Starting phenix.real_space_refine (version: dev) on Sat Apr 9 10:01:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oic_12925/04_2022/7oic_12925_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oic_12925/04_2022/7oic_12925.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oic_12925/04_2022/7oic_12925_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oic_12925/04_2022/7oic_12925_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oic_12925/04_2022/7oic_12925_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oic_12925/04_2022/7oic_12925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oic_12925/04_2022/7oic_12925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oic_12925/04_2022/7oic_12925_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oic_12925/04_2022/7oic_12925_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "E PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F ASP 220": "OD1" <-> "OD2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 92": "OD1" <-> "OD2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "I ASP 137": "OD1" <-> "OD2" Residue "I GLU 158": "OE1" <-> "OE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "K PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K GLU 157": "OE1" <-> "OE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K ASP 164": "OD1" <-> "OD2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "L ASP 71": "OD1" <-> "OD2" 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 GLU 131": "OE1" <-> "OE2" Residue "L TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M GLU 56": "OE1" <-> "OE2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M GLU 68": "OE1" <-> "OE2" Residue "M ASP 111": "OD1" <-> "OD2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ASP 135": "OD1" <-> "OD2" Residue "M ASP 146": "OD1" <-> "OD2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M GLU 209": "OE1" <-> "OE2" Residue "M ASP 225": "OD1" <-> "OD2" Residue "M ASP 250": "OD1" <-> "OD2" Residue "M PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ASP 71": "OD1" <-> "OD2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 103": "OE1" <-> "OE2" Residue "N ASP 114": "OD1" <-> "OD2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "N PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "N ASP 201": "OD1" <-> "OD2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "N GLU 204": "OE1" <-> "OE2" Residue "N PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O GLU 57": "OE1" <-> "OE2" Residue "O ASP 67": "OD1" <-> "OD2" Residue "O ASP 77": "OD1" <-> "OD2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ASP 116": "OD1" <-> "OD2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 53": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 74": "NH1" <-> "NH2" Residue "P ARG 79": "NH1" <-> "NH2" Residue "P ARG 107": "NH1" <-> "NH2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P ASP 155": "OD1" <-> "OD2" Residue "P ARG 176": "NH1" <-> "NH2" Residue "Q PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q ASP 98": "OD1" <-> "OD2" Residue "Q GLU 101": "OE1" <-> "OE2" Residue "Q PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 173": "OE1" <-> "OE2" Residue "Q TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 256": "OE1" <-> "OE2" Residue "Q GLU 279": "OE1" <-> "OE2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "S ASP 68": "OD1" <-> "OD2" Residue "S GLU 72": "OE1" <-> "OE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 104": "NH1" <-> "NH2" Residue "S GLU 119": "OE1" <-> "OE2" Residue "S GLU 126": "OE1" <-> "OE2" Residue "S PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S GLU 162": "OE1" <-> "OE2" Residue "S PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 72": "OE1" <-> "OE2" Residue "T TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T GLU 135": "OE1" <-> "OE2" Residue "T GLU 144": "OE1" <-> "OE2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "T ARG 157": "NH1" <-> "NH2" Residue "T TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 11": "NH1" <-> "NH2" Residue "U PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "V ARG 20": "NH1" <-> "NH2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V ASP 51": "OD1" <-> "OD2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V ASP 53": "OD1" <-> "OD2" Residue "V ASP 69": "OD1" <-> "OD2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "V TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "V ASP 127": "OD1" <-> "OD2" Residue "V GLU 134": "OE1" <-> "OE2" Residue "V GLU 139": "OE1" <-> "OE2" Residue "V ARG 145": "NH1" <-> "NH2" Residue "V ASP 176": "OD1" <-> "OD2" Residue "V GLU 184": "OE1" <-> "OE2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "V GLU 196": "OE1" <-> "OE2" Residue "V GLU 197": "OE1" <-> "OE2" Residue "V TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 102": "OE1" <-> "OE2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W ASP 115": "OD1" <-> "OD2" Residue "W TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X ASP 95": "OD1" <-> "OD2" Residue "X GLU 111": "OE1" <-> "OE2" Residue "X TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 160": "OD1" <-> "OD2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X ASP 173": "OD1" <-> "OD2" Residue "X GLU 179": "OE1" <-> "OE2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X GLU 193": "OE1" <-> "OE2" Residue "X GLU 209": "OE1" <-> "OE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ASP 222": "OD1" <-> "OD2" Residue "X PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 66": "OE1" <-> "OE2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y GLU 130": "OE1" <-> "OE2" Residue "Y ASP 137": "OD1" <-> "OD2" Residue "Y GLU 150": "OE1" <-> "OE2" Residue "Y ASP 151": "OD1" <-> "OD2" Residue "Y ARG 162": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Y ARG 228": "NH1" <-> "NH2" Residue "Y PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "Z GLU 144": "OE1" <-> "OE2" Residue "0 GLU 88": "OE1" <-> "OE2" Residue "0 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 128": "OE1" <-> "OE2" Residue "0 GLU 136": "OE1" <-> "OE2" Residue "0 GLU 167": "OE1" <-> "OE2" Residue "0 GLU 176": "OE1" <-> "OE2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "1 GLU 39": "OE1" <-> "OE2" Residue "1 GLU 58": "OE1" <-> "OE2" Residue "1 ARG 63": "NH1" <-> "NH2" Residue "2 ARG 49": "NH1" <-> "NH2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "5 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 79": "OD1" <-> "OD2" Residue "5 ARG 80": "NH1" <-> "NH2" Residue "5 TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 95": "OE1" <-> "OE2" Residue "5 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 110": "NH1" <-> "NH2" Residue "5 GLU 115": "OE1" <-> "OE2" Residue "5 GLU 134": "OE1" <-> "OE2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "5 GLU 254": "OE1" <-> "OE2" Residue "5 TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 272": "OD1" <-> "OD2" Residue "5 GLU 281": "OE1" <-> "OE2" Residue "5 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "5 PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 379": "OD1" <-> "OD2" Residue "5 TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 399": "OE1" <-> "OE2" Residue "5 PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 27": "NH1" <-> "NH2" Residue "6 ARG 28": "NH1" <-> "NH2" Residue "6 ASP 55": "OD1" <-> "OD2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 58": "NH1" <-> "NH2" Residue "6 ARG 60": "NH1" <-> "NH2" Residue "6 ARG 72": "NH1" <-> "NH2" Residue "6 ARG 136": "NH1" <-> "NH2" Residue "6 GLU 138": "OE1" <-> "OE2" Residue "6 TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 ASP 160": "OD1" <-> "OD2" Residue "6 GLU 181": "OE1" <-> "OE2" Residue "6 GLU 192": "OE1" <-> "OE2" Residue "6 GLU 207": "OE1" <-> "OE2" Residue "6 ASP 222": "OD1" <-> "OD2" Residue "6 GLU 231": "OE1" <-> "OE2" Residue "6 GLU 247": "OE1" <-> "OE2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 276": "OD1" <-> "OD2" Residue "6 PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 336": "OD1" <-> "OD2" 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 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 46": "OD1" <-> "OD2" Residue "7 GLU 63": "OE1" <-> "OE2" Residue "7 ASP 114": "OD1" <-> "OD2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 217": "OE1" <-> "OE2" Residue "7 GLU 220": "OE1" <-> "OE2" Residue "7 TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 238": "OD1" <-> "OD2" Residue "7 ARG 250": "NH1" <-> "NH2" Residue "7 ASP 259": "OD1" <-> "OD2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "7 TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 100": "OE1" <-> "OE2" Residue "8 GLU 110": "OE1" <-> "OE2" Residue "8 GLU 112": "OE1" <-> "OE2" Residue "8 ASP 134": "OD1" <-> "OD2" Residue "8 ARG 137": "NH1" <-> "NH2" Residue "8 GLU 141": "OE1" <-> "OE2" Residue "8 GLU 148": "OE1" <-> "OE2" Residue "8 GLU 160": "OE1" <-> "OE2" Residue "8 ASP 165": "OD1" <-> "OD2" Residue "8 PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 172": "OE1" <-> "OE2" Residue "9 ARG 25": "NH1" <-> "NH2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 49": "NH1" <-> "NH2" Residue "9 PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 82": "OE1" <-> "OE2" Residue "9 GLU 94": "OE1" <-> "OE2" Residue "9 ASP 