: chain '0' and resid 155 through 161 removed outlier: 4.377A pdb=" N THR 0 161 " --> pdb=" O ARG 0 177 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '1' and resid 28 through 33 removed outlier: 5.576A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 59 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '1' and resid 15 through 18 removed outlier: 4.482A pdb=" N ASN 1 15 " --> pdb=" O LEU 1 65 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '3' and resid 122 through 125 removed outlier: 5.079A pdb=" N TRP 3 122 " --> pdb=" O CYS 3 150 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '4' and resid 79 through 84 removed outlier: 6.816A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '5' and resid 126 through 130 removed outlier: 4.939A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '5' and resid 201 through 205 removed outlier: 6.874A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '5' and resid 208 through 214 removed outlier: 5.344A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '6' and resid 183 through 187 Processing sheet with id= 52, first strand: chain '6' and resid 235 through 238 removed outlier: 8.303A pdb=" N THR 6 310 " --> pdb=" O ASP 6 276 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain '6' and resid 265 through 272 No H-bonds generated for sheet with id= 53 Processing sheet with id= 54, first strand: chain '7' and resid 75 through 82 removed outlier: 6.750A pdb=" N GLY 7 71 " --> pdb=" O PRO 7 75 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS 7 123 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS 7 126 " --> pdb=" O LEU 7 107 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain '7' and resid 164 through 167 removed outlier: 6.983A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN 7 298 " --> pdb=" O SER 7 281 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain '7' and resid 217 through 221 Processing sheet with id= 57, first strand: chain '9' and resid 42 through 45 Processing sheet with id= 58, first strand: chain 'a' and resid 47 through 52 removed outlier: 6.055A 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 67 removed outlier: 4.666A 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 258 removed outlier: 6.897A pdb=" N PHE c 271 " --> pdb=" O THR c 258 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'd' and resid 212 through 219 Processing sheet with id= 62, first strand: chain 'e' and resid 174 through 178 removed outlier: 5.122A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'e' and resid 211 through 216 removed outlier: 3.981A pdb=" N PHE e 215 " --> pdb=" O ALA e 229 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA e 229 " --> pdb=" O PHE e 215 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'f' and resid 123 through 130 removed outlier: 4.117A pdb=" N THR f 129 " --> pdb=" O THR f 152 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N THR f 152 " --> pdb=" O THR f 129 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR f 96 " --> pdb=" O ARG f 183 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.557A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'k' and resid 49 through 56 Processing sheet with id= 67, first strand: chain 'm' and resid 63 through 67 removed outlier: 3.627A pdb=" N MET m 77 " --> pdb=" O VAL m 57 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'p' and resid 78 through 82 Processing sheet with id= 69, first strand: chain 'r' and resid 35 through 41 Processing sheet with id= 70, first strand: chain 's' and resid 112 through 116 Processing sheet with id= 71, first strand: chain 's' and resid 198 through 202 removed outlier: 6.671A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 's' and resid 206 through 216 removed outlier: 7.540A pdb=" N MET s 89 " --> pdb=" O ASP s 228 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG s 230 " --> pdb=" O MET s 89 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE s 274 " --> pdb=" O MET s 92 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 's' and resid 297 through 302 removed outlier: 5.498A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'u' and resid 107 through 114 removed outlier: 5.210A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) 2795 hydrogen bonds defined for protein. 8226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1031 hydrogen bonds 1758 hydrogen bond angles 0 basepair planarities 423 basepair parallelities 837 stacking parallelities Total time for adding SS restraints: 56.00 Time building geometry restraints manager: 39.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 12747 1.30 - 1.43: 38473 1.43 - 1.56: 51926 1.56 - 1.70: 3155 1.70 - 1.83: 452 Bond restraints: 106753 Sorted by residual: bond pdb=" C ILE X 52 " pdb=" N ASN X 53 " ideal model delta sigma weight residual 1.329 1.221 0.107 1.35e-02 5.49e+03 6.32e+01 bond pdb=" CA TYR 6 155 " pdb=" C TYR 6 155 " ideal model delta sigma weight residual 1.522 1.416 0.106 1.39e-02 5.18e+03 5.86e+01 bond pdb=" CA ARG U 43 " pdb=" CB ARG U 43 " ideal model delta sigma weight residual 1.531 1.431 0.099 1.52e-02 4.33e+03 4.28e+01 bond pdb=" CA ARG H 75 " pdb=" C ARG H 75 " ideal model delta sigma weight residual 1.522 1.442 0.081 1.38e-02 5.25e+03 3.42e+01 bond pdb=" C LEU 9 70 " pdb=" N LYS 9 71 " ideal model delta sigma weight residual 1.325 1.255 0.070 1.25e-02 6.40e+03 3.10e+01 ... (remaining 106748 not shown) Histogram of bond angle deviations from ideal: 86.72 - 97.52: 16 97.52 - 108.31: 21738 108.31 - 119.10: 76993 119.10 - 129.90: 51614 129.90 - 140.69: 1599 Bond angle restraints: 151960 Sorted by residual: angle pdb=" CG ARG F 76 " pdb=" CD ARG F 76 " pdb=" NE ARG F 76 " ideal model delta sigma weight residual 112.00 96.13 15.87 2.20e+00 2.07e-01 5.21e+01 angle pdb=" N GLY H 66 " pdb=" CA GLY H 66 " pdb=" C GLY H 66 " ideal model delta sigma weight residual 110.38 119.43 -9.05 1.28e+00 6.10e-01 5.00e+01 angle pdb=" N VAL i 98 " pdb=" CA VAL i 98 " pdb=" C VAL i 98 " ideal model delta sigma weight residual 112.17 105.54 6.63 9.50e-01 1.11e+00 4.88e+01 angle pdb=" CA PRO 5 85 " pdb=" N PRO 5 85 " pdb=" CD PRO 5 85 " ideal model delta sigma weight residual 112.00 102.36 9.64 1.40e+00 5.10e-01 4.74e+01 angle pdb=" N GLU H 142 " pdb=" CA GLU H 142 " pdb=" CB GLU H 142 " ideal model delta sigma weight residual 110.30 120.81 -10.51 1.54e+00 4.22e-01 4.66e+01 ... (remaining 151955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 61349 35.88 - 71.76: 4027 71.76 - 107.64: 509 107.64 - 143.52: 29 143.52 - 179.40: 44 Dihedral angle restraints: 65958 sinusoidal: 42022 harmonic: 23936 Sorted by residual: dihedral pdb=" C5' U A1074 " pdb=" C4' U A1074 " pdb=" C3' U A1074 " pdb=" O3' U A1074 " ideal model delta sinusoidal sigma weight residual 147.00 74.07 72.93 1 8.00e+00 1.56e-02 1.06e+02 dihedral pdb=" C4' U A1074 " pdb=" C3' U A1074 " pdb=" C2' U A1074 " pdb=" C1' U A1074 " ideal model delta sinusoidal sigma weight residual -35.00 35.17 -70.17 1 8.00e+00 1.56e-02 9.91e+01 dihedral pdb=" CA GLU 6 49 " pdb=" C GLU 6 49 " pdb=" N LYS 6 50 " pdb=" CA LYS 6 50 " ideal model delta harmonic sigma weight residual -180.00 -132.92 -47.08 0 5.00e+00 4.00e-02 8.87e+01 ... (remaining 65955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 16363 0.116 - 0.232: 1438 0.232 - 0.348: 97 0.348 - 0.465: 12 0.465 - 0.581: 3 Chirality restraints: 17913 Sorted by residual: chirality pdb=" CB VAL E 218 " pdb=" CA VAL E 218 " pdb=" CG1 VAL E 218 " pdb=" CG2 VAL E 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CB ILE O 123 " pdb=" CA ILE O 123 " pdb=" CG1 ILE O 123 " pdb=" CG2 ILE O 123 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CB VAL i 98 " pdb=" CA VAL i 98 " pdb=" CG1 VAL i 98 " pdb=" CG2 VAL i 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 17910 not shown) Planarity restraints: 13567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 265 " 0.067 2.00e-02 2.50e+03 6.39e-02 1.02e+02 pdb=" CG TRP D 265 " -0.165 2.00e-02 2.50e+03 pdb=" CD1 TRP D 265 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TRP D 265 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP D 265 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 265 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP D 265 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 265 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 265 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP D 265 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 74 " 0.051 2.00e-02 2.50e+03 4.96e-02 6.15e+01 pdb=" CG TRP Y 74 " -0.131 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 74 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 74 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 74 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 74 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 74 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 74 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 74 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 74 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 150 " -0.059 2.00e-02 2.50e+03 4.27e-02 4.56e+01 pdb=" CG TRP U 150 " 0.112 2.00e-02 2.50e+03 pdb=" CD1 TRP U 150 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP U 150 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP U 150 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP U 150 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP U 150 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 150 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 150 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP U 150 " -0.017 2.00e-02 2.50e+03 ... (remaining 13564 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 23 2.20 - 2.87: 36025 2.87 - 3.55: 144481 3.55 - 4.22: 270282 4.22 - 4.90: 413362 Nonbonded interactions: 864173 Sorted by model distance: nonbonded pdb=" OG SER w 112 " pdb=" O23 PNS v 101 " model vdw 1.521 2.440 nonbonded pdb=" OG SER w 112 " pdb=" P24 PNS v 101 " model vdw 1.555 3.400 nonbonded pdb=" O4 U A 360 " pdb=" C6 A A 454 " model vdw 1.840 3.260 nonbonded pdb=" CB SER w 112 " pdb=" P24 PNS v 101 " model vdw 1.919 3.800 nonbonded pdb=" O4 U A 360 " pdb=" N6 A A 454 " model vdw 1.987 2.520 ... (remaining 864168 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: 3.410 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: 0.060 Extract box with map and model: 13.140 Check model and map are aligned: 1.120 Set scattering table: 0.710 Process input model: 282.330 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.330 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 306.