Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 19 06:09:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5h_11643/07_2023/7a5h_11643_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5h_11643/07_2023/7a5h_11643.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5h_11643/07_2023/7a5h_11643_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5h_11643/07_2023/7a5h_11643_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5h_11643/07_2023/7a5h_11643_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5h_11643/07_2023/7a5h_11643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5h_11643/07_2023/7a5h_11643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5h_11643/07_2023/7a5h_11643_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5h_11643/07_2023/7a5h_11643_updated.pdb" } resolution = 3.3 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1586 5.49 5 Mg 92 5.21 5 S 285 5.16 5 C 59002 2.51 5 N 18662 2.21 5 O 22981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ASP 180": "OD1" <-> "OD2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 324": "OD1" <-> "OD2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "E TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ASP 185": "OD1" <-> "OD2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 137": "OD1" <-> "OD2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I ASP 182": "OD1" <-> "OD2" Residue "I ASP 183": "OD1" <-> "OD2" Residue "I PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J ASP 127": "OD1" <-> "OD2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K ASP 164": "OD1" <-> "OD2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 174": "OE1" <-> "OE2" Residue "K ASP 175": "OD1" <-> "OD2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "L ARG 37": "NH1" <-> "NH2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "L GLU 133": "OE1" <-> "OE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ASP 135": "OD1" <-> "OD2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M GLU 161": "OE1" <-> "OE2" Residue "M TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 180": "OD1" <-> "OD2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 225": "OD1" <-> "OD2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M ARG 259": "NH1" <-> "NH2" Residue "M ASP 279": "OD1" <-> "OD2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N ASP 148": "OD1" <-> "OD2" Residue "N TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "N GLU 171": "OE1" <-> "OE2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "N GLU 204": "OE1" <-> "OE2" Residue "N GLU 206": "OE1" <-> "OE2" Residue "N GLU 216": "OE1" <-> "OE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ASP 139": "OD1" <-> "OD2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "P GLU 40": "OE1" <-> "OE2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P GLU 57": "OE1" <-> "OE2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 75": "NH1" <-> "NH2" Residue "P GLU 76": "OE1" <-> "OE2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "P GLU 126": "OE1" <-> "OE2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "Q ARG 74": "NH1" <-> "NH2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q GLU 101": "OE1" <-> "OE2" Residue "Q TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q GLU 161": "OE1" <-> "OE2" Residue "Q GLU 165": "OE1" <-> "OE2" Residue "Q ASP 184": "OD1" <-> "OD2" Residue "Q ASP 185": "OD1" <-> "OD2" Residue "Q ARG 191": "NH1" <-> "NH2" Residue "Q ASP 201": "OD1" <-> "OD2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q ASP 246": "OD1" <-> "OD2" Residue "Q GLU 251": "OE1" <-> "OE2" Residue "Q GLU 256": "OE1" <-> "OE2" Residue "Q GLU 266": "OE1" <-> "OE2" Residue "Q ARG 271": "NH1" <-> "NH2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "Q GLU 279": "OE1" <-> "OE2" Residue "Q GLU 287": "OE1" <-> "OE2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ASP 16": "OD1" <-> "OD2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R ASP 104": "OD1" <-> "OD2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "R ASP 134": "OD1" <-> "OD2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S GLU 72": "OE1" <-> "OE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 104": "NH1" <-> "NH2" Residue "S ASP 112": "OD1" <-> "OD2" Residue "S GLU 119": "OE1" <-> "OE2" Residue "S ASP 121": "OD1" <-> "OD2" Residue "S GLU 126": "OE1" <-> "OE2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 66": "OE1" <-> "OE2" Residue "T ASP 