103": "OD1" <-> "OD2" Residue "9 GLU 120": "OE1" <-> "OE2" Residue "9 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 41": "OD1" <-> "OD2" Residue "a TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 48": "OE1" <-> "OE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "a GLU 110": "OE1" <-> "OE2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a ARG 131": "NH1" <-> "NH2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a ARG 142": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b ASP 106": "OD1" <-> "OD2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 163": "OE1" <-> "OE2" Residue "c PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "c GLU 244": "OE1" <-> "OE2" Residue "c GLU 254": "OE1" <-> "OE2" Residue "c PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 277": "OD1" <-> "OD2" Residue "c GLU 287": "OE1" <-> "OE2" Residue "c PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 309": "OE1" <-> "OE2" Residue "c TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "d PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "d ASP 175": "OD1" <-> "OD2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 249": "OE1" <-> "OE2" Residue "d TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 78": "OE1" <-> "OE2" Residue "e ASP 86": "OD1" <-> "OD2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e ASP 104": "OD1" <-> "OD2" Residue "e ASP 119": "OD1" <-> "OD2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 139": "OE1" <-> "OE2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "e ASP 167": "OD1" <-> "OD2" Residue "e GLU 182": "OE1" <-> "OE2" Residue "e TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 104": "OE1" <-> "OE2" Residue "f GLU 133": "OE1" <-> "OE2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f GLU 168": "OE1" <-> "OE2" Residue "f GLU 180": "OE1" <-> "OE2" Residue "f GLU 191": "OE1" <-> "OE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g ASP 154": "OD1" <-> "OD2" Residue "g GLU 163": "OE1" <-> "OE2" Residue "h TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 71": "OE1" <-> "OE2" Residue "h GLU 76": "OE1" <-> "OE2" Residue "h ASP 93": "OD1" <-> "OD2" Residue "h ASP 106": "OD1" <-> "OD2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "h ASP 128": "OD1" <-> "OD2" Residue "h PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i GLU 49": "OE1" <-> "OE2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i GLU 87": "OE1" <-> "OE2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "j PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j GLU 83": "OE1" <-> "OE2" Residue "j ARG 94": "NH1" <-> "NH2" Residue "j ARG 103": "NH1" <-> "NH2" Residue "k PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 28": "OE1" <-> "OE2" Residue "k ARG 31": "NH1" <-> "NH2" Residue "k PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 40": "OE1" <-> "OE2" Residue "k PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 77": "NH1" <-> "NH2" Residue "k PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 115": "NH1" <-> "NH2" Residue "l GLU 116": "OE1" <-> "OE2" Residue "l ARG 120": "NH1" <-> "NH2" Residue "l ARG 128": "NH1" <-> "NH2" Residue "l ARG 131": "NH1" <-> "NH2" Residue "m TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 72": "NH1" <-> "NH2" Residue "o ARG 23": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o GLU 57": "OE1" <-> "OE2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o GLU 69": "OE1" <-> "OE2" Residue "p PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 56": "OD1" <-> "OD2" Residue "p ASP 74": "OD1" <-> "OD2" Residue "p PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 113": "OE1" <-> "OE2" Residue "p GLU 132": "OE1" <-> "OE2" Residue "p ASP 149": "OD1" <-> "OD2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 80": "OE1" <-> "OE2" Residue "q GLU 88": "OE1" <-> "OE2" Residue "q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r GLU 110": "OE1" <-> "OE2" Residue "r ARG 132": "NH1" <-> "NH2" Residue "r ARG 153": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s ARG 158": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s ARG 162": "NH1" <-> "NH2" Residue "s TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 212": "NH1" <-> "NH2" Residue "s ARG 219": "NH1" <-> "NH2" Residue "s ARG 222": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s ARG 230": "NH1" <-> "NH2" Residue "s ARG 242": "NH1" <-> "NH2" Residue "s ASP 269": "OD1" <-> "OD2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s GLU 279": "OE1" <-> "OE2" Residue "s PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 304": "OD1" <-> "OD2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s GLU 309": "OE1" <-> "OE2" Residue "s PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 384": "OD1" <-> "OD2" Residue "s ARG 389": "NH1" <-> "NH2" Residue "s TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 407": "OD1" <-> "OD2" Residue "u PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 95": "OD1" <-> "OD2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 154": "OD1" <-> "OD2" Residue "u ASP 165": "OD1" <-> "OD2" Residue "u ASP 171": "OD1" <-> "OD2" Residue "u GLU 186": "OE1" <-> "OE2" Residue "u TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 14": "NH1" <-> "NH2" Residue "v ARG 24": "NH1" <-> "NH2" Residue "v ARG 28": "NH1" <-> "NH2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v GLU 52": "OE1" <-> "OE2" Residue "v GLU 56": "OE1" <-> "OE2" Residue "w ASP 94": "OD1" <-> "OD2" Residue "w ASP 111": "OD1" <-> "OD2" Residue "w GLU 123": "OE1" <-> "OE2" Residue "w ASP 124": "OD1" <-> "OD2" Residue "w GLU 125": "OE1" <-> "OE2" Residue "w ASP 134": "OD1" <-> "OD2" Residue "w GLU 143": "OE1" <-> "OE2" Residue "w ASP 146": "OD1" <-> "OD2" Residue "x PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 58": "OD1" <-> "OD2" Residue "x GLU 70": "OE1" <-> "OE2" Residue "x TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 101": "OE1" <-> "OE2" Residue "x PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 154": "OE1" <-> "OE2" Residue "x TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 159": "OD1" <-> "OD2" Residue "x GLU 224": "OE1" <-> "OE2" Residue "x GLU 243": "OE1" <-> "OE2" Residue "x GLU 245": "OE1" <-> "OE2" Residue "x TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 250": "OD1" <-> "OD2" Residue "x GLU 267": "OE1" <-> "OE2" Residue "x GLU 268": "OE1" <-> "OE2" Residue "x PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 318": "OE1" <-> "OE2" Residue "x GLU 326": "OE1" <-> "OE2" Residue "x ASP 340": "OD1" <-> "OD2" Residue "x PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 203": "OE1" <-> "OE2" Residue "y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 225": "OE1" <-> "OE2" Residue "y PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 269": "OE1" <-> "OE2" Residue "y TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 278": "OD1" <-> "OD2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 100859 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 29374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1383, 29374 Classifications: {'RNA': 1383} Modifications used: {'rna3p_pyr': 547, 'rna2p_pur': 151, 'rna3p_pur': 583, 'rna2p_pyr': 102} Link IDs: {'rna3p': 1130, 'rna2p': 252} 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: {'rna3p_pyr': 26, 'rna2p_pur': 1, 'rna3p_pur': 29} Link IDs: {'rna3p': 54, 'rna2p': 1} Chain breaks: 4 Chain: "D" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1692 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain: "E" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2365 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 24, 'CIS': 1, 'TRANS': 274} Chain breaks: 1 Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 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, 'CIS': 1, 'TRANS': 129} 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: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1080 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 126, 'PCIS': 1} Chain breaks: 1 Chain: "Q" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1822 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 14, 'TRANS': 204} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'CIS': 1, 'TRANS': 135} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 145, 'PCIS': 1} Chain: "T" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1368 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "U" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 922 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "V" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1551 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 15, 'CIS': 1, 'TRANS': 172} Chain breaks: 2 Chain: "W" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "X" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2027 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 17, 'TRANS': 225} Chain: "Y" Number of atoms: 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: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 376 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 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: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3064 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 30, 'CIS': 2, 'TRANS': 342, 'PCIS': 1} Chain