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.176 106753 Z= 0.847 Angle : 1.335 17.673 151960 Z= 0.690 Chirality : 0.068 0.581 17913 Planarity : 0.008 0.143 13567 Dihedral : 20.889 179.401 50452 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.81 % Favored : 93.16 % Rotamer: Outliers : 0.07 % Allowed : 0.90 % Favored : 99.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.08), residues: 8059 helix: -1.12 (0.09), residues: 2905 sheet: -1.43 (0.15), residues: 1031 loop : -1.71 (0.09), residues: 4123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.165 0.004 TRP D 265 HIS 0.020 0.003 HIS s 300 PHE 0.057 0.004 PHE I 90 TYR 0.075 0.004 TYR r 150 ARG 0.043 0.002 ARG L 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1408 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1403 time to evaluate : 6.625 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: D 104 TYR cc_start: 0.8735 (t80) cc_final: 0.8445 (t80) REVERT: E 90 TRP cc_start: 0.8555 (t60) cc_final: 0.8292 (t60) REVERT: H 128 LEU cc_start: 0.7235 (mm) cc_final: 0.7009 (mm) REVERT: I 48 MET cc_start: 0.8343 (mmm) cc_final: 0.8120 (mtp) REVERT: K 131 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6959 (mm-30) REVERT: P 132 LEU cc_start: 0.8431 (tt) cc_final: 0.8104 (tt) REVERT: P 158 MET cc_start: 0.7249 (mmp) cc_final: 0.6885 (mmt) REVERT: P 178 ILE cc_start: 0.9309 (mm) cc_final: 0.8788 (mt) REVERT: Q 123 ASP cc_start: 0.6452 (t0) cc_final: 0.6183 (t0) REVERT: R 21 ILE cc_start: 0.7423 (mm) cc_final: 0.7176 (mt) REVERT: R 89 ASN cc_start: 0.8548 (m-40) cc_final: 0.8248 (m110) REVERT: R 123 ARG cc_start: 0.8322 (tpt90) cc_final: 0.7894 (tpt90) REVERT: S 108 VAL cc_start: 0.8186 (t) cc_final: 0.7938 (m) REVERT: S 131 GLU cc_start: 0.8573 (pp20) cc_final: 0.8300 (pp20) REVERT: W 117 ILE cc_start: 0.8989 (mm) cc_final: 0.8771 (mm) REVERT: X 191 TYR cc_start: 0.8175 (m-80) cc_final: 0.7457 (m-80) REVERT: Y 86 THR cc_start: 0.7523 (p) cc_final: 0.6113 (p) REVERT: Y 115 LEU cc_start: 0.8845 (tp) cc_final: 0.8524 (tp) REVERT: 3 130 LYS cc_start: 0.7258 (pttt) cc_final: 0.6285 (ttpt) REVERT: 6 355 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7551 (mttp) REVERT: 7 193 MET cc_start: 0.6641 (tpt) cc_final: 0.6382 (tpt) REVERT: 9 134 ASN cc_start: 0.8115 (m110) cc_final: 0.7765 (m-40) REVERT: a 122 ARG cc_start: 0.8601 (tpt90) cc_final: 0.8395 (tpt-90) REVERT: d 165 THR cc_start: 0.6206 (p) cc_final: 0.5908 (p) REVERT: d 169 PHE cc_start: 0.7775 (t80) cc_final: 0.7543 (t80) REVERT: d 241 ASP cc_start: 0.5876 (t0) cc_final: 0.5525 (t0) REVERT: e 200 MET cc_start: 0.0136 (mtm) cc_final: -0.0528 (mpp) REVERT: h 99 ASN cc_start: 0.7523 (m110) cc_final: 0.6914 (m-40) REVERT: p 111 ILE cc_start: 0.7609 (mm) cc_final: 0.7328 (mm) REVERT: r 170 ASN cc_start: 0.8024 (t0) cc_final: 0.7334 (t0) REVERT: s 66 TRP cc_start: 0.7925 (t60) cc_final: 0.7672 (t60) REVERT: s 154 HIS cc_start: 0.8002 (m-70) cc_final: 0.7734 (m90) REVERT: s 294 TYR cc_start: 0.7505 (m-10) cc_final: 0.7196 (m-10) REVERT: s 321 GLU cc_start: 0.6789 (pm20) cc_final: 0.6498 (pm20) outliers start: 5 outliers final: 1 residues processed: 1407 average time/residue: 0.9378 time to fit residues: 2242.5237 Evaluate side-chains 1179 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1178 time to evaluate : 6.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 118 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 955 random chunks: chunk 806 optimal weight: 0.6980 chunk 723 optimal weight: 30.0000 chunk 401 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 chunk 488 optimal weight: 4.9990 chunk 386 optimal weight: 0.9980 chunk 748 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 455 optimal weight: 0.9990 chunk 557 optimal weight: 3.9990 chunk 867 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 237 HIS E 339 GLN F 74 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 GLN K 9 GLN M 30 ASN ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN N 208 ASN P 50 ASN P 97 GLN ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN S 84 ASN S 105 GLN S 179 ASN T 55 ASN T 75 HIS T 151 GLN X 172 GLN X 177 HIS ** Y 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 100 GLN 5 165 GLN 5 186 GLN 5 324 GLN 6 174 HIS ** 6 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 284 HIS 8 144 GLN a 46 ASN b 66 ASN b 129 GLN c 310 ASN d 217 HIS ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 46 GLN h 103 HIS ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 96 HIS ** r 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 154 HIS s 246 GLN s 298 GLN u 148 HIS ** w 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 106753 Z= 0.195 Angle : 0.710 15.268 151960 Z= 0.361 Chirality : 0.042 0.367 17913 Planarity : 0.006 0.071 13567 Dihedral : 22.156 179.717 33080 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.44 % Favored : 95.55 % Rotamer: Outliers : 1.05 % Allowed : 9.88 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.09), residues: 8059 helix: -0.20 (0.09), residues: 2951 sheet: -1.23 (0.15), residues: 1047 loop : -1.35 (0.09), residues: 4061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP D 265 HIS 0.011 0.001 HIS u 148 PHE 0.026 0.002 PHE I 90 TYR 0.042 0.002 TYR 6 51 ARG 0.018 0.001 ARG P 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1443 time to evaluate : 6.535 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: D 104 TYR cc_start: 0.8618 (t80) cc_final: 0.8159 (t80) REVERT: D 285 LYS cc_start: 0.7198 (pttm) cc_final: 0.6941 (pttp) REVERT: D 292 MET cc_start: 0.7236 (tmm) cc_final: 0.7022 (ttm) REVERT: F 143 SER cc_start: 0.8971 (t) cc_final: 0.8542 (p) REVERT: K 55 ASP cc_start: 0.8033 (m-30) cc_final: 0.7792 (m-30) REVERT: K 121 MET cc_start: 0.8891 (mtt) cc_final: 0.8438 (mtt) REVERT: L 101 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: O 58 LYS cc_start: 0.8334 (ttmt) cc_final: 0.8027 (ttmt) REVERT: P 178 ILE cc_start: 0.9079 (mm) cc_final: 0.8522 (mt) REVERT: Q 120 THR cc_start: 0.8224 (t) cc_final: 0.7946 (m) REVERT: R 21 ILE cc_start: 0.7180 (mm) cc_final: 0.6931 (mt) REVERT: R 89 ASN cc_start: 0.8372 (m-40) cc_final: 0.8148 (m110) REVERT: R 94 GLN cc_start: 0.8371 (tt0) cc_final: 0.8101 (tt0) REVERT: T 133 ASN cc_start: 0.8284 (t0) cc_final: 0.7998 (t0) REVERT: T 151 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8443 (mt0) REVERT: U 61 TYR cc_start: 0.8129 (m-80) cc_final: 0.7920 (m-10) REVERT: W 69 THR cc_start: 0.9291 (p) cc_final: 0.8965 (m) REVERT: X 151 GLU cc_start: 0.7907 (pm20) cc_final: 0.7691 (pm20) REVERT: X 191 TYR cc_start: 0.8050 (m-80) cc_final: 0.7641 (m-80) REVERT: Z 140 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7297 (mmtm) REVERT: 3 130 LYS cc_start: 0.6978 (pttt) cc_final: 0.6263 (ttpt) REVERT: 5 114 LEU cc_start: 0.7150 (tt) cc_final: 0.6823 (tt) REVERT: 5 418 TYR cc_start: 0.8337 (t80) cc_final: 0.7980 (t80) REVERT: 6 355 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7490 (mttp) REVERT: 9 134 ASN cc_start: 0.7890 (m110) cc_final: 0.7644 (m-40) REVERT: a 108 MET cc_start: 0.8120 (tpt) cc_final: 0.7886 (tpt) REVERT: a 110 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6993 (mt-10) REVERT: a 122 ARG cc_start: 0.8394 (tpt90) cc_final: 0.8176 (tpt-90) REVERT: c 47 ARG cc_start: 0.6296 (ttp80) cc_final: 0.6061 (ttp-110) REVERT: c 59 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7898 (ptp-170) REVERT: c 275 TYR cc_start: 0.7919 (m-80) cc_final: 0.7415 (m-80) REVERT: d 169 PHE cc_start: 0.7718 (t80) cc_final: 0.7507 (t80) REVERT: d 241 ASP cc_start: 0.6094 (t0) cc_final: 0.5613 (t0) REVERT: h 151 ASN cc_start: 0.8765 (p0) cc_final: 0.8404 (p0) REVERT: h 154 ILE cc_start: 0.8615 (mm) cc_final: 0.8411 (mm) REVERT: p 111 ILE cc_start: 0.7592 (mm) cc_final: 0.7358 (mm) REVERT: r 121 MET cc_start: 0.8097 (mtp) cc_final: 0.7891 (mtp) REVERT: r 170 ASN cc_start: 0.8042 (t0) cc_final: 0.7271 (t0) REVERT: v 26 THR cc_start: 0.8679 (m) cc_final: 0.8453 (t) outliers start: 76 outliers final: 45 residues processed: 1468 average time/residue: 0.9387 time to fit residues: 2351.4219 Evaluate side-chains 1294 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1247 time to evaluate : 8.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 163 CYS Chi-restraints excluded: chain S residue 75 HIS Chi-restraints excluded: chain S residue 118 ASN Chi-restraints excluded: chain T residue 151 GLN Chi-restraints excluded: chain T residue 205 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 5 residue 169 GLU Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 138 VAL Chi-restraints excluded: chain 7 residue 154 ILE Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain k residue 19 GLN Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain r residue 158 SER Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 321 GLU Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 170 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 955 random chunks: chunk 481 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 721 optimal weight: 40.0000 chunk 590 optimal weight: 0.0970 chunk 239 optimal weight: 10.0000 chunk 868 optimal weight: 10.0000 chunk 938 optimal weight: 20.0000 chunk 773 optimal weight: 3.9990 chunk 861 optimal weight: 10.0000 chunk 296 optimal weight: 0.2980 chunk 696 optimal weight: 0.