110": "OD1" <-> "OD2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "T ARG 157": "NH1" <-> "NH2" Residue "T PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U ASP 38": "OD1" <-> "OD2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 109": "OD1" <-> "OD2" Residue "U GLU 131": "OE1" <-> "OE2" Residue "U GLU 133": "OE1" <-> "OE2" Residue "U ARG 143": "NH1" <-> "NH2" Residue "U PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 20": "NH1" <-> "NH2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V ASP 53": "OD1" <-> "OD2" Residue "V TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "V TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 103": "OD1" <-> "OD2" Residue "V GLU 112": "OE1" <-> "OE2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "V ASP 127": "OD1" <-> "OD2" Residue "V GLU 132": "OE1" <-> "OE2" Residue "V PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 139": "OE1" <-> "OE2" Residue "V ARG 145": "NH1" <-> "NH2" Residue "V GLU 180": "OE1" <-> "OE2" Residue "V ASP 181": "OD1" <-> "OD2" Residue "V GLU 184": "OE1" <-> "OE2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "V GLU 200": "OE1" <-> "OE2" Residue "V GLU 206": "OE1" <-> "OE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 139": "OE1" <-> "OE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X GLU 33": "OE1" <-> "OE2" Residue "X GLU 35": "OE1" <-> "OE2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X ASP 95": "OD1" <-> "OD2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X ASP 152": "OD1" <-> "OD2" Residue "X ASP 160": "OD1" <-> "OD2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X GLU 179": "OE1" <-> "OE2" Residue "X GLU 182": "OE1" <-> "OE2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X ASP 189": "OD1" <-> "OD2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 233": "OE1" <-> "OE2" Residue "Y GLU 66": "OE1" <-> "OE2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y GLU 130": "OE1" <-> "OE2" Residue "Y ASP 133": "OD1" <-> "OD2" Residue "Y GLU 148": "OE1" <-> "OE2" Residue "Y GLU 150": "OE1" <-> "OE2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 206": "OD1" <-> "OD2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Y GLU 224": "OE1" <-> "OE2" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "0 GLU 112": "OE1" <-> "OE2" Residue "0 GLU 128": "OE1" <-> "OE2" Residue "0 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 169": "OD1" <-> "OD2" Residue "0 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "1 GLU 39": "OE1" <-> "OE2" Residue "2 ARG 49": "NH1" <-> "NH2" Residue "2 GLU 52": "OE1" <-> "OE2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 ASP 182": "OD1" <-> "OD2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "5 GLU 32": "OE1" <-> "OE2" Residue "5 GLU 42": "OE1" <-> "OE2" Residue "5 ASP 47": "OD1" <-> "OD2" Residue "5 ASP 79": "OD1" <-> "OD2" Residue "5 ASP 84": "OD1" <-> "OD2" Residue "5 GLU 95": "OE1" <-> "OE2" Residue "5 ASP 101": "OD1" <-> "OD2" Residue "5 GLU 115": "OE1" <-> "OE2" Residue "5 GLU 130": "OE1" <-> "OE2" Residue "5 GLU 148": "OE1" <-> "OE2" Residue "5 GLU 152": "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 243": "OE1" <-> "OE2" Residue "5 GLU 254": "OE1" <-> "OE2" Residue "5 ASP 276": "OD1" <-> "OD2" Residue "5 GLU 281": "OE1" <-> "OE2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ASP 307": "OD1" <-> "OD2" Residue "5 ASP 332": "OD1" <-> "OD2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "5 PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 363": "OD1" <-> "OD2" Residue "5 GLU 368": "OE1" <-> "OE2" Residue "5 ASP 377": "OD1" <-> "OD2" Residue "5 PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 27": "NH1" <-> "NH2" Residue "6 ASP 41": "OD1" <-> "OD2" Residue "6 ASP 55": "OD1" <-> "OD2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 58": "NH1" <-> "NH2" Residue "6 ARG 60": "NH1" <-> "NH2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "6 ARG 72": "NH1" <-> "NH2" Residue "6 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 124": "NH1" <-> "NH2" Residue "6 ASP 133": "OD1" <-> "OD2" Residue "6 ARG 136": "NH1" <-> "NH2" Residue "6 GLU 140": "OE1" <-> "OE2" Residue "6 GLU 153": "OE1" <-> "OE2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 ASP 160": "OD1" <-> "OD2" Residue "6 GLU 181": "OE1" <-> "OE2" Residue "6 ASP 183": "OD1" <-> "OD2" Residue "6 GLU 209": "OE1" <-> "OE2" Residue "6 ASP 229": "OD1" <-> "OD2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 GLU 