breaks: 3 Chain: "6" Number of atoms: 2636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2636 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 30, 'CIS': 2, 'TRANS': 292} Chain breaks: 5 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "7" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2158 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 15, 'CIS': 1, 'TRANS': 249} Chain breaks: 3 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: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain breaks: 1 Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 10, 'TRANS': 71} Chain breaks: 1 Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 15, 'TRANS': 258, 'PCIS': 1} Chain breaks: 1 Chain: "d" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1347 Classifications: {'peptide': 162} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 148, 'PCIS': 1} Chain breaks: 2 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: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1039 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 2 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 13, 'TRANS': 113, 'PCIS': 2} Chain: "h" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 91} 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: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 655 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'CIS': 1, 'TRANS': 80} 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: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 797 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 Chain: "q" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1002 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 14, 'TRANS': 104} 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: "x" Number of atoms: 2701 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 342, 2669 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 323, 'PCIS': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 342, 2669 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 323, 'PCIS': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2692 Chain: "y" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1602 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 196} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 114 Unusual residues: {' MG': 72} Classifications: {'undetermined': 72, 'RNA': 2} Modifications used: {'rna3p_pyr': 1, 'rna2p_pur': 1} Link IDs: {None: 71, 'MG-O1P': 1, 'rna3p': 1} Not linked: pdbres=" MG A1601 " pdbres=" MG A1602 " Not linked: pdbres=" MG A1602 " pdbres=" MG A1603 " Not linked: pdbres=" MG A1603 " pdbres=" MG A1604 " Not linked: pdbres=" MG A1604 " pdbres=" MG A1605 " Not linked: pdbres=" MG A1605 " pdbres=" MG A1606 " ... (remaining 66 not shown) Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "x" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Modifications used: {'COO': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 90230 SG CYS r 70 145.046 98.641 61.720 1.00 23.65 S ATOM 90545 SG CYS r 108 143.172 100.806 62.525 1.00 16.96 S ATOM 62213 SG CYS 0 123 161.725 86.962 174.535 1.00 4.82 S ATOM 62236 SG CYS 0 126 163.491 86.870 177.978 1.00 4.82 S ATOM 64450 SG CYS 4 76 144.704 136.406 75.448 1.00 31.71 S ATOM 64473 SG CYS 4 79 144.511 132.737 76.471 1.00 26.59 S ATOM 64597 SG CYS 4 92 147.730 134.608 76.964 1.00 23.29 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N SAM x 401 " occ=0.99 ... (25 atoms not shown) pdb=" O4* SAM x 401 " occ=0.99 Time building chain proxies: 44.83, per 1000 atoms: 0.44 Number of scatterers: 100859 At special positions: 0 Unit cell: (211.38, 223.304, 254.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Se 2 33.99 Zn 3 29.99 S 306 16.00 P 1442 15.00 Mg 76 11.99 O 22205 8.00 N 18329 7.00 C 58496 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 34.58 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" ND1 HIS 0 115 " pdb=" ZN 4 200 " pdb="ZN ZN 4 200 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN I 301 " - pdb=" SG CYS r 108 " Number of angles added : 3 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16268 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 291 helices and 75 sheets defined 43.0% alpha, 13.3% beta 394 base pairs and 799 stacking pairs defined. Time for finding SS restraints: 41.22 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 'D' and resid 249 through 254 removed outlier: 6.296A pdb=" N ASN D 253 " --> pdb=" O VAL D 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 4.803A 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 153 through 158 removed outlier: 5.748A pdb=" N ALA E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'F' and resid 92 through 108 removed outlier: 4.691A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 6.540A pdb=" N ARG F 121 " --> pdb=" O ARG F 117 " (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: 4.860A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 4.899A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'H' and resid 74 through 80 removed outlier: 5.971A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'H' and resid 133 through 147 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 93 Processing helix chain 'I' and resid 105 through 120 Processing helix chain 'I' and resid 127 through 139 Proline residue: I 133 - end of helix Processing helix chain 'I' and resid 142 through 147 removed outlier: 4.564A pdb=" N LEU I 146 " --> pdb=" O ASN I 142 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 142 through 147' 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: 4.822A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 Processing helix chain 'J' and resid 86 through 96 Processing helix chain 'J' and resid 113 through 128 removed outlier: 4.660A pdb=" N ASP J 127 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLU J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) 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 40 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: 4.491A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 Processing helix chain 'K' and resid 154 through 159 removed outlier: 5.006A pdb=" N THR K 159 " --> pdb=" O LEU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 167 Proline residue: K 167 - end of helix Processing helix chain 'L' and resid 44 through 49 Processing helix chain 'L' and resid 125 through 131 removed outlier: 4.173A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 removed outlier: 4.800A pdb=" N LEU L 138 " --> pdb=" O TYR L 134 " (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 79 Proline residue: M 79 - end of helix 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 215 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 69 through 74 removed outlier: 5.054A pdb=" N GLY N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 170 through 184 removed outlier: 4.997A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Proline residue: N 184 - end of helix 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: 5.011A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 66 Processing helix chain 'O' and resid 69 through 81 removed outlier: 5.370A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 98 Proline residue: O 87 - end of helix Proline residue: O 95 - end of helix Processing helix chain 'O' and resid 143 through 160 Processing helix chain 'P' and resid 53 through 59 Processing helix chain 'P' and resid 108 through 113 removed outlier: 5.938A pdb=" N LYS P 112 " --> pdb=" O GLU P 108 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS P 113 " --> pdb=" O TRP P 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 108 through 113' Processing helix chain 'P' and resid 120 through 139 Processing helix chain 'P' and resid 148 through 155 removed outlier: 5.861A pdb=" N ASP P 155 " --> pdb=" O GLU P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 168 Processing helix chain 'Q' and resid 77 through 82 Proline residue: Q 82 - end of helix Processing helix chain 'Q' and resid 88 through 106 Processing helix chain 'Q' and resid 187 through 193 removed outlier: 4.800A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 Processing helix chain 'Q' and resid 244 through 249 Processing helix chain 'Q' and resid 250 through 268 removed outlier: 5.889A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Proline residue: Q 263 - end of helix Processing helix chain 'Q' and resid 275 through 292 Processing helix chain 'R' and resid 16 through 29 Processing helix chain 'R' and resid 46 through 80 removed outlier: 4.447A 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 'T' and resid 49 through 57 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 'V' and resid 28 through 36 Proline residue: V 36 - end of helix 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 7 through 19 removed outlier: 4.716A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 25 Proline residue: X 25 - end of helix Processing helix chain 'X' and resid 26 through 35 Processing helix chain 'X' and resid 72 through 79 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: 4.691A 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: 4.901A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 94 removed outlier: 5.124A 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 