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 ASN E 339 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN K 9 GLN K 56 HIS L 48 ASN L 80 GLN M 102 GLN ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN P 50 ASN ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN S 84 ASN T 55 ASN T 133 ASN W 80 HIS X 177 HIS ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 96 ASN 1 45 HIS ** 5 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 165 GLN ** 6 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS 6 277 GLN 7 255 HIS 7 285 ASN a 46 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 107 GLN b 129 GLN c 168 HIS ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 ASN ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 152 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 423 HIS u 148 HIS ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 106753 Z= 0.191 Angle : 0.659 13.409 151960 Z= 0.335 Chirality : 0.041 0.413 17913 Planarity : 0.005 0.067 13567 Dihedral : 21.925 178.359 33080 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.80 % Favored : 95.19 % Rotamer: Outliers : 2.20 % Allowed : 13.28 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.09), residues: 8059 helix: 0.27 (0.09), residues: 2936 sheet: -1.16 (0.15), residues: 1084 loop : -1.18 (0.10), residues: 4039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP D 265 HIS 0.013 0.001 HIS X 177 PHE 0.056 0.002 PHE v 32 TYR 0.044 0.002 TYR 6 51 ARG 0.013 0.000 ARG L 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1510 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1351 time to evaluate : 6.584 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: D 104 TYR cc_start: 0.8631 (t80) cc_final: 0.8071 (t80) REVERT: D 208 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.6728 (mtm-85) REVERT: D 231 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7750 (mttt) REVERT: D 292 MET cc_start: 0.7322 (tmm) cc_final: 0.7073 (ttm) REVERT: E 279 LYS cc_start: 0.7892 (ptmt) cc_final: 0.7539 (ttpt) REVERT: F 143 SER cc_start: 0.8940 (t) cc_final: 0.8489 (p) REVERT: I 37 ARG cc_start: 0.7537 (ttm110) cc_final: 0.6477 (ttt180) REVERT: I 45 GLN cc_start: 0.7993 (tt0) cc_final: 0.7737 (mt0) REVERT: K 55 ASP cc_start: 0.7974 (m-30) cc_final: 0.7615 (m-30) REVERT: K 121 MET cc_start: 0.8861 (mtt) cc_final: 0.8368 (mtt) REVERT: M 88 SER cc_start: 0.8837 (p) cc_final: 0.8566 (m) REVERT: O 58 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8157 (ttmt) REVERT: P 158 MET cc_start: 0.6991 (mmp) cc_final: 0.6612 (mmt) REVERT: P 178 ILE cc_start: 0.9003 (mm) cc_final: 0.8424 (mt) REVERT: Q 120 THR cc_start: 0.8189 (t) cc_final: 0.7956 (m) REVERT: R 21 ILE cc_start: 0.7324 (mm) cc_final: 0.7031 (mt) REVERT: S 119 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6074 (mt-10) REVERT: T 133 ASN cc_start: 0.8644 (t0) cc_final: 0.8186 (t0) REVERT: U 61 TYR cc_start: 0.8092 (m-80) cc_final: 0.7885 (m-10) REVERT: W 69 THR cc_start: 0.9289 (p) cc_final: 0.8977 (m) REVERT: X 191 TYR cc_start: 0.7941 (m-80) cc_final: 0.7666 (m-80) REVERT: Y 233 ILE cc_start: 0.8083 (tt) cc_final: 0.7880 (tt) REVERT: 3 130 LYS cc_start: 0.7004 (pttt) cc_final: 0.6282 (ttpt) REVERT: 5 106 ILE cc_start: 0.7422 (mm) cc_final: 0.7075 (mt) REVERT: 6 355 LYS cc_start: 0.7727 (mtmt) cc_final: 0.7414 (mttp) REVERT: 6 374 GLU cc_start: 0.7745 (pm20) cc_final: 0.7530 (pm20) REVERT: 7 143 TRP cc_start: 0.8896 (OUTLIER) cc_final: 0.7731 (m-90) REVERT: 9 134 ASN cc_start: 0.7939 (m110) cc_final: 0.7667 (m-40) REVERT: a 110 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7008 (mt-10) REVERT: c 81 GLU cc_start: 0.7034 (pm20) cc_final: 0.6832 (pm20) REVERT: g 118 TRP cc_start: 0.8015 (m100) cc_final: 0.7753 (m100) REVERT: h 73 TYR cc_start: 0.6587 (m-80) cc_final: 0.6338 (t80) REVERT: h 103 HIS cc_start: 0.6248 (m90) cc_final: 0.5862 (m90) REVERT: h 142 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6253 (pp20) REVERT: h 154 ILE cc_start: 0.8582 (mm) cc_final: 0.8373 (mm) REVERT: j 29 LEU cc_start: 0.7948 (mt) cc_final: 0.7681 (mt) REVERT: p 113 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7623 (mm-30) REVERT: r 170 ASN cc_start: 0.8015 (t0) cc_final: 0.7134 (t0) REVERT: r 182 ARG cc_start: 0.7581 (ttm170) cc_final: 0.6720 (tpp-160) REVERT: s 149 CYS cc_start: 0.7859 (t) cc_final: 0.7629 (t) REVERT: s 179 GLN cc_start: 0.7064 (pt0) cc_final: 0.6813 (pt0) REVERT: v 26 THR cc_start: 0.8728 (m) cc_final: 0.8505 (t) outliers start: 159 outliers final: 94 residues processed: 1421 average time/residue: 0.9325 time to fit residues: 2263.9949 Evaluate side-chains 1347 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1250 time to evaluate : 6.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 163 CYS Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 75 HIS Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 74 TRP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 49 VAL Chi-restraints excluded: chain 5 residue 137 LEU Chi-restraints excluded: chain 5 residue 169 GLU Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 6 residue 141 ARG Chi-restraints excluded: chain 7 residue 42 GLU Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 138 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 285 ASN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 142 GLU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 86 MET Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 139 GLN Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 158 SER Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain r residue 192 TRP Chi-restraints excluded: chain s residue 321 GLU Chi-restraints excluded: chain s residue 322 VAL Chi-restraints excluded: chain s residue 332 LEU Chi-restraints excluded: chain s residue 418 LEU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 955 random chunks: chunk 858 optimal weight: 7.9990 chunk 653 optimal weight: 0.3980 chunk 450 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 chunk 414 optimal weight: 3.9990 chunk 583 optimal weight: 40.0000 chunk 871 optimal weight: 5.9990 chunk 923 optimal weight: 20.0000 chunk 455 optimal weight: 10.0000 chunk 826 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 ASN E 339 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN L 43 ASN L 80 GLN ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN N 202 GLN O 39 HIS P 115 HIS ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN S 118 ASN T 55 ASN T 151 GLN U 23 ASN V 94 HIS ** W 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 177 HIS ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 96 ASN 1 45 HIS 4 68 ASN 4 100 GLN 5 109 HIS ** 5 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 255 HIS 7 285 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN c 310 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 123 HIS ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 176 GLN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 113 GLN u 148 HIS ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 106753 Z= 0.373 Angle : 0.740 14.514 151960 Z= 0.372 Chirality : 0.045 0.395 17913 Planarity : 0.006 0.073 13567 Dihedral : 21.881 179.959 33078 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.58 % Favored : 94.40 % Rotamer: Outliers : 2.94 % Allowed : 14.99 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.09), residues: 8059 helix: 0.32 (0.09), residues: 2960 sheet: -1.14 (0.15), residues: 1084 loop : -1.19 (0.10), residues: 4015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 265 HIS 0.010 0.001 HIS o 46 PHE 0.041 0.002 PHE E 224 TYR 0.031 0.002 TYR 6 51 ARG 0.014 0.001 ARG K 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1259 time to evaluate : 6.600 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: D 104 TYR cc_start: 0.8650 (t80) cc_final: 0.8220 (t80) REVERT: E 275 ARG cc_start: 0.8206 (ttt180) cc_final: 0.7764 (ttt180) REVERT: E 279 LYS cc_start: 0.8100 (ptmt) cc_final: 0.7813 (ttpt) REVERT: K 25 MET cc_start: 0.9029 (mmm) cc_final: 0.8747 (mmt) REVERT: M 143 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8373 (tp30) REVERT: O 58 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8213 (ttmt) REVERT: P 158 MET cc_start: 0.6798 (mmp) cc_final: 0.6552 (mmm) REVERT: P 178 ILE cc_start: 0.8953 (mm) cc_final: 0.8395 (mt) REVERT: Q 120 THR cc_start: 0.8226 (t) cc_final: 0.7983 (m) REVERT: R 21 ILE cc_start: 0.7370 (mm) cc_final: 0.7108 (mt) REVERT: T 85 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: T 133 ASN cc_start: 0.8752 (t0) cc_final: 0.8314 (t0) REVERT: W 69 THR cc_start: 0.9372 (p) cc_final: 0.9016 (m) REVERT: X 142 ASP cc_start: 0.7020 (t0) cc_final: 0.6776 (t0) REVERT: Y 100 LYS cc_start: 0.8355 (ptpp) cc_final: 0.7955 (ptpp) REVERT: 3 130 LYS cc_start: 0.7262 (pttt) cc_final: 0.6466 (ttpt) REVERT: 5 106 ILE cc_start: 0.7368 (mm) cc_final: 0.7038 (mt) REVERT: 6 155 TYR cc_start: 0.8114 (m-80) cc_final: 0.7784 (m-80) REVERT: 6 355 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7388 (mttp) REVERT: 7 143 TRP cc_start: 0.8953 (OUTLIER) cc_final: 0.7900 (m-90) REVERT: a 108 MET cc_start: 0.8203 (tpt) cc_final: 0.7923 (tpt) REVERT: g 43 ASP cc_start: 0.6582 (p0) cc_final: 0.6367 (p0) REVERT: g 44 GLU cc_start: 0.6575 (mm-30) cc_final: 0.6232 (mm-30) REVERT: h 103 HIS cc_start: 0.6303 (m90) cc_final: 0.5842 (m90) REVERT: j 29 LEU cc_start: 0.8183 (mt) cc_final: 0.7868 (mt) REVERT: p 113 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7625 (mm-30) REVERT: r 170 ASN cc_start: 0.8068 (t0) cc_final: 0.7199 (t0) REVERT: v 26 THR cc_start: 0.8764 (m) cc_final: 0.8514 (t) outliers start: 213 outliers final: 147 residues processed: 1366 average time/residue: 0.9324 time to fit residues: 2176.8580 Evaluate side-chains 1354 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1204 time to evaluate : 6.