Processing helix chain 'Y' and resid 191 through 198 removed outlier: 5.228A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 238 removed outlier: 4.556A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 47 Processing helix chain 'Z' and resid 49 through 57 Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 114 Processing helix chain '0' and resid 86 through 95 Processing helix chain '0' and resid 124 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: 5.523A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 138 through 146 Processing helix chain '3' and resid 151 through 163 removed outlier: 5.216A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 5.062A pdb=" N ASP 3 182 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 4.866A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 53 removed outlier: 4.272A 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 141 Processing helix chain '5' and resid 150 through 163 Processing helix chain '5' and resid 172 through 196 Proline residue: 5 178 - end of helix removed outlier: 5.903A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.280A 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: 4.854A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 5.192A pdb=" N LEU 5 304 " --> pdb=" O ARG 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 329 Processing helix chain '5' and resid 407 through 420 removed outlier: 4.675A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 5.319A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 removed outlier: 5.068A 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 118 Processing helix chain '6' and resid 131 through 143 Processing helix chain '6' and resid 144 through 156 Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 244 through 249 Processing helix chain '6' and resid 292 through 297 Processing helix chain '6' and resid 299 through 307 Processing helix chain '6' and resid 324 through 333 Processing helix chain '6' and resid 362 through 370 removed outlier: 4.670A pdb=" N LEU 6 366 " --> pdb=" O PRO 6 362 " (cutoff:3.500A) Processing helix chain '6' and resid 157 through 163 Processing helix chain '7' and resid 36 through 59 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 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 Processing helix chain '7' and resid 271 through 276 removed outlier: 5.161A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 91 through 98 Processing helix chain '8' and resid 107 through 154 Processing helix chain '8' and resid 155 through 164 removed outlier: 5.358A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 166 through 171 Proline residue: 8 170 - end of helix No H-bonds generated for 'chain '8' and resid 166 through 171' Processing helix chain '9' and resid 27 through 35 removed outlier: 4.781A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 Proline residue: 9 58 - end of helix Processing helix chain '9' and resid 87 through 103 Proline residue: 9 98 - end of helix Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 119 through 125 Proline residue: a 125 - end of helix Processing helix chain 'a' and resid 127 through 134 Processing helix chain 'b' and resid 16 through 21 Processing helix chain 'b' and resid 37 through 50 removed outlier: 5.021A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.107A 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 108 removed outlier: 5.587A pdb=" N SER b 108 " --> pdb=" O LEU b 104 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 53 removed outlier: 5.039A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 59 through 64 Proline residue: c 64 - end of helix Processing helix chain 'c' and resid 67 through 80 Processing helix chain 'c' and resid 84 through 94 removed outlier: 5.731A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 107 Processing helix chain 'c' and resid 123 through 146 Proline residue: c 146 - end of helix Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 163 through 174 Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 225 removed outlier: 4.973A pdb=" N GLY c 225 " --> pdb=" O THR c 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 Processing helix chain 'c' and resid 236 through 249 Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 117 through 130 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 177 Proline residue: d 170 - end of helix removed outlier: 5.578A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE d 176 " --> pdb=" O MET d 172 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 85 through 104 Processing helix chain 'e' and resid 116 through 132 removed outlier: 5.616A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 137 through 143 removed outlier: 4.964A pdb=" N ASP e 141 " --> pdb=" O ILE e 137 " (cutoff:3.500A) removed outlier: 5.353A 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 256 through 264 Processing helix chain 'e' and resid 266 through 277 removed outlier: 5.665A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 58 through 64 removed outlier: 5.817A pdb=" N LEU f 62 " --> pdb=" O LYS f 58 " (cutoff:3.500A) removed outlier: 4.970A 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 44 through 53 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 66 through 78 Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 113 through 121 removed outlier: 5.169A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 5.042A 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 147 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: 6.132A 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 25 through 32 removed outlier: 4.600A pdb=" N LEU j 29 " --> pdb=" O GLY j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 41 through 46 Processing helix chain 'j' and resid 60 through 108 removed outlier: 4.914A pdb=" N ALA j 108 " --> pdb=" O LYS j 104 " (cutoff:3.500A) Processing helix chain 'k' and resid 27 through 36 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 Processing helix chain 'm' and resid 34 through 40 removed outlier: 4.887A pdb=" N ALA m 38 " --> pdb=" O ASP m 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 52 Proline residue: o 52 - end of helix Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 63 through 81 Processing helix chain 'o' and resid 87 through 98 removed outlier: 5.122A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (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 removed outlier: 4.111A pdb=" N ALA p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 77 removed outlier: 5.134A pdb=" N THR p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) Processing helix chain 'p' and resid 112 through 124 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 Processing helix chain 'q' and resid 54 through 65 Processing helix chain 'q' and resid 71 through 77 Proline residue: q 77 - end of helix Processing helix chain 'q' and resid 78 through 93 Processing helix chain 'q' and resid 95 through 143 Proline residue: q 129 - end of helix 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: 4.671A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ASP r 183 " --> pdb=" O PRO r 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 178 through 183' Processing helix chain 's' and resid 55 through 73 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 193 removed outlier: 5.091A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLU s 170 " --> pdb=" O TYR s 166 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU s 174 " --> pdb=" O GLU s 170 " (cutoff:3.500A) 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 removed outlier: 4.775A pdb=" N LEU s 271 " --> pdb=" O LYS s 267 " (cutoff:3.500A) Proline residue: s 272 - end of helix No H-bonds generated for 'chain 's' and resid 267 through 272' Processing helix chain 's' and resid 307 through 315 Processing helix chain 's' and resid 318 through 344 Processing helix chain 's' and resid 380 through 387 removed outlier: 5.474A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN s 387 " --> pdb=" O ALA s 383 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 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 197 Processing helix chain 'v' and resid 5 through 23 Processing helix chain 'v' and resid 27 through 42 Processing helix chain 'v' and resid 47 through 64 Processing helix chain 'w' and resid 75 through 91 removed outlier: 5.376A pdb=" N ASP w 91 " --> pdb=" O LEU w 87 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 5.438A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 4.901A 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 'x' and resid 39 through 56 Processing helix chain 'x' and resid 59 through 70 removed outlier: 5.050A pdb=" N GLU x 70 " --> pdb=" O SER x 66 " (cutoff:3.500A) Processing helix chain 'x' and resid 82 through 94 Processing helix chain 'x' and resid 97 through 109 removed outlier: 4.476A pdb=" N GLU x 107 " --> pdb=" O ILE x 103 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU x 108 " --> pdb=" O SER x 104 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN x 109 " --> pdb=" O HIS x 105 " (cutoff:3.500A) Processing helix chain 'x' and resid 120 through 125 Processing helix chain 'x' and resid 159 through 170 Proline residue: x 165 - end of helix Processing helix chain 'x' and resid 185A through 195 Processing helix chain 'x' and resid 206 through 221 Processing helix chain 'x' and resid 222 through 227 removed outlier: 4.635A pdb=" N ASP x 227 " --> pdb=" O GLU x 223 " (cutoff:3.500A) Processing helix chain 'x' and resid 240 through 245 Processing helix chain 'x' and resid 260 through 267 Processing helix chain 'x' and resid 274 through 300 removed outlier: 3.504A pdb=" N LYS x 278 " --> pdb=" O LYS x 274 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS x 279 " --> pdb=" O ARG x 275 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU x 280 " --> pdb=" O SER x 276 " (cutoff:3.500A) Proline residue: x 285 - end of helix removed outlier: 5.359A pdb=" N LYS x 300 " --> pdb=" O LEU x 296 " (cutoff:3.500A) Processing helix chain 'x' and resid 313 through 331 removed outlier: 5.135A pdb=" N VAL x 320 " --> pdb=" O GLN x 316 " (cutoff:3.500A) Processing helix chain 'x' and resid 341 through 350 Processing helix chain 'y' and resid 122 through 135 Processing helix chain 'y' and resid 137 through 148 removed outlier: 4.984A pdb=" N SER y 148 " --> pdb=" O VAL y 144 " (cutoff:3.500A) Processing helix chain 'y' and resid 149 through 155 Proline residue: y 155 - end of helix Processing helix chain 'y' and resid 156 through 170 Processing helix chain 'y' and resid 173 through 183 removed outlier: 6.681A pdb=" N LYS y 177 " --> pdb=" O GLU y 173 " (cutoff:3.500A) Processing helix chain 'y' and resid 184 through 189 Processing helix chain 'y' and resid 190 through 203 Processing helix chain 'y' and resid 208 through 219 Processing helix chain 'y' and resid 220 through 226 removed outlier: 4.881A pdb=" N ASP y 226 " --> pdb=" O VAL y 222 " (cutoff:3.500A) Processing helix chain 'y' and resid 227 through 239 removed outlier: 6.333A pdb=" N GLU y 231 " --> pdb=" O LEU y 227 " (cutoff:3.500A) Processing helix chain 'y' and resid 244 through 252 removed outlier: 5.031A pdb=" N GLU y 252 " --> pdb=" O ILE y 248 " (cutoff:3.500A) Processing helix chain 'y' and resid 257 through 272 Processing helix chain 'y' and resid 289 through 294 Processing helix chain 'y' and resid 297 through 305 Processing helix chain 'y' and resid 309 through 328 Processing sheet with id= 1, first strand: chain 'D' and resid 121 through 126 removed outlier: 4.507A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 128 through 131 removed outlier: 4.794A pdb=" N ASP D 138 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 191 through 194 removed outlier: 6.886A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 98 through 101 Processing sheet with id= 5, first strand: chain 'E' and resid 105 through 111 removed outlier: 5.791A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 131 through 135 removed outlier: 7.238A pdb=" N MET E 142 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 143 through 149 removed outlier: 6.338A pdb=" N THR E 175 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 201 through 205 Processing sheet with id= 9, first strand: chain 'F' and resid 61 through 67 Processing sheet with id= 10, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 11, first strand: chain 'H' and resid 53 through 56 removed outlier: 4.725A pdb=" N THR H 53 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU H 84 " --> pdb=" O ILE H 55 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 109 through 113 removed outlier: 3.773A pdb=" N ASP H 110 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 94 through 100 Processing sheet with id= 14, first strand: chain 'J' and resid 18 through 24 removed outlier: 4.500A pdb=" N LYS J 81 " --> pdb=" O LYS J 69 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'K' and resid 17 through 22 Processing sheet with id= 16, first strand: chain 'K' and resid 77 through 81 removed outlier: 4.779A pdb=" N GLY K 86 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 55 through 58 removed outlier: 4.208A pdb=" N THR L 36 " --> pdb=" O CYS L 57 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN L 103 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 19, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 20, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 21, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.688A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'N' and resid 128 through 132 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'O' and resid 41 through 45 Processing sheet with id= 24, first strand: chain 'P' and resid 78 through 84 removed outlier: 6.677A pdb=" N VAL P 89 " --> pdb=" O THR P 106 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Q' and resid 130 through 135 removed outlier: 6.514A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Q' and resid 139 through 142 Processing sheet with id= 27, first strand: chain 'S' and resid 105 through 109 removed outlier: 7.475A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'S' and resid 111 through 117 removed outlier: 6.443A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 153 through 157 removed outlier: 5.727A pdb=" N LEU S 153 " --> pdb=" O ALA S 201 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER S 197 " --> pdb=" O GLU S 157 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S' and resid 162 through 165 Processing sheet with id= 31, first strand: chain 'S' and resid 168 through 175 Processing sheet with id= 32, first strand: chain 'T' and resid 71 through 78 removed outlier: 5.004A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'U' and resid 26 through 29 removed outlier: 4.318A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'V' and resid 62 through 65 Processing sheet with id= 35, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.836A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'W' and resid 81 through 84 removed outlier: 5.045A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 97 through 103 Processing sheet with id= 38, first strand: chain 'X' and resid 85 through 92 removed outlier: 7.077A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 40, first strand: chain 'Z' and resid 97 through 101 removed outlier: 4.550A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '0' and resid 155 through 159 Processing sheet with id= 42, first strand: chain '1' and resid 29 through 34 removed outlier: 6.377A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '3' and resid 122 through 125 removed outlier: 5.573A pdb=" N TRP 3 122 " --> pdb=" O CYS 3 150 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '4' and resid 88 through 91 removed outlier: 6.970A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '5' and resid 104 through 108 Processing sheet with id= 46, first strand: chain '5' and resid 126 through 130 removed outlier: 4.923A pdb=" N HIS 5 353 " --> pdb=" O GLY 5 346 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N ARG 5 200 " --> pdb=" O LYS 5 233 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '5' and resid 230 through 233 removed outlier: 6.773A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '6' and resid 183 through 187 Processing sheet with id= 49, first strand: chain '6' and resid 235 through 238 removed outlier: 6.263A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N THR 6 310 " --> pdb=" O ASP 6 276 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '6' and resid 265 through 272 Processing sheet with id= 51, first strand: chain '7' and resid 76 through 82 removed outlier: 5.548A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '7' and resid 178 through 184 removed outlier: 6.896A pdb=" N GLN 7 298 " --> pdb=" O SER 7 281 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain '7' and resid 217 through 221 removed outlier: 4.796A pdb=" N LYS 7 253 " --> pdb=" O SER 7 264 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain '9' and resid 42 through 45 Processing sheet with id= 55, first strand: chain 'a' and resid 44 through 52 removed outlier: 6.000A pdb=" N ASN a 44 " --> pdb=" O VAL a 65 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN a 46 " --> pdb=" O PRO a 63 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'b' and resid 61 through 67 removed outlier: 6.309A pdb=" N VAL b 75 " --> pdb=" O GLU b 86 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA b 77 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR b 79 " --> pdb=" O GLY b 82 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 58, first strand: chain 'c' and resid 269 through 275 Processing sheet with id= 59, first strand: chain 'd' and resid 192 through 195 removed outlier: 6.986A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL d 247 " --> pdb=" O HIS d 262 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'd' and resid 244 through 247 Processing sheet with id= 61, first strand: chain 'e' and resid 198 through 201 Processing sheet with id= 62, first strand: chain 'e' and resid 211 through 217 removed outlier: 5.604A pdb=" N LEU e 227 " --> pdb=" O PHE e 217 " (cutoff:3.500A) removed outlier: 15.177A pdb=" N GLY e 49 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 13.370A pdb=" N GLU e 163 " --> pdb=" O GLY e 49 " (cutoff:3.500A) removed outlier: 11.503A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'f' and resid 78 through 81 removed outlier: 7.781A pdb=" N ARG f 78 " --> pdb=" O