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 142 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 163 CYS Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 75 HIS Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 118 ASN Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain T residue 83 SER Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 205 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 74 TRP Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 2 residue 71 SER Chi-restraints excluded: chain 2 residue 89 SER Chi-restraints excluded: chain 4 residue 78 ASP Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 49 VAL Chi-restraints excluded: chain 5 residue 137 LEU Chi-restraints excluded: chain 5 residue 169 GLU Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 87 THR Chi-restraints excluded: chain 7 residue 138 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 158 PHE Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 285 ASN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 65 VAL Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 70 CYS Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 223 MET Chi-restraints excluded: chain c residue 291 VAL Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 79 SER Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 139 GLN Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 158 SER Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain r residue 192 TRP Chi-restraints excluded: chain s residue 92 MET Chi-restraints excluded: chain s residue 168 GLU Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 321 GLU Chi-restraints excluded: chain s residue 322 VAL Chi-restraints excluded: chain s residue 332 LEU Chi-restraints excluded: chain s residue 418 LEU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 159 ILE Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 175 MET Chi-restraints excluded: chain u residue 176 VAL Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 955 random chunks: chunk 768 optimal weight: 3.9990 chunk 524 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 687 optimal weight: 0.6980 chunk 380 optimal weight: 4.9990 chunk 787 optimal weight: 40.0000 chunk 638 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 471 optimal weight: 2.9990 chunk 828 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN L 43 ASN L 80 GLN M 53 HIS ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN T 55 ASN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN Y 160 GLN 4 100 GLN ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 63 GLN 6 174 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN 7 284 HIS 7 285 ASN 9 134 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN ** d 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 179 GLN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 113 GLN ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 106753 Z= 0.262 Angle : 0.676 14.250 151960 Z= 0.341 Chirality : 0.041 0.392 17913 Planarity : 0.005 0.058 13567 Dihedral : 21.820 179.798 33078 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.14 % Favored : 94.85 % Rotamer: Outliers : 3.12 % Allowed : 16.80 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.09), residues: 8059 helix: 0.43 (0.09), residues: 2976 sheet: -1.06 (0.15), residues: 1095 loop : -1.12 (0.10), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP D 265 HIS 0.010 0.001 HIS u 148 PHE 0.030 0.002 PHE v 32 TYR 0.027 0.002 TYR 6 51 ARG 0.012 0.000 ARG h 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1502 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1276 time to evaluate : 6.641 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: D 92 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6434 (mtm180) REVERT: D 104 TYR cc_start: 0.8658 (t80) cc_final: 0.8229 (t80) REVERT: D 231 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7597 (mttt) REVERT: E 275 ARG cc_start: 0.8242 (ttt180) cc_final: 0.7841 (ttt180) REVERT: E 279 LYS cc_start: 0.7981 (ptmt) cc_final: 0.7669 (ttpt) REVERT: F 135 ARG cc_start: 0.6617 (mmt-90) cc_final: 0.6365 (mmp-170) REVERT: F 191 ASP cc_start: 0.8480 (p0) cc_final: 0.8260 (p0) REVERT: I 45 GLN cc_start: 0.7848 (tt0) cc_final: 0.7564 (mt0) REVERT: I 123 MET cc_start: 0.2991 (mpp) cc_final: 0.2701 (mpp) REVERT: K 121 MET cc_start: 0.8816 (mtt) cc_final: 0.8401 (mtt) REVERT: M 88 SER cc_start: 0.8786 (p) cc_final: 0.8550 (m) REVERT: M 143 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8347 (tp30) REVERT: M 293 TYR cc_start: 0.8123 (t80) cc_final: 0.7905 (t80) REVERT: O 58 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8241 (ttmt) REVERT: P 57 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7661 (mm-30) REVERT: P 178 ILE cc_start: 0.8910 (mm) cc_final: 0.8334 (mt) REVERT: Q 95 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6729 (mm-30) REVERT: Q 197 TYR cc_start: 0.8009 (m-80) cc_final: 0.7738 (m-80) REVERT: R 21 ILE cc_start: 0.7308 (mm) cc_final: 0.7026 (mt) REVERT: R 58 TYR cc_start: 0.7163 (m-80) cc_final: 0.5788 (m-80) REVERT: T 54 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7426 (mtmt) REVERT: T 85 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: T 133 ASN cc_start: 0.8700 (t0) cc_final: 0.8311 (t0) REVERT: W 69 THR cc_start: 0.9368 (p) cc_final: 0.9019 (m) REVERT: X 177 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.6576 (t-90) REVERT: 0 133 GLU cc_start: 0.8150 (tp30) cc_final: 0.7865 (tp30) REVERT: 3 130 LYS cc_start: 0.7276 (pttt) cc_final: 0.6459 (ttpt) REVERT: 5 98 LEU cc_start: 0.2599 (OUTLIER) cc_final: 0.1982 (pt) REVERT: 5 106 ILE cc_start: 0.7292 (mm) cc_final: 0.6975 (mt) REVERT: 6 141 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6865 (tmm-80) REVERT: 6 338 ARG cc_start: 0.6056 (tmt170) cc_final: 0.5041 (ptm160) REVERT: 6 355 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7370 (mttp) REVERT: 7 143 TRP cc_start: 0.8947 (OUTLIER) cc_final: 0.7689 (m-90) REVERT: 7 193 MET cc_start: 0.6769 (tpt) cc_final: 0.6532 (tpt) REVERT: a 108 MET cc_start: 0.8089 (tpt) cc_final: 0.7868 (tpt) REVERT: b 106 ASP cc_start: 0.6973 (t0) cc_final: 0.6491 (t0) REVERT: d 169 PHE cc_start: 0.7785 (t80) cc_final: 0.7409 (t80) REVERT: d 241 ASP cc_start: 0.6172 (t0) cc_final: 0.5839 (t0) REVERT: k 33 PHE cc_start: 0.7165 (t80) cc_final: 0.6616 (t80) REVERT: k 87 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7651 (tt) REVERT: p 113 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7627 (mm-30) REVERT: r 170 ASN cc_start: 0.8006 (t0) cc_final: 0.7146 (t0) REVERT: r 182 ARG cc_start: 0.7674 (ttm170) cc_final: 0.6717 (tpp-160) REVERT: s 149 CYS cc_start: 0.7920 (t) cc_final: 0.7662 (t) REVERT: u 191 GLU cc_start: 0.7730 (pm20) cc_final: 0.7479 (pm20) REVERT: v 26 THR cc_start: 0.8757 (m) cc_final: 0.8469 (t) outliers start: 226 outliers final: 158 residues processed: 1392 average time/residue: 0.9327 time to fit residues: 2220.2052 Evaluate side-chains 1394 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1228 time to evaluate : 6.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 142 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 62 TYR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 163 CYS Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 75 HIS Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain T residue 83 SER Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 205 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain U residue 103 GLN Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 128 THR Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 74 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 2 residue 89 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 49 VAL Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 137 LEU Chi-restraints excluded: chain 5 residue 169 GLU Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 6 residue 55 ASP Chi-restraints excluded: chain 6 residue 141 ARG Chi-restraints excluded: chain 6 residue 192 GLU Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 84 ASN Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 158 PHE Chi-restraints excluded: chain 7 residue 285 ASN Chi-restraints excluded: chain 9 residue 44 LEU Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 96 VAL Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 140 LYS Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 70 CYS Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 90 HIS Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 223 MET Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 65 HIS Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 73 TYR Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 54 MET Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 139 GLN Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 158 SER Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 92 MET Chi-restraints excluded: chain s residue 168 GLU Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 211 VAL Chi-restraints excluded: chain s residue 321 GLU Chi-restraints excluded: chain s residue 322 VAL Chi-restraints excluded: chain s residue 332 LEU Chi-restraints excluded: chain s residue 418 LEU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 159 ILE Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 176 VAL Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 955 random chunks: chunk 310 optimal weight: 50.0000 chunk 831 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 541 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 924 optimal weight: 10.0000 chunk 767 optimal weight: 6.9990 chunk 427 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 305 optimal weight: 30.0000 chunk 485 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 195 HIS ** W 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN ** Y 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 GLN 0 96 ASN 1 45 HIS 4 100 GLN ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 55 GLN 7 255 HIS 7 285 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 ASN b 123 ASN ** b 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 240 GLN ** s 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 HIS ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 106753 Z= 0.461 Angle : 0.791 17.702 151960 Z= 0.396 Chirality : 0.047 0.389 17913 Planarity : 0.006 0.099 13567 Dihedral : 21.865 179.192 33078 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.15 % Favored : 93.83 % Rotamer: Outliers : 3.76 % Allowed : 17.71 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.09), residues: 8059 helix: 0.36 (0.09), residues: 2966 sheet: -1.15 (0.15), residues: 1089 loop : -1.21 (0.10), residues: 4004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 265 HIS 0.014 0.001 HIS h 103 PHE 0.041 0.002 PHE E 224 TYR 0.025 0.002 TYR E 284 ARG 0.013 0.001 ARG h 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1516 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1244 time to evaluate : 6.726 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: D 92 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6638 (mtm180) REVERT: D 104 TYR cc_start: 0.8723 (t80) cc_final: 