GLY f 89 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY f 89 " --> pdb=" O ARG f 78 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'f' and resid 123 through 131 removed outlier: 5.177A pdb=" N GLU f 123 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR f 152 " --> pdb=" O THR f 129 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU f 150 " --> pdb=" O THR f 131 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.957A pdb=" N ARG g 105 " --> pdb=" O THR g 101 " (cutoff:3.500A) removed outlier: 5.414A 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 55 removed outlier: 5.160A pdb=" N SER k 50 " --> pdb=" O LYS k 14 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE k 68 " --> pdb=" O HIS k 72 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'm' and resid 63 through 67 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 removed outlier: 6.507A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 's' and resid 213 through 217 removed outlier: 4.752A pdb=" N GLY s 213 " --> pdb=" O LEU s 229 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG s 225 " --> pdb=" O ILE s 217 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET s 89 " --> pdb=" O ASP s 228 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG s 230 " --> pdb=" O MET s 89 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE s 274 " --> pdb=" O MET s 92 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'u' and resid 107 through 114 removed outlier: 4.896A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'x' and resid 130 through 133 removed outlier: 5.292A pdb=" N ARG x 130 " --> pdb=" O VAL x 77 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'x' and resid 198 through 203 removed outlier: 6.860A pdb=" N ASP x 255 " --> pdb=" O LEU x 180 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ASP x 250 " --> pdb=" O GLY x 302 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N CYS x 310 " --> pdb=" O VAL x 256 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN x 335 " --> pdb=" O LEU x 383 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'x' and resid 361 through 365 3052 hydrogen bonds defined for protein. 8991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 960 hydrogen bonds 1652 hydrogen bond angles 0 basepair planarities 394 basepair parallelities 799 stacking parallelities Total time for adding SS restraints: 57.85 Time building geometry restraints manager: 37.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 23968 1.33 - 1.49: 44996 1.49 - 1.64: 36622 1.64 - 1.80: 326 1.80 - 1.95: 161 Bond restraints: 106073 Sorted by residual: bond pdb=" CA THR f 50 " pdb=" C THR f 50 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.41e-02 5.03e+03 2.37e+01 bond pdb=" N9 A A 158 " pdb=" C4 A A 158 " ideal model delta sigma weight residual 1.374 1.284 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CB ASP R 16 " pdb=" CG ASP R 16 " ideal model delta sigma weight residual 1.516 1.416 0.100 2.50e-02 1.60e+03 1.60e+01 bond pdb=" CB VAL T 209 " pdb=" CG2 VAL T 209 " ideal model delta sigma weight residual 1.521 1.393 0.128 3.30e-02 9.18e+02 1.51e+01 bond pdb=" CB VAL M 141 " pdb=" CG1 VAL M 141 " ideal model delta sigma weight residual 1.521 1.397 0.124 3.30e-02 9.18e+02 1.42e+01 ... (remaining 106068 not shown) Histogram of bond angle deviations from ideal: 93.38 - 102.89: 3549 102.89 - 112.40: 59468 112.40 - 121.91: 64567 121.91 - 131.42: 21974 131.42 - 140.93: 734 Bond angle restraints: 150292 Sorted by residual: angle pdb=" N VAL 7 304 " pdb=" CA VAL 7 304 " pdb=" C VAL 7 304 " ideal model delta sigma weight residual 110.05 99.97 10.08 1.09e+00 8.42e-01 8.55e+01 angle pdb=" N ILE M 76 " pdb=" CA ILE M 76 " pdb=" C ILE M 76 " ideal model delta sigma weight residual 113.53 104.73 8.80 9.80e-01 1.04e+00 8.07e+01 angle pdb=" C GLN Z 61 " pdb=" N ASN Z 62 " pdb=" CA ASN Z 62 " ideal model delta sigma weight residual 121.80 140.93 -19.13 2.44e+00 1.68e-01 6.15e+01 angle pdb=" CA ARG v 14 " pdb=" CB ARG v 14 " pdb=" CG ARG v 14 " ideal model delta sigma weight residual 114.10 128.97 -14.87 2.00e+00 2.50e-01 5.53e+01 angle pdb=" C ASP h 136 " pdb=" N ARG h 137 " pdb=" CA ARG h 137 " ideal model delta sigma weight residual 121.54 134.79 -13.25 1.91e+00 2.74e-01 4.81e+01 ... (remaining 150287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 58865 35.96 - 71.91: 2064 71.91 - 107.87: 169 107.87 - 143.82: 13 143.82 - 179.78: 41 Dihedral angle restraints: 61152 sinusoidal: 36041 harmonic: 25111 Sorted by residual: dihedral pdb=" CA GLU R 137 " pdb=" C GLU R 137 " pdb=" N PRO R 138 " pdb=" CA PRO R 138 " ideal model delta harmonic sigma weight residual -180.00 -130.53 -49.47 0 5.00e+00 4.00e-02 9.79e+01 dihedral pdb=" CA LYS Q 227 " pdb=" C LYS Q 227 " pdb=" N PRO Q 228 " pdb=" CA PRO Q 228 " ideal model delta harmonic sigma weight residual 180.00 133.54 46.46 0 5.00e+00 4.00e-02 8.64e+01 dihedral pdb=" O4' U A1228 " pdb=" C1' U A1228 " pdb=" N1 U A1228 " pdb=" C2 U A1228 " ideal model delta sinusoidal sigma weight residual -160.00 19.78 -179.78 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 61149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 17210 0.174 - 0.349: 389 0.349 - 0.523: 14 0.523 - 0.697: 3 0.697 - 0.871: 2 Chirality restraints: 17618 Sorted by residual: chirality pdb=" CB VAL E 218 " pdb=" CA VAL E 218 " pdb=" CG1 VAL E 218 " pdb=" CG2 VAL E 218 " both_signs ideal model delta sigma weight residual False -2.63 -1.76 -0.87 2.00e-01 2.50e+01 1.90e+01 chirality pdb=" CG LEU R 10 " pdb=" CB LEU R 10 " pdb=" CD1 LEU R 10 " pdb=" CD2 LEU R 10 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 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 -1.99 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 17615 not shown) Planarity restraints: 13942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 1 " -0.070 2.00e-02 2.50e+03 2.95e-02 2.61e+01 pdb=" N9 G A 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 G A 1 " 0.018 2.00e-02 2.50e+03 pdb=" N7 G A 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 1 " -0.006 2.00e-02 2.50e+03 pdb=" C6 G A 1 " -0.025 2.00e-02 2.50e+03 pdb=" O6 G A 1 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G A 1 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G A 1 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G A 1 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G A 1 " 0.019 2.00e-02 2.50e+03 pdb=" C4 G A 1 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 619 " -0.062 2.00e-02 2.50e+03 2.70e-02 2.19e+01 pdb=" N9 G A 619 " 0.039 2.00e-02 2.50e+03 pdb=" C8 G A 619 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G A 619 " 0.014 2.00e-02 2.50e+03 pdb=" C5 G A 619 " 0.022 2.00e-02 2.50e+03 pdb=" C6 G A 619 " -0.032 2.00e-02 2.50e+03 pdb=" O6 G A 619 " -0.014 2.00e-02 2.50e+03 pdb=" N1 G A 619 " -0.021 2.00e-02 2.50e+03 pdb=" C2 G A 619 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A 619 " 0.020 2.00e-02 2.50e+03 pdb=" N3 G A 619 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G A 619 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1027 " 0.063 2.00e-02 2.50e+03 2.67e-02 2.14e+01 pdb=" N9 G A1027 " -0.061 2.00e-02 2.50e+03 pdb=" C8 G A1027 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A1027 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G A1027 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G A1027 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A1027 " 0.022 2.00e-02 2.50e+03 pdb=" N1 G A1027 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G A1027 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A1027 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G A1027 " -0.014 2.00e-02 2.50e+03 pdb=" C4 G A1027 " -0.005 2.00e-02 2.50e+03 ... (remaining 13939 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 774 2.51 - 3.11: 68712 3.11 - 3.71: 172933 3.71 - 4.30: 253334 4.30 - 4.90: 383920 Nonbonded interactions: 879673 Sorted by model distance: nonbonded pdb=" O4 U A 805 " pdb="MG MG A1634 " model vdw 1.916 2.170 nonbonded pdb=" OP1 A A 291 " pdb="MG MG A1615 " model vdw 1.963 2.170 nonbonded pdb=" OP1 C A 430 " pdb="MG MG A1649 " model vdw 1.976 2.170 nonbonded pdb=" OP2 A A 580 " pdb="MG MG A1614 " model vdw 1.989 2.170 nonbonded pdb=" O6 G A1264 " pdb="MG MG A1672 " model vdw 1.991 2.170 ... (remaining 879668 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 Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Se 2 7.20 5 Zn 3 6.06 5 P 1442 5.49 5 Mg 76 5.21 5 S 306 5.16 5 C 58496 2.51 5 N 18329 2.21 5 O 22205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 16.570 Check model and map are aligned: 1.150 Convert atoms to be neutral: 0.680 Process input model: 271.460 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 300.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.014 0.142 106073 Z= 0.871 Angle : 1.271 21.256 150292 Z= 0.648 Chirality : 0.070 0.871 17618 Planarity : 0.009 0.108 13942 Dihedral : 17.048 179.779 44884 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.74 % Favored : 92.19 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.14 % Twisted Proline : 0.72 % Twisted General : 0.29 % 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: -1.98 (0.08), residues: 8444 helix: -0.63 (0.08), residues: 3216 sheet: -1.07 (0.15), residues: 1065 loop : -1.93 (0.09), residues: 4163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1065 time to evaluate : 7.116 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 outliers start: 6 outliers final: 0 residues processed: 1069 average time/residue: 0.9419 time to fit residues: 1686.8852 Evaluate side-chains 932 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 932 time to evaluate : 7.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.2789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 825 optimal weight: 1.9990 chunk 741 optimal weight: 20.0000 chunk 411 optimal weight: 0.7980 chunk 253 optimal weight: 50.0000 chunk 500 optimal weight: 1.9990 chunk 396 optimal weight: 5.9990 chunk 766 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 466 optimal weight: 3.9990 chunk 570 optimal weight: 3.9990 chunk 888 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN M 219 ASN ** N 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 GLN P 141 ASN P 146 GLN ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN R 89 ASN T 210 HIS U 77 ASN X 175 GLN ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 5 206 ASN ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN 9 123 GLN a 137 ASN c 48 GLN ** c 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 87 HIS ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 115 ASN h 118 HIS ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 423 HIS ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 106073 Z= 0.232 Angle : 0.728 16.005 150292 Z= 0.368 Chirality : 0.042 0.304 17618 Planarity : 0.006 0.078 13942 Dihedral : 15.671 179.156 26846 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.67 % Favored : 93.28 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.15 % Twisted Proline : 0.72 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.09), residues: 8444 helix: 0.27 (0.09), residues: 3237 sheet: -0.93 (0.15), residues: 1045 loop : -1.71 (0.09), residues: 4162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1048 time to evaluate : 7.117 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 outliers start: 79 outliers final: 48 residues processed: 1084 average time/residue: 0.9536 time to fit residues: 1736.8314 Evaluate side-chains 992 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 944 time to evaluate : 7.055 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.7054 time to fit residues: 73.5438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 493 optimal weight: 0.9990 chunk 275 optimal weight: 9.9990 chunk 739 optimal weight: 7.9990 chunk 604 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 889 optimal weight: 0.7980 chunk 961 optimal weight: 9.9990 chunk 792 optimal weight: 1.9990 chunk 882 optimal weight: 10.0000 chunk 303 optimal weight: 0.0020 chunk 713 optimal weight: 4.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN I 43 GLN I 45 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN L 33 GLN ** N 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 141 ASN P 146 GLN Q 261 ASN R 77 GLN T 62 GLN U 62 ASN X 175 GLN ** Y 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 77 GLN 5 206 ASN ** 5 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 147 HIS ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN ** c 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 236 ASN d 149 HIS ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 33 GLN ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 423 HIS ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 106073 Z= 0.185 Angle : 0.653 17.437 150292 Z= 0.329 Chirality : 0.040 0.324 17618 Planarity : 0.005 0.078 13942 Dihedral : 15.353 179.962 26846 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.38 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.15 % Twisted Proline : 0.54 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.09), residues: 8444 helix: 0.77 (0.09), residues: 3243 sheet: -0.80 (0.15), residues: 1069 loop : -1.51 (0.09), residues: 4132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1017 time to evaluate : 7.183 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 outliers start: 70 outliers final: 32 residues processed: 1055 average time/residue: 0.9649 time to fit residues: 1708.8660 Evaluate side-chains 983 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 951 time to evaluate : 7.074 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.7346 time to fit residues: 52.9679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 879 optimal weight: 2.9990 chunk 668 optimal weight: 2.9990 chunk 461 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 424 optimal weight: 0.9980 chunk 597 optimal weight: 2.9990 chunk 892 optimal weight: 2.9990 chunk 945 optimal weight: 50.0000 chunk 466 optimal weight: 2.9990 chunk 846 optimal weight: 20.0000 chunk 254 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN M 219 ASN ** N 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 141 ASN S 84 ASN X 89 GLN X 175 GLN 0 118 GLN ** 5 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 147 HIS ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN b 135 ASN c 48 GLN ** c 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 91 GLN s 298 GLN s 358 GLN s 423 HIS ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.005 0.089 106073 Z= 0.305 Angle : 0.692 17.380 150292 Z= 0.348 Chirality : 0.042 0.325 17618 Planarity : 0.006 0.093 13942 Dihedral : 15.318 179.873 26846 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.10 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.15 % Twisted Proline : 0.54 % Twisted General : 0.08 % 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: -0.67 (0.09), residues: 8444 helix: 0.88 (0.09), residues: 3259 sheet: -0.70 (0.15), residues: 1075 loop : -1.49 (0.09), residues: 4110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 977 time to evaluate : 7.144 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 outliers start: 112 outliers final: 68 residues processed: 1036 average time/residue: 0.9554 time to fit residues: 1669.8857 Evaluate side-chains 1004 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 936 time to evaluate : 7.074 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.7020 time to fit residues: 100.2183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 787 optimal weight: 0.0770 chunk 536 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 703 optimal weight: 5.9990 chunk 390 optimal weight: 0.9990 chunk 806 optimal weight: 9.9990 chunk 653 optimal weight: 50.0000 chunk 1 optimal weight: 4.9990 chunk 482 optimal weight: 0.8980 chunk 848 optimal weight: 5.9990 chunk 238 optimal weight: 0.0070 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN I 43 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN M 26 ASN ** N 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN X 175 GLN ** Y 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 31 ASN ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 298 ASN 6 147 HIS a 137 ASN ** c 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 245 GLN ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 GLN s 423 HIS ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.139 106073 Z= 0.167 Angle : 0.626 17.493 150292 Z= 0.315 Chirality : 0.039 0.331 17618 Planarity : 0.005 0.075 13942 Dihedral : 15.161 179.972 26846 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.65 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.15 % Twisted Proline : 0.54 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.09), residues: 8444 helix: 1.13 (0.09), residues: 3256 sheet: -0.69 (0.15), residues: 1052 loop : -1.35 (0.10), residues: 4136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 996 time to evaluate : 7.653 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 outliers start: 89 outliers final: 41 residues processed: 1057 average time/residue: 1.0546 time to fit residues: 1900.6768 Evaluate side-chains 996 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 955 time to evaluate : 7.019 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.8616 time to fit residues: 72.6775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 318 optimal weight: 10.0000 chunk 851 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 555 optimal weight: 0.7980 chunk 233 optimal weight: 10.0000 chunk 946 optimal weight: 6.9990 chunk 785 optimal weight: 5.9990 chunk 438 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 chunk 496 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN H 88 HIS I 43 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN M 219 ASN ** N 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN S 84 ASN T 151 GLN U 74 HIS Y 183 GLN Z 62 ASN 6 147 HIS a 137 ASN b 58 ASN c 48 GLN c 192 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 152 GLN ** r 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 423 HIS ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.141 106073 Z= 0.425 Angle : 0.761 19.212 150292 Z= 0.380 Chirality : 0.046 0.358 17618 Planarity : 0.006 0.096 13942 Dihedral : 15.300 179.112 26846 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.15 % Twisted Proline : 0.36 % Twisted General : 0.08 % 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: -0.57 (0.09), residues: 8444 helix: 0.98 (0.09), residues: 3258 sheet: -0.68 (0.15), residues: 1083 loop : -1.42 (0.10), residues: 4103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 967 time to evaluate : 7.624 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 outliers start: 108 outliers final: 68 residues processed: 1027 average time/residue: 0.9486 time to fit residues: 1645.9908 Evaluate side-chains 1007 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 939 time to evaluate : 7.118 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.7075 time to fit residues: 100.8792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 912 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 539 optimal weight: 0.7980 chunk 691 optimal weight: 0.5980 chunk 535 optimal weight: 3.9990 chunk 796 optimal weight: 0.8980 chunk 528 optimal weight: 9.9990 chunk 942 optimal weight: 30.0000 chunk 589 optimal weight: 0.0040 chunk 574 optimal weight: 0.0030 chunk 435 optimal weight: 0.0470 overall best weight: 0.