0.8239 (t80) REVERT: D 266 LEU cc_start: 0.7740 (mm) cc_final: 0.7504 (mm) REVERT: D 292 MET cc_start: 0.7239 (tmm) cc_final: 0.6464 (ttm) REVERT: E 275 ARG cc_start: 0.8269 (ttt180) cc_final: 0.7801 (ttt180) REVERT: E 279 LYS cc_start: 0.8191 (ptmt) cc_final: 0.7939 (ttpt) REVERT: E 302 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7692 (m) REVERT: I 123 MET cc_start: 0.3170 (mpp) cc_final: 0.2844 (mpp) REVERT: L 142 GLN cc_start: 0.7824 (pp30) cc_final: 0.7491 (pp30) REVERT: M 143 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8367 (tp30) REVERT: N 78 GLU cc_start: 0.7113 (pm20) cc_final: 0.6193 (pm20) REVERT: N 83 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.7063 (t) REVERT: O 58 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8321 (ttmt) REVERT: P 158 MET cc_start: 0.7009 (mmp) cc_final: 0.6761 (mmm) REVERT: P 178 ILE cc_start: 0.8946 (mm) cc_final: 0.8374 (mt) REVERT: Q 95 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6990 (mm-30) REVERT: R 21 ILE cc_start: 0.7401 (mm) cc_final: 0.7104 (mt) REVERT: T 133 ASN cc_start: 0.8569 (t0) cc_final: 0.8145 (t0) REVERT: W 69 THR cc_start: 0.9404 (p) cc_final: 0.9040 (m) REVERT: X 97 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7053 (mp) REVERT: X 118 ILE cc_start: 0.9078 (mm) cc_final: 0.8869 (mm) REVERT: X 160 ASP cc_start: 0.7613 (m-30) cc_final: 0.7148 (m-30) REVERT: X 177 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.6744 (t-90) REVERT: Y 126 MET cc_start: 0.6555 (tpp) cc_final: 0.6345 (tpt) REVERT: 0 133 GLU cc_start: 0.8170 (tp30) cc_final: 0.7903 (tp30) REVERT: 3 130 LYS cc_start: 0.7406 (pttt) cc_final: 0.6544 (ttpt) REVERT: 5 33 TRP cc_start: 0.7927 (OUTLIER) cc_final: 0.6662 (m-10) REVERT: 5 98 LEU cc_start: 0.2911 (OUTLIER) cc_final: 0.2324 (pt) REVERT: 5 106 ILE cc_start: 0.7322 (mm) cc_final: 0.7021 (mt) REVERT: 6 155 TYR cc_start: 0.8433 (m-80) cc_final: 0.8056 (m-80) REVERT: 6 338 ARG cc_start: 0.6095 (tmt170) cc_final: 0.5056 (ptm160) REVERT: 6 355 LYS cc_start: 0.7875 (mtmt) cc_final: 0.7373 (mttp) REVERT: 7 55 GLN cc_start: 0.7566 (mm110) cc_final: 0.7291 (mm-40) REVERT: 7 143 TRP cc_start: 0.9018 (OUTLIER) cc_final: 0.7686 (m-90) REVERT: 9 90 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7545 (pp30) REVERT: a 108 MET cc_start: 0.8328 (tpt) cc_final: 0.8052 (tpt) REVERT: b 58 ASN cc_start: 0.9265 (OUTLIER) cc_final: 0.8779 (p0) REVERT: c 219 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9174 (mt) REVERT: c 283 GLU cc_start: 0.7809 (tp30) cc_final: 0.7520 (tt0) REVERT: c 287 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6913 (pm20) REVERT: d 169 PHE cc_start: 0.7865 (t80) cc_final: 0.7510 (t80) REVERT: d 241 ASP cc_start: 0.6324 (t0) cc_final: 0.6019 (t0) REVERT: g 44 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6185 (mm-30) REVERT: h 87 GLN cc_start: 0.7379 (mm110) cc_final: 0.7050 (mm110) REVERT: h 151 ASN cc_start: 0.8965 (p0) cc_final: 0.8448 (p0) REVERT: k 87 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7775 (tt) REVERT: p 113 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7677 (mm-30) REVERT: r 170 ASN cc_start: 0.8052 (t0) cc_final: 0.7153 (t0) REVERT: s 149 CYS cc_start: 0.7924 (t) cc_final: 0.7574 (t) REVERT: v 26 THR cc_start: 0.8779 (m) cc_final: 0.8529 (t) outliers start: 272 outliers final: 198 residues processed: 1396 average time/residue: 0.9567 time to fit residues: 2288.0894 Evaluate side-chains 1409 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1197 time to evaluate : 6.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 142 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 163 CYS Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 75 HIS Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain T residue 83 SER Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 144 GLU Chi-restraints excluded: chain T residue 205 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 128 THR Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 74 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 2 residue 71 SER Chi-restraints excluded: chain 2 residue 89 SER Chi-restraints excluded: chain 3 residue 111 ILE Chi-restraints excluded: chain 3 residue 151 ASN Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 33 TRP Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 137 LEU Chi-restraints excluded: chain 5 residue 169 GLU Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 269 ASN Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 185 MET Chi-restraints excluded: chain 6 residue 192 GLU Chi-restraints excluded: chain 6 residue 239 ASN Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 6 residue 311 MET Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 87 THR Chi-restraints excluded: chain 7 residue 138 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 158 PHE Chi-restraints excluded: chain 7 residue 165 ASN Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 227 LEU Chi-restraints excluded: chain 7 residue 285 ASN Chi-restraints excluded: chain 9 residue 44 LEU Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 90 GLN Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 65 VAL Chi-restraints excluded: chain a residue 66 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 70 CYS Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 223 MET Chi-restraints excluded: chain c residue 287 GLU Chi-restraints excluded: chain c residue 291 VAL Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 279 THR Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 65 HIS Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 73 TYR Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 139 GLN Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 158 SER Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain r residue 192 TRP Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 92 MET Chi-restraints excluded: chain s residue 168 GLU Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 321 GLU Chi-restraints excluded: chain s residue 322 VAL Chi-restraints excluded: chain s residue 332 LEU Chi-restraints excluded: chain s residue 418 LEU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 159 ILE Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 176 VAL Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 955 random chunks: chunk 890 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 526 optimal weight: 1.9990 chunk 674 optimal weight: 20.0000 chunk 522 optimal weight: 5.9990 chunk 777 optimal weight: 5.9990 chunk 515 optimal weight: 30.0000 chunk 920 optimal weight: 4.9990 chunk 576 optimal weight: 1.9990 chunk 561 optimal weight: 3.9990 chunk 424 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN T 55 ASN ** W 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN ** Y 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 255 HIS 7 285 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 ASN ** b 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 152 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 106753 Z= 0.348 Angle : 0.730 19.931 151960 Z= 0.366 Chirality : 0.044 0.387 17913 Planarity : 0.005 0.074 13567 Dihedral : 21.832 179.905 33078 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.58 % Favored : 94.40 % Rotamer: Outliers : 3.47 % Allowed : 19.04 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.09), residues: 8059 helix: 0.43 (0.09), residues: 2970 sheet: -1.06 (0.15), residues: 1046 loop : -1.17 (0.10), residues: 4043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 265 HIS 0.032 0.001 HIS h 103 PHE 0.033 0.002 PHE E 224 TYR 0.030 0.002 TYR c 275 ARG 0.014 0.001 ARG h 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1492 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1241 time to evaluate : 6.975 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: D 92 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6569 (mtm180) REVERT: D 104 TYR cc_start: 0.8704 (t80) cc_final: 0.8152 (t80) REVERT: D 231 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7615 (mttt) REVERT: D 266 LEU cc_start: 0.7639 (mm) cc_final: 0.7433 (mm) REVERT: D 292 MET cc_start: 0.7408 (tmm) cc_final: 0.6459 (ttm) REVERT: E 275 ARG cc_start: 0.8234 (ttt180) cc_final: 0.7998 (ttt180) REVERT: E 302 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7753 (m) REVERT: K 55 ASP cc_start: 0.8019 (m-30) cc_final: 0.7670 (m-30) REVERT: L 142 GLN cc_start: 0.7945 (pp30) cc_final: 0.7597 (pp30) REVERT: M 143 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: N 78 GLU cc_start: 0.7123 (pm20) cc_final: 0.6225 (pm20) REVERT: N 83 THR cc_start: 0.7434 (OUTLIER) cc_final: 0.7216 (t) REVERT: O 58 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8333 (ttmt) REVERT: P 178 ILE cc_start: 0.8910 (mm) cc_final: 0.8355 (mt) REVERT: Q 95 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6972 (mm-30) REVERT: R 21 ILE cc_start: 0.7351 (mm) cc_final: 0.7063 (mt) REVERT: R 58 TYR cc_start: 0.7379 (m-80) cc_final: 0.6056 (m-80) REVERT: T 133 ASN cc_start: 0.8653 (t0) cc_final: 0.8284 (t0) REVERT: W 69 THR cc_start: 0.9402 (p) cc_final: 0.9058 (m) REVERT: X 160 ASP cc_start: 0.7549 (m-30) cc_final: 0.7248 (m-30) REVERT: X 177 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.6916 (t-90) REVERT: X 230 TYR cc_start: 0.7861 (m-10) cc_final: 0.7579 (m-80) REVERT: 0 133 GLU cc_start: 0.8193 (tp30) cc_final: 0.7912 (tp30) REVERT: 3 130 LYS cc_start: 0.7358 (pttt) cc_final: 0.6544 (ttpt) REVERT: 5 33 TRP cc_start: 0.7902 (OUTLIER) cc_final: 0.6604 (m-10) REVERT: 5 98 LEU cc_start: 0.3013 (OUTLIER) cc_final: 0.2465 (pt) REVERT: 5 106 ILE cc_start: 0.7297 (mm) cc_final: 0.7023 (mt) REVERT: 6 155 TYR cc_start: 0.8393 (m-80) cc_final: 0.8022 (m-80) REVERT: 6 338 ARG cc_start: 0.6040 (tmt170) cc_final: 0.5081 (ptm160) REVERT: 6 355 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7502 (mttp) REVERT: 7 143 TRP cc_start: 0.9002 (OUTLIER) cc_final: 0.7614 (m-90) REVERT: 7 193 MET cc_start: 0.6764 (tpt) cc_final: 0.6540 (tpt) REVERT: 7 285 ASN cc_start: 0.5730 (OUTLIER) cc_final: 0.5523 (m110) REVERT: 9 90 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7480 (pp30) REVERT: b 58 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8901 (p0) REVERT: c 71 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: c 219 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9140 (mt) REVERT: c 283 GLU cc_start: 0.7826 (tp30) cc_final: 0.7427 (tt0) REVERT: d 169 PHE cc_start: 0.7746 (t80) cc_final: 0.7433 (t80) REVERT: d 241 ASP cc_start: 0.6382 (t0) cc_final: 0.6075 (t0) REVERT: d 274 GLN cc_start: 0.7542 (pm20) cc_final: 0.7267 (pm20) REVERT: g 44 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6159 (mm-30) REVERT: h 87 GLN cc_start: 0.7352 (mm110) cc_final: 0.7000 (mm110) REVERT: h 151 ASN cc_start: 0.8924 (p0) cc_final: 0.8468 (p0) REVERT: i 49 GLU cc_start: 0.6551 (mp0) cc_final: 0.6345 (mp0) REVERT: k 86 MET cc_start: 0.6978 (pmm) cc_final: 0.6302 (mpp) REVERT: p 113 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7604 (mm-30) REVERT: r 170 ASN cc_start: 0.8071 (t0) cc_final: 0.7224 (t0) REVERT: r 182 ARG cc_start: 0.7744 (ttm170) cc_final: 0.6717 (tpp-160) REVERT: s 149 CYS cc_start: 0.7954 (t) cc_final: 0.7689 (t) REVERT: u 96 MET cc_start: 0.6596 (ppp) cc_final: 0.6159 (ppp) REVERT: v 26 THR cc_start: 0.8804 (m) cc_final: 0.8502 (t) outliers start: 251 outliers final: 190 residues processed: 1385 average time/residue: 0.9303 time to fit residues: 2206.6091 Evaluate side-chains 1395 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1192 time to evaluate : 6.