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 ASN H 121 ASN I 43 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN ** Y 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 183 GLN 5 165 GLN ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 206 ASN 6 359 HIS a 137 ASN c 192 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 423 HIS ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 80 GLN ** x 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.268 106073 Z= 0.164 Angle : 0.633 21.126 150292 Z= 0.318 Chirality : 0.038 0.329 17618 Planarity : 0.005 0.081 13942 Dihedral : 15.079 179.761 26846 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.19 % Favored : 93.78 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.15 % Twisted Proline : 0.54 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.09), residues: 8444 helix: 1.20 (0.09), residues: 3273 sheet: -0.67 (0.15), residues: 1079 loop : -1.27 (0.10), residues: 4092 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1017 time to evaluate : 7.274 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 outliers start: 52 outliers final: 26 residues processed: 1045 average time/residue: 0.9455 time to fit residues: 1666.7746 Evaluate side-chains 992 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 966 time to evaluate : 7.149 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.7159 time to fit residues: 44.4640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 583 optimal weight: 20.0000 chunk 376 optimal weight: 0.7980 chunk 562 optimal weight: 20.0000 chunk 283 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 599 optimal weight: 9.9990 chunk 642 optimal weight: 1.9990 chunk 466 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 740 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN I 43 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 ASN R 77 GLN S 84 ASN U 35 GLN Y 99 HIS Y 183 GLN ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 206 ASN a 137 ASN c 48 GLN c 192 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 72 HIS ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 91 GLN ** r 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 423 HIS ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.151 106073 Z= 0.335 Angle : 0.702 18.148 150292 Z= 0.350 Chirality : 0.043 0.332 17618 Planarity : 0.006 0.082 13942 Dihedral : 15.112 179.955 26846 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.84 % Favored : 93.13 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.15 % Twisted Proline : 0.36 % 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: -0.38 (0.09), residues: 8444 helix: 1.14 (0.09), residues: 3258 sheet: -0.64 (0.15), residues: 1081 loop : -1.31 (0.10), residues: 4105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 961 time to evaluate : 7.172 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 outliers start: 76 outliers final: 45 residues processed: 1002 average time/residue: 0.9792 time to fit residues: 1661.3422 Evaluate side-chains 977 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 932 time to evaluate : 7.204 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.7332 time to fit residues: 71.8315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 857 optimal weight: 1.9990 chunk 903 optimal weight: 8.9990 chunk 823 optimal weight: 0.9980 chunk 878 optimal weight: 4.9990 chunk 902 optimal weight: 0.0270 chunk 528 optimal weight: 0.0470 chunk 382 optimal weight: 0.6980 chunk 689 optimal weight: 40.0000 chunk 269 optimal weight: 0.9990 chunk 793 optimal weight: 0.5980 chunk 830 optimal weight: 10.0000 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN Y 183 GLN ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 206 ASN ** 6 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN c 48 GLN c 192 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 423 HIS ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 1.274 106073 Z= 0.356 Angle : 0.743 106.098 150292 Z= 0.360 Chirality : 0.040 0.444 17618 Planarity : 0.005 0.102 13942 Dihedral : 15.112 179.903 26846 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.86 % Favored : 93.10 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.15 % Twisted Proline : 0.54 % 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: -0.36 (0.09), residues: 8444 helix: 1.15 (0.09), residues: 3265 sheet: -0.65 (0.15), residues: 1079 loop : -1.28 (0.10), residues: 4100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 955 time to evaluate : 7.135 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 outliers start: 38 outliers final: 28 residues processed: 969 average time/residue: 0.9738 time to fit residues: 1596.3249 Evaluate side-chains 969 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 941 time to evaluate : 7.399 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.7228 time to fit residues: 47.9132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 875 optimal weight: 3.9990 chunk 576 optimal weight: 10.0000 chunk 928 optimal weight: 8.9990 chunk 566 optimal weight: 0.4980 chunk 440 optimal weight: 2.9990 chunk 645 optimal weight: 3.9990 chunk 974 optimal weight: 0.6980 chunk 896 optimal weight: 9.9990 chunk 775 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 599 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 ASN R 77 GLN S 84 ASN Y 183 GLN ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 206 ASN ** 6 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN c 48 GLN c 192 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 423 HIS ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 1.274 106073 Z= 0.356 Angle : 0.743 106.098 150292 Z= 0.360 Chirality : 0.040 0.444 17618 Planarity : 0.005 0.102 13942 Dihedral : 15.112 179.903 26846 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.86 % Favored : 93.10 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.15 % Twisted Proline : 0.54 % 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: -0.36 (0.09), residues: 8444 helix: 1.15 (0.09), residues: 3265 sheet: -0.65 (0.15), residues: 1079 loop : -1.28 (0.10), residues: 4100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16888 Ramachandran restraints generated. 8444 Oldfield, 0 Emsley, 8444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 946 time to evaluate : 7.175 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 outliers start: 4 outliers final: 3 residues processed: 948 average time/residue: 0.9810 time to fit residues: 1571.5935 Evaluate side-chains 942 residues out of total 7606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 939 time to evaluate : 7.068 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.7353 time to fit residues: 13.5204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 475 optimal weight: 6.9990 chunk 616 optimal weight: 8.9990 chunk 826 optimal weight: 10.0000 chunk 237 optimal weight: 0.6980 chunk 715 optimal weight: 40.0000 chunk 114 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 777 optimal weight: 4.9990 chunk 325 optimal weight: 10.0000 chunk 797 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN Y 183 GLN Z 62 ASN ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 206 ASN ** 6 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN c 48 GLN c 192 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 423 HIS ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.197707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.153905 restraints weight = 135949.652| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.88 r_work: 0.3450 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 1.274 106073 Z= 0.356 Angle : 0.743 106.098 150292 Z= 0.360 Chirality : 0.040 0.444 17618 Planarity : 0.005 0.102 13942 Dihedral : 15.112 179.903 26846 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.86 % Favored : 93.10 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.15 % Twisted Proline : 0.54 % 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: -0.36 (0.09), residues: 8444 helix: 1.15 (0.09), residues: 3265 sheet: -0.65 (0.15), residues: 1079 loop : -1.28 (0.10), residues: 4100 =============================================================================== Job complete usr+sys time: 23481.83 seconds wall clock time: 414 minutes 37.93 seconds (24877.93 seconds total)