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 142 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 163 CYS Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 75 HIS Chi-restraints excluded: chain S residue 118 ASN Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain T residue 83 SER Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 144 GLU Chi-restraints excluded: chain T residue 205 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 74 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 2 residue 71 SER Chi-restraints excluded: chain 2 residue 89 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 33 TRP Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 137 LEU Chi-restraints excluded: chain 5 residue 169 GLU Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 269 ASN Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 185 MET Chi-restraints excluded: chain 6 residue 192 GLU Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 6 residue 293 LEU Chi-restraints excluded: chain 6 residue 374 GLU Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 138 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 158 PHE Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 227 LEU Chi-restraints excluded: chain 7 residue 285 ASN Chi-restraints excluded: chain 9 residue 44 LEU Chi-restraints excluded: chain 9 residue 51 VAL Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 90 GLN Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 65 VAL Chi-restraints excluded: chain a residue 66 ASP Chi-restraints excluded: chain a residue 140 LYS Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 70 CYS Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 71 GLU Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 223 MET Chi-restraints excluded: chain d residue 123 ARG Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 279 THR Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 65 HIS Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 73 TYR Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 96 LEU Chi-restraints excluded: chain q residue 139 GLN Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 158 SER Chi-restraints excluded: chain r residue 176 VAL Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 92 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 168 GLU Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 184 LEU Chi-restraints excluded: chain s residue 211 VAL Chi-restraints excluded: chain s residue 321 GLU Chi-restraints excluded: chain s residue 322 VAL Chi-restraints excluded: chain s residue 332 LEU Chi-restraints excluded: chain s residue 418 LEU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 159 ILE Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 176 VAL Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 955 random chunks: chunk 569 optimal weight: 1.9990 chunk 367 optimal weight: 0.8980 chunk 549 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 585 optimal weight: 10.0000 chunk 627 optimal weight: 40.0000 chunk 455 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 723 optimal weight: 0.0970 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN E 339 GLN H 121 ASN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN O 39 HIS ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN ** W 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN ** Y 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 100 GLN 5 338 GLN ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 55 GLN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 285 ASN a 46 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 ASN ** b 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN ** d 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 GLN p 152 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 386 ASN ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 106753 Z= 0.182 Angle : 0.655 20.077 151960 Z= 0.328 Chirality : 0.040 0.396 17913 Planarity : 0.005 0.073 13567 Dihedral : 21.716 179.936 33078 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.12 % Allowed : 19.70 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.09), residues: 8059 helix: 0.64 (0.10), residues: 2975 sheet: -0.98 (0.15), residues: 1074 loop : -1.04 (0.10), residues: 4010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP D 265 HIS 0.030 0.001 HIS h 103 PHE 0.023 0.001 PHE b 54 TYR 0.037 0.002 TYR u 146 ARG 0.015 0.000 ARG h 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1295 time to evaluate : 6.648 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: D 92 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6469 (mtm180) REVERT: D 104 TYR cc_start: 0.8613 (t80) cc_final: 0.8048 (t80) REVERT: D 231 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7505 (mttt) REVERT: D 292 MET cc_start: 0.7379 (tmm) cc_final: 0.6583 (ttm) REVERT: F 143 SER cc_start: 0.9071 (t) cc_final: 0.8468 (p) REVERT: I 37 ARG cc_start: 0.7613 (ttm110) cc_final: 0.6707 (ttt180) REVERT: K 55 ASP cc_start: 0.7991 (m-30) cc_final: 0.7647 (m-30) REVERT: K 121 MET cc_start: 0.8738 (mtt) cc_final: 0.8400 (mtt) REVERT: L 142 GLN cc_start: 0.7941 (pp30) cc_final: 0.7601 (pp30) REVERT: M 143 GLU cc_start: 0.8558 (tt0) cc_final: 0.8327 (tp30) REVERT: N 78 GLU cc_start: 0.6958 (pm20) cc_final: 0.6162 (pm20) REVERT: N 83 THR cc_start: 0.7444 (OUTLIER) cc_final: 0.7149 (t) REVERT: O 58 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8380 (ttmt) REVERT: P 178 ILE cc_start: 0.8859 (mm) cc_final: 0.8362 (mt) REVERT: R 21 ILE cc_start: 0.7221 (mm) cc_final: 0.6896 (mt) REVERT: R 58 TYR cc_start: 0.6960 (m-80) cc_final: 0.5656 (m-80) REVERT: T 133 ASN cc_start: 0.8809 (t0) cc_final: 0.8442 (t0) REVERT: U 50 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7563 (mtm-85) REVERT: V 202 MET cc_start: 0.8186 (mmm) cc_final: 0.7809 (mmm) REVERT: W 69 THR cc_start: 0.9372 (p) cc_final: 0.9061 (m) REVERT: W 147 MET cc_start: 0.1405 (tpt) cc_final: 0.1197 (tpt) REVERT: X 160 ASP cc_start: 0.7579 (m-30) cc_final: 0.7226 (m-30) REVERT: X 177 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.6687 (t-90) REVERT: X 230 TYR cc_start: 0.7834 (m-10) cc_final: 0.7583 (m-80) REVERT: Y 160 GLN cc_start: 0.7053 (pp30) cc_final: 0.6223 (pt0) REVERT: Y 161 GLU cc_start: 0.6917 (tp30) cc_final: 0.6497 (tp30) REVERT: Y 233 ILE cc_start: 0.8067 (tt) cc_final: 0.7659 (tt) REVERT: 0 133 GLU cc_start: 0.8144 (tp30) cc_final: 0.7852 (tp30) REVERT: 0 163 GLU cc_start: 0.5294 (mp0) cc_final: 0.5016 (mp0) REVERT: 2 56 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.7967 (m) REVERT: 3 130 LYS cc_start: 0.7153 (pttt) cc_final: 0.6406 (ttpt) REVERT: 5 98 LEU cc_start: 0.2979 (OUTLIER) cc_final: 0.2407 (pt) REVERT: 5 106 ILE cc_start: 0.7147 (mm) cc_final: 0.6918 (mt) REVERT: 6 155 TYR cc_start: 0.8166 (m-80) cc_final: 0.7912 (m-80) REVERT: 6 338 ARG cc_start: 0.5810 (tmt170) cc_final: 0.4750 (ptm160) REVERT: 6 355 LYS cc_start: 0.7746 (mtmt) cc_final: 0.7407 (mttp) REVERT: 7 143 TRP cc_start: 0.8934 (OUTLIER) cc_final: 0.7543 (m-90) REVERT: c 44 GLU cc_start: 0.6792 (tp30) cc_final: 0.6430 (tp30) REVERT: c 67 ASP cc_start: 0.7392 (t0) cc_final: 0.6743 (t0) REVERT: c 219 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9126 (mt) REVERT: c 283 GLU cc_start: 0.7869 (tp30) cc_final: 0.7510 (tt0) REVERT: c 287 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6721 (pm20) REVERT: d 232 MET cc_start: 0.7314 (mtp) cc_final: 0.7039 (ttp) REVERT: d 241 ASP cc_start: 0.6385 (t0) cc_final: 0.6062 (t0) REVERT: d 274 GLN cc_start: 0.7524 (pm20) cc_final: 0.7247 (pm20) REVERT: g 43 ASP cc_start: 0.6098 (p0) cc_final: 0.5865 (p0) REVERT: g 44 GLU cc_start: 0.6270 (mm-30) cc_final: 0.5932 (mm-30) REVERT: h 87 GLN cc_start: 0.7322 (mm110) cc_final: 0.7078 (mm110) REVERT: h 153 LYS cc_start: 0.8068 (mmmm) cc_final: 0.7452 (mmmt) REVERT: k 33 PHE cc_start: 0.7127 (t80) cc_final: 0.6713 (t80) REVERT: k 74 LEU cc_start: 0.6320 (mt) cc_final: 0.5995 (mp) REVERT: k 86 MET cc_start: 0.7028 (pmm) cc_final: 0.6312 (mpp) REVERT: r 93 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8021 (mm) REVERT: r 170 ASN cc_start: 0.7957 (t0) cc_final: 0.7212 (t0) REVERT: r 182 ARG cc_start: 0.7542 (ttm170) cc_final: 0.6660 (tpp-160) REVERT: s 149 CYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7691 (t) REVERT: u 93 ASP cc_start: 0.7072 (t0) cc_final: 0.6572 (t0) REVERT: u 96 MET cc_start: 0.6591 (ppp) cc_final: 0.6132 (ppp) REVERT: u 104 GLU cc_start: 0.6245 (mm-30) cc_final: 0.5338 (mm-30) REVERT: u 123 TYR cc_start: 0.7075 (m-10) cc_final: 0.6811 (m-10) REVERT: u 141 TYR cc_start: 0.7014 (t80) cc_final: 0.6781 (t80) REVERT: v 26 THR cc_start: 0.8823 (m) cc_final: 0.8495 (t) outliers start: 226 outliers final: 161 residues processed: 1430 average time/residue: 0.9234 time to fit residues: 2263.9342 Evaluate side-chains 1406 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1235 time to evaluate : 6.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 122 ARG Chi-restraints excluded: chain J residue 142 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 62 TYR Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 75 HIS Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain T residue 83 SER Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 144 GLU Chi-restraints excluded: chain T residue 205 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 74 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 2 residue 89 SER Chi-restraints excluded: chain 3 residue 111 ILE Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 169 GLU Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 269 ASN Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 185 MET Chi-restraints excluded: chain 6 residue 192 GLU Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 293 LEU Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 374 GLU Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 158 PHE Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 285 ASN Chi-restraints excluded: chain 9 residue 44 LEU Chi-restraints excluded: chain 9 residue 51 VAL Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain 9 residue 96 VAL Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 66 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 90 HIS Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 81 GLU Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 223 MET Chi-restraints excluded: chain c residue 287 GLU Chi-restraints excluded: chain d residue 123 ARG Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 217 HIS Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain f residue 129 THR Chi-restraints excluded: chain g residue 65 HIS Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 73 TYR Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 139 GLN Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 158 SER Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 149 CYS Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 168 GLU Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 184 LEU Chi-restraints excluded: chain s residue 211 VAL Chi-restraints excluded: chain s residue 321 GLU Chi-restraints excluded: chain s residue 332 LEU Chi-restraints excluded: chain s residue 418 LEU Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 159 ILE Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 955 random chunks: chunk 837 optimal weight: 5.9990 chunk 881 optimal weight: 30.0000 chunk 804 optimal weight: 7.9990 chunk 857 optimal weight: 4.9990 chunk 516 optimal weight: 10.0000 chunk 373 optimal weight: 1.9990 chunk 673 optimal weight: 0.5980 chunk 263 optimal weight: 0.9990 chunk 775 optimal weight: 6.9990 chunk 811 optimal weight: 4.9990 chunk 854 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 339 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN ** W 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN ** Y 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 45 HIS 4 68 ASN 5 338 GLN ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 63 GLN 6 174 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 55 GLN 7 285 ASN 9 134 ASN a 46 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 61 HIS h 67 GLN ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 152 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 386 ASN u 148 HIS ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 106753 Z= 0.300 Angle : 0.704 19.353 151960 Z= 0.353 Chirality : 0.042 0.400 17913 Planarity : 0.005 0.066 13567 Dihedral : 21.660 179.543 33078 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.37 % Favored : 94.61 % Rotamer: Outliers : 2.90 % Allowed : 20.42 % Favored : 76.68 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.09), residues: 8059 helix: 0.66 (0.10), residues: 2969 sheet: -1.01 (0.15), residues: 1086 loop : -1.03 (0.10), residues: 4004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP D 265 HIS 0.029 0.001 HIS h 103 PHE 0.047 0.002 PHE v 39 TYR 0.070 0.002 TYR v 13 ARG 0.011 0.001 ARG h 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1438 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1228 time to evaluate : 6.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6414 (mtm180) REVERT: D 104 TYR cc_start: 0.8652 (t80) cc_final: 0.8086 (t80) REVERT: D 292 MET cc_start: 0.7410 (tmm) cc_final: 0.6601 (ttm) REVERT: E 227 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8579 (mp10) REVERT: E 302 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7740 (m) REVERT: F 184 GLN cc_start: 0.8676 (mt0) cc_final: 0.8476 (mt0) REVERT: F 191 ASP cc_start: 0.8546 (p0) cc_final: 0.8325 (p0) REVERT: K 55 ASP cc_start: 0.8011 (m-30) cc_final: 0.7662 (m-30) REVERT: K 121 MET cc_start: 0.8734 (mtt) cc_final: 0.8335 (mtt) REVERT: K 131 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7084 (mm-30) REVERT: M 19 LEU cc_start: 0.9160 (mt) cc_final: 0.8790 (mt) REVERT: M 143 GLU cc_start: 0.8650 (tt0) cc_final: 0.8397 (tp30) REVERT: O 58 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8350 (ttmt) REVERT: P 158 MET cc_start: 0.6953 (mmp) cc_final: 0.6654 (mmm) REVERT: P 178 ILE cc_start: 0.8958 (mm) cc_final: 0.8400 (mt) REVERT: R 21 ILE cc_start: 0.7495 (mm) cc_final: 0.7148 (mt) REVERT: R 58 TYR cc_start: 0.7373 (m-80) cc_final: 0.5999 (m-80) REVERT: T 133 ASN cc_start: 0.8765 (t0) cc_final: 0.8431 (t0) REVERT: V 202 MET cc_start: 0.8328 (mmm) cc_final: 0.7927 (mmm) REVERT: W 69 THR cc_start: 0.9406 (p) cc_final: 0.9057 (m) REVERT: X 160 ASP cc_start: 0.7590 (m-30) cc_final: 0.7289 (m-30) REVERT: X 177 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.6710 (t-90) REVERT: Y 233 ILE cc_start: 0.8030 (tt) cc_final: 0.7807 (tt) REVERT: 0 133 GLU cc_start: 0.8171 (tp30) cc_final: 0.7863 (tp30) REVERT: 0 163 GLU cc_start: 0.5293 (mp0) cc_final: 0.5091 (mp0) REVERT: 3 130 LYS cc_start: 0.7287 (pttt) cc_final: 0.6593 (ttpt) REVERT: 5 98 LEU cc_start: 0.2980 (OUTLIER) cc_final: 0.2409 (pt) REVERT: 5 106 ILE cc_start: 0.7095 (mm) cc_final: 0.6858 (mt) REVERT: 6 155 TYR cc_start: 0.8378 (m-80) cc_final: 0.8057 (m-80) REVERT: 6 338 ARG cc_start: 0.5906 (tmt170) cc_final: 0.4830 (ptm160) REVERT: 6 355 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7435 (mttp) REVERT: 7 143 TRP cc_start: 0.8975 (OUTLIER) cc_final: 0.7596 (m-90) REVERT: c 67 ASP cc_start: 0.7470 (t0) cc_final: 0.7246 (t0) REVERT: c 219 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9139 (mt) REVERT: c 283 GLU cc_start: 0.7900 (tp30) cc_final: 0.7542 (tt0) REVERT: c 287 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6789 (pm20) REVERT: d 232 MET cc_start: 0.7307 (mtp) cc_final: 0.7022 (ttp) REVERT: d 241 ASP cc_start: 0.6538 (t0) cc_final: 0.6243 (t0) REVERT: d 274 GLN cc_start: 0.7536 (pm20) cc_final: 0.7229 (pm20) REVERT: g 44 GLU cc_start: 0.6395 (mm-30) cc_final: 0.6041 (mm-30) REVERT: h 87 GLN cc_start: 0.7360 (mm110) cc_final: 0.7106 (mm110) REVERT: h 151 ASN cc_start: 0.8805 (p0) cc_final: 0.8495 (p0) REVERT: h 153 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7587 (mmmt) REVERT: k 33 PHE cc_start: 0.7126 (t80) cc_final: 0.6720 (t80) REVERT: r 170 ASN cc_start: 0.8106 (t0) cc_final: 0.7232 (t0) REVERT: r 182 ARG cc_start: 0.7672 (ttm170) cc_final: 0.6681 (tpp-160) REVERT: s 149 CYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7597 (t) REVERT: u 93 ASP cc_start: 0.7141 (t0) cc_final: 0.6706 (t0) REVERT: u 96 MET cc_start: 0.6665 (ppp) cc_final: 0.6228 (ppp) REVERT: u 104 GLU cc_start: 0.6351 (mm-30) cc_final: 0.5480 (mm-30) REVERT: u 193 LEU cc_start: 0.8111 (mm) cc_final: 0.7819 (mp) REVERT: v 26 THR cc_start: 0.8868 (m) cc_final: 0.8548 (t) outliers start: 210 outliers final: 173 residues processed: 1355 average time/residue: 0.9493 time to fit residues: 2210.1876 Evaluate side-chains 1388 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1206 time to evaluate : 6.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 122 ARG Chi-restraints excluded: chain J residue 142 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 163 CYS Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 75 HIS Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain T residue 83 SER Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 144 GLU Chi-restraints excluded: chain T residue 205 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 74 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 2 residue 89 SER Chi-restraints excluded: chain 3 residue 111 ILE Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 169 GLU Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 269 ASN Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 185 MET Chi-restraints excluded: chain 6 residue 192 GLU Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 293 LEU Chi-restraints excluded: chain 6 residue 300 THR Chi-restraints excluded: chain 6 residue 374 GLU Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 158 PHE Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 227 LEU Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 9 residue 44 LEU Chi-restraints excluded: chain 9 residue 51 VAL Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 66 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 70 CYS Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 81 GLU Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 223 MET Chi-restraints excluded: chain c residue 287 GLU Chi-restraints excluded: chain d residue 123 ARG Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 65 HIS Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 73 TYR Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain p residue 174 LYS Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 139 GLN Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 158 SER Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 149 CYS Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 168 GLU Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 184 LEU Chi-restraints excluded: chain s residue 211 VAL Chi-restraints excluded: chain s residue 321 GLU Chi-restraints excluded: chain s residue 322 VAL Chi-restraints excluded: chain s residue 332 LEU Chi-restraints excluded: chain s residue 418 LEU Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 159 ILE Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 13 TYR Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 955 random chunks: chunk 563 optimal weight: 0.0970 chunk 907 optimal weight: 20.0000 chunk 553 optimal weight: 4.9990 chunk 430 optimal weight: 20.0000 chunk 630 optimal weight: 30.0000 chunk 951 optimal weight: 40.0000 chunk 875 optimal weight: 10.0000 chunk 757 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 585 optimal weight: 20.0000 chunk 464 optimal weight: 0.9980 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 233 GLN E 339 GLN H 121 ASN K 9 GLN ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN O 39 HIS ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 133 ASN ** W 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN ** Y 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 55 GLN 7 255 HIS a 46 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN c 134 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 152 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 386 ASN ** u 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 HIS ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 106753 Z= 0.235 Angle : 0.682 19.520 151960 Z= 0.342 Chirality : 0.041 0.397 17913 Planarity : 0.005 0.066 13567 Dihedral : 21.630 179.942 33078 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.88 % Favored : 95.11 % Rotamer: Outliers : 2.78 % Allowed : 20.72 % Favored : 76.50 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.09), residues: 8059 helix: 0.69 (0.10), residues: 2970 sheet: -0.93 (0.15), residues: 1083 loop : -1.02 (0.10), residues: 4006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP D 265 HIS 0.029 0.001 HIS h 103 PHE 0.034 0.002 PHE d 169 TYR 0.061 0.002 TYR 5 418 ARG 0.008 0.000 ARG 6 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1229 time to evaluate : 6.661 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: D 92 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6391 (mtm180) REVERT: D 104 TYR cc_start: 0.8620 (t80) cc_final: 0.8056 (t80) REVERT: D 231 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7652 (mttt) REVERT: D 292 MET cc_start: 0.7370 (tmm) cc_final: 0.6602 (ttm) REVERT: E 302 SER cc_start: 0.8033 (OUTLIER) cc_final: 0.7733 (m) REVERT: K 55 ASP cc_start: 0.8003 (m-30) cc_final: 0.7650 (m-30) REVERT: K 121 MET cc_start: 0.8776 (mtt) cc_final: 0.8430 (mtt) REVERT: M 19 LEU cc_start: 0.9105 (mt) cc_final: 0.8777 (mt) REVERT: M 143 GLU cc_start: 0.8620 (tt0) cc_final: 0.8368 (tp30) REVERT: O 58 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8346 (ttmt) REVERT: P 158 MET cc_start: 0.6883 (mmp) cc_final: 0.6526 (mmm) REVERT: P 178 ILE cc_start: 0.8949 (mm) cc_final: 0.8434 (mt) REVERT: R 21 ILE cc_start: 0.7331 (mm) cc_final: 0.7001 (mt) REVERT: R 58 TYR cc_start: 0.7155 (m-80) cc_final: 0.5808 (m-80) REVERT: T 133 ASN cc_start: 0.8790 (t0) cc_final: 0.8452 (t0) REVERT: V 108 MET cc_start: 0.2376 (mmp) cc_final: 0.1997 (mmp) REVERT: V 202 MET cc_start: 0.8317 (mmm) cc_final: 0.7905 (mmm) REVERT: W 69 THR cc_start: 0.9393 (p) cc_final: 0.9054 (m) REVERT: X 160 ASP cc_start: 0.7577 (m-30) cc_final: 0.7308 (m-30) REVERT: X 177 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.6688 (t-90) REVERT: Y 93 LYS cc_start: 0.7953 (mmmt) cc_final: 0.6902 (mmmm) REVERT: Y 160 GLN cc_start: 0.7031 (pp30) cc_final: 0.6131 (pt0) REVERT: Y 161 GLU cc_start: 0.7009 (tp30) cc_final: 0.6453 (tp30) REVERT: 0 133 GLU cc_start: 0.8143 (tp30) cc_final: 0.7865 (tp30) REVERT: 3 129 TYR cc_start: 0.8581 (p90) cc_final: 0.8356 (p90) REVERT: 3 130 LYS cc_start: 0.7261 (pttt) cc_final: 0.6524 (ttpt) REVERT: 5 98 LEU cc_start: 0.2826 (OUTLIER) cc_final: 0.2154 (pt) REVERT: 5 106 ILE cc_start: 0.7087 (mm) cc_final: 0.6857 (mt) REVERT: 6 155 TYR cc_start: 0.8296 (m-80) cc_final: 0.8000 (m-80) REVERT: 6 338 ARG cc_start: 0.5855 (tmt170) cc_final: 0.4847 (ptm160) REVERT: 6 355 LYS cc_start: 0.7768 (mtmt) cc_final: 0.7412 (mttp) REVERT: 7 143 TRP cc_start: 0.8970 (OUTLIER) cc_final: 0.7575 (m-90) REVERT: 7 193 MET cc_start: 0.6808 (tpt) cc_final: 0.6495 (tpt) REVERT: a 122 ARG cc_start: 0.8081 (tpt-90) cc_final: 0.7831 (ttt90) REVERT: c 44 GLU cc_start: 0.6831 (tp30) cc_final: 0.6480 (tp30) REVERT: c 67 ASP cc_start: 0.7331 (t0) cc_final: 0.7082 (t0) REVERT: c 219 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9110 (mt) REVERT: c 283 GLU cc_start: 0.7873 (tp30) cc_final: 0.7533 (tt0) REVERT: c 287 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6735 (pm20) REVERT: d 232 MET cc_start: 0.7288 (mtp) cc_final: 0.7056 (ttp) REVERT: d 241 ASP cc_start: 0.6516 (t0) cc_final: 0.6199 (t0) REVERT: d 274 GLN cc_start: 0.7530 (pm20) cc_final: 0.7234 (pm20) REVERT: g 44 GLU cc_start: 0.6256 (mm-30) cc_final: 0.5900 (mm-30) REVERT: h 87 GLN cc_start: 0.7435 (mm110) cc_final: 0.6932 (mm110) REVERT: h 151 ASN cc_start: 0.8810 (p0) cc_final: 0.8479 (p0) REVERT: h 153 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7607 (mmmt) REVERT: k 33 PHE cc_start: 0.7053 (t80) cc_final: 0.6735 (t80) REVERT: p 118 LYS cc_start: 0.8566 (mmmm) cc_final: 0.8215 (mmmm) REVERT: r 170 ASN cc_start: 0.8093 (t0) cc_final: 0.7222 (t0) REVERT: r 182 ARG cc_start: 0.7620 (ttm170) cc_final: 0.6661 (tpp-160) REVERT: s 149 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7592 (t) REVERT: u 93 ASP cc_start: 0.7171 (t0) cc_final: 0.6638 (t0) REVERT: u 96 MET cc_start: 0.6605 (ppp) cc_final: 0.6187 (ppp) REVERT: u 193 LEU cc_start: 0.8021 (mm) cc_final: 0.7767 (mp) REVERT: v 26 THR cc_start: 0.8845 (m) cc_final: 0.8524 (t) outliers start: 201 outliers final: 170 residues processed: 1348 average time/residue: 0.9461 time to fit residues: 2175.8482 Evaluate side-chains 1390 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1212 time to evaluate : 6.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 122 ARG Chi-restraints excluded: chain J residue 142 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 163 CYS Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 75 HIS Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain T residue 83 SER Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 144 GLU Chi-restraints excluded: chain T residue 205 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 74 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 2 residue 89 SER Chi-restraints excluded: chain 3 residue 111 ILE Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 104 CYS Chi-restraints excluded: chain 5 residue 169 GLU Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 185 MET Chi-restraints excluded: chain 6 residue 192 GLU Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 293 LEU Chi-restraints excluded: chain 6 residue 300 THR Chi-restraints excluded: chain 6 residue 374 GLU Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 158 PHE Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 227 LEU Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 9 residue 44 LEU Chi-restraints excluded: chain 9 residue 51 VAL Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 86 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 66 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 90 HIS Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 81 GLU Chi-restraints excluded: chain c residue 98 ILE Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 223 MET Chi-restraints excluded: chain c residue 287 GLU Chi-restraints excluded: chain d residue 123 ARG Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 65 HIS Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 73 TYR Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain p residue 174 LYS Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 158 SER Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 149 CYS Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 168 GLU Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 184 LEU Chi-restraints excluded: chain s residue 211 VAL Chi-restraints excluded: chain s residue 321 GLU Chi-restraints excluded: chain s residue 332 LEU Chi-restraints excluded: chain s residue 418 LEU Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 159 ILE Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 176 VAL Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 955 random chunks: chunk 601 optimal weight: 30.0000 chunk 807 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 698 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 chunk 210 optimal weight: 0.9980 chunk 758 optimal weight: 1.9990 chunk 317 optimal weight: 0.1980 chunk 779 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 339 GLN H 121 ASN K 9 GLN ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN T 133 ASN ** W 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN ** Y 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 96 ASN 1 45 HIS 5 269 ASN ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 55 GLN 7 255 HIS 9 134 ASN a 46 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 152 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 314 GLN s 386 ASN ** u 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 HIS ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.154351 restraints weight = 150149.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152764 restraints weight = 315052.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149281 restraints weight = 169487.908| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 106753 Z= 0.249 Angle : 0.686 19.677 151960 Z= 0.343 Chirality : 0.041 0.396 17913 Planarity : 0.005 0.059 13567 Dihedral : 21.590 179.754 33078 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.29 % Favored : 94.70 % Rotamer: Outliers : 2.78 % Allowed : 20.86 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.09), residues: 8059 helix: 0.71 (0.10), residues: 2970 sheet: -0.94 (0.15), residues: 1086 loop : -1.00 (0.10), residues: 4003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP D 265 HIS 0.037 0.001 HIS u 148 PHE 0.053 0.002 PHE d 169 TYR 0.053 0.002 TYR v 13 ARG 0.013 0.000 ARG h 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28884.03 seconds wall clock time: 506 minutes 13.45 seconds (30373.45 seconds total)