309": "OE1" <-> "OE2" Residue "6 PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 ASP 324": "OD1" <-> "OD2" Residue "6 ASP 325": "OD1" <-> "OD2" Residue "6 GLU 339": "OE1" <-> "OE2" Residue "6 GLU 343": "OE1" <-> "OE2" Residue "6 ARG 364": "NH1" <-> "NH2" Residue "6 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 367": "OD1" <-> "OD2" Residue "6 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 51": "OE1" <-> "OE2" Residue "7 GLU 66": "OE1" <-> "OE2" Residue "7 ASP 74": "OD1" <-> "OD2" Residue "7 ASP 132": "OD1" <-> "OD2" Residue "7 GLU 137": "OE1" <-> "OE2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 ASP 182": "OD1" <-> "OD2" Residue "7 GLU 191": "OE1" <-> "OE2" Residue "7 ASP 213": "OD1" <-> "OD2" Residue "7 GLU 217": "OE1" <-> "OE2" Residue "7 GLU 222": "OE1" <-> "OE2" Residue "7 TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 242": "OE1" <-> "OE2" Residue "7 ARG 250": "NH1" <-> "NH2" Residue "7 ASP 259": "OD1" <-> "OD2" Residue "7 ASP 262": "OD1" <-> "OD2" Residue "7 GLU 265": "OE1" <-> "OE2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "7 GLU 279": "OE1" <-> "OE2" Residue "8 ASP 87": "OD1" <-> "OD2" Residue "8 PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 105": "OE1" <-> "OE2" Residue "8 GLU 109": "OE1" <-> "OE2" Residue "8 GLU 110": "OE1" <-> "OE2" Residue "8 GLU 112": "OE1" <-> "OE2" Residue "8 ARG 137": "NH1" <-> "NH2" Residue "8 GLU 145": "OE1" <-> "OE2" Residue "8 GLU 148": "OE1" <-> "OE2" Residue "8 GLU 160": "OE1" <-> "OE2" Residue "8 ASP 165": "OD1" <-> "OD2" Residue "8 PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 174": "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 ASP 64": "OD1" <-> "OD2" Residue "9 GLU 94": "OE1" <-> "OE2" Residue "9 GLU 101": "OE1" <-> "OE2" Residue "9 ASP 103": "OD1" <-> "OD2" Residue "9 ASP 106": "OD1" <-> "OD2" Residue "9 GLU 115": "OE1" <-> "OE2" Residue "9 GLU 120": "OE1" <-> "OE2" Residue "a ASP 41": "OD1" <-> "OD2" Residue "a ASP 42": "OD1" <-> "OD2" 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 ASP 141": "OD1" <-> "OD2" Residue "a ARG 142": "NH1" <-> "NH2" Residue "b PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 36": "OD1" <-> "OD2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b GLU 45": "OE1" <-> "OE2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b GLU 96": "OE1" <-> "OE2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "b GLU 147": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c GLU 71": "OE1" <-> "OE2" Residue "c PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 86": "OD1" <-> "OD2" Residue "c GLU 102": "OE1" <-> "OE2" Residue "c GLU 164": "OE1" <-> "OE2" Residue "c GLU 182": "OE1" <-> "OE2" Residue "c GLU 209": "OE1" <-> "OE2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "c ASP 217": "OD1" <-> "OD2" Residue "c GLU 254": "OE1" <-> "OE2" Residue "c TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 287": "OE1" <-> "OE2" Residue "c GLU 294": "OE1" <-> "OE2" Residue "c GLU 309": "OE1" <-> "OE2" Residue "c TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 70": "OE1" <-> "OE2" Residue "d ARG 74": "NH1" <-> "NH2" Residue "d ASP 129": "OD1" <-> "OD2" Residue "d GLU 147": "OE1" <-> "OE2" Residue "d ASP 156": "OD1" <-> "OD2" Residue "d ASP 158": "OD1" <-> "OD2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "d GLU 187": "OE1" <-> "OE2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 237": "OD1" <-> "OD2" Residue "d GLU 244": "OE1" <-> "OE2" Residue "d GLU 294": "OE1" <-> "OE2" Residue "e GLU 80": "OE1" <-> "OE2" Residue "e GLU 88": "OE1" <-> "OE2" Residue "e ASP 93": "OD1" <-> "OD2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e ASP 104": "OD1" <-> "OD2" Residue "e ASP 119": "OD1" <-> "OD2" Residue "e ASP 154": "OD1" <-> "OD2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "e GLU 189": "OE1" <-> "OE2" Residue "e PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 262": "OD1" <-> "OD2" Residue "e PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 278": "OD1" <-> "OD2" Residue "f GLU 66": "OE1" <-> "OE2" Residue "f GLU 87": "OE1" <-> "OE2" Residue "f TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f GLU 172": "OE1" <-> "OE2" Residue "g GLU 44": "OE1" <-> "OE2" Residue "g ASP 77": "OD1" <-> "OD2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ASP 99": "OD1" <-> "OD2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "g ASP 123": "OD1" <-> "OD2" Residue "g GLU 156": "OE1" <-> "OE2" Residue "h GLU 64": "OE1" <-> "OE2" Residue "h ASP 65": "OD1" <-> "OD2" Residue "h ARG 69": "NH1" <-> "NH2" 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 125": "OD1" <-> "OD2" Residue "h GLU 142": "OE1" <-> "OE2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i GLU 67": "OE1" <-> "OE2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i ASP 105": "OD1" <-> "OD2" Residue "i ASP 106": "OD1" <-> "OD2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j ARG 94": "NH1" <-> "NH2" Residue "j GLU 100": "OE1" <-> "OE2" Residue "j GLU 101": "OE1" <-> "OE2" Residue "j ARG 103": "NH1" <-> "NH2" Residue "k ARG 31": "NH1" <-> "NH2" Residue "k GLU 40": "OE1" <-> "OE2" Residue "k ASP 54": "OD1" <-> "OD2" Residue "k ASP 70": "OD1" <-> "OD2" Residue "k ARG 77": "NH1" <-> "NH2" 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 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 70": "OE1" <-> "OE2" Residue "o ARG 23": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o GLU 72": "OE1" <-> "OE2" Residue "o PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 90": "OD1" <-> "OD2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "p GLU 51": "OE1" <-> "OE2" Residue "p ASP 74": "OD1" <-> "OD2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q GLU 43": "OE1" <-> "OE2" Residue "q ASP 44": "OD1" <-> "OD2" Residue "q TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q GLU 80": "OE1" <-> "OE2" Residue "q GLU 88": "OE1" <-> "OE2" Residue "q GLU 89": "OE1" <-> "OE2" Residue "q GLU 101": "OE1" <-> "OE2" Residue "q GLU 111": "OE1" <-> "OE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "q GLU 141": "OE1" <-> "OE2" Residue "q GLU 151": "OE1" <-> "OE2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 85": "OD1" <-> "OD2" Residue "r ARG 132": "NH1" <-> "NH2" Residue "r ARG 153": "NH1" <-> "NH2" Residue "r ARG 168": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "s ASP 77": "OD1" <-> "OD2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 103": "OD1" <-> "OD2" Residue "s ASP 148": "OD1" <-> "OD2" Residue "s ARG 158": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s ARG 162": "NH1" <-> "NH2" Residue "s GLU 167": "OE1" <-> "OE2" Residue "s ASP 201": "OD1" <-> "OD2" Residue "s ARG 212": "NH1" <-> "NH2" Residue "s GLU 215": "OE1" <-> "OE2" Residue "s ARG 219": "NH1" <-> "NH2" Residue "s ARG 222": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s ASP 227": "OD1" <-> "OD2" Residue "s ASP 228": "OD1" <-> "OD2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 234": "OD1" <-> "OD2" Residue "s ARG 242": "NH1" <-> "NH2" Residue "s GLU 260": "OE1" <-> "OE2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s ASP 290": "OD1" <-> "OD2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s ASP 318": "OD1" <-> "OD2" Residue "s GLU 321": "OE1" <-> "OE2" Residue "s GLU 348": "OE1" <-> "OE2" Residue "s TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 389": "NH1" <-> "NH2" Residue "s GLU 406": "OE1" <-> "OE2" Residue "s PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 415": "OD1" <-> "OD2" Residue "u ASP 95": "OD1" <-> "OD2" Residue "u GLU 117": "OE1" <-> "OE2" Residue "u ASP 122": "OD1" <-> "OD2" Residue "u ASP 163": "OD1" <-> "OD2" Residue "u ASP 165": "OD1" <-> "OD2" Residue "u GLU 183": "OE1" <-> "OE2" Residue "u GLU 191": "OE1" <-> "OE2" Residue "v ARG 6": "NH1" <-> "NH2" Residue "v TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 14": "NH1" <-> "NH2" Residue "v ARG 24": "NH1" <-> "NH2" Residue "v ARG 28": "NH1" <-> "NH2" Residue "v ASP 29": "OD1" <-> "OD2" Residue "v ASP 47": "OD1" <-> "OD2" Residue "v GLU 52": "OE1" <-> "OE2" Residue "v GLU 56": "OE1" <-> "OE2" Residue "w GLU 77": "OE1" <-> "OE2" Residue "w ASP 81": "OD1" <-> "OD2" Residue "w ASP 94": "OD1" <-> "OD2" Residue "w GLU 96": "OE1" <-> "OE2" Residue "w GLU 117": "OE1" <-> "OE2" Residue "w GLU 125": "OE1" <-> "OE2" Residue "w GLU 136": "OE1" <-> "OE2" Residue "w ASP 146": "OD1" <-> "OD2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "G ASP 134": "OD1" <-> "OD2" Residue "G TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 145": "OD1" <-> "OD2" Residue "G ASP 153": "OD1" <-> "OD2" Residue "G ASP 161": "OD1" <-> "OD2" Residue "G PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G GLU 214": "OE1" <-> "OE2" Residue "G TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 222": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 102610 Number of models: 1 Model: "" Number of chains: 66 Chain: "D" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1842 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 12, 'TRANS': 223} Chain: "E" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2396 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 24, 'TRANS': 279} Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} Chain breaks: 1 Chain: "J" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1061 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "P" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1148 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain: "Q" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1805 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 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: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1218 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "V" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1624 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 183} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "W" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2035 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "5" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3156 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 354} Chain breaks: 1 Chain: "6" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2640 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "8" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 890 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 97} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Chain: "a" Number of atoms: 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: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} Chain breaks: 1 Chain: "d" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1741 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain breaks: 3 Chain: "e" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1762 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "f" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 915 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} Chain: "h" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "l" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 221 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "m" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "o" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 771 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} 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: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1076 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 14, 'TRANS': 113} 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: "t" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "u" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 927 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 30945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1457, 30945 Classifications: {'RNA': 1457} Modifications used: {'rna2p_pur': 155, 'rna2p_pyr': 116, 'rna3p_pur': 615, 'rna3p_pyr': 571} Link IDs: {'rna2p': 270, 'rna3p': 1186} Chain breaks: 15 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 54} Chain breaks: 4 Chain: "24" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'rna2p': 14, 'rna3p': 58} Chain: "Y2" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 157 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 928 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 917 Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 809 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "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: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Unusual residues: {' MG': 89} Classifications: {'undetermined': 89} Link IDs: {None: 88} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 32143 SG CYS 0 110 167.304 147.082 169.468 1.00 33.93 S ATOM 32165 SG CYS 0 113 167.461 150.450 167.217 1.00 33.47 S ATOM 32245 SG CYS 0 123 167.423 147.294 165.359 1.00 24.29 S ATOM 32268 SG CYS 0 126 170.566 148.153 167.811 1.00 27.82 S ATOM 7322 SG CYS I 64 65.053 95.191 154.402 1.00 49.23 S ATOM 60621 SG CYS r 70 66.158 93.785 158.279 1.00 27.37 S ATOM 60642 SG CYS r 73 62.979 95.454 158.601 1.00 26.97 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG C 109 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 109 " occ=0.50 Time building chain proxies: 35.11, per 1000 atoms: 0.34 Number of scatterers: 102610 At special positions: 0 Unit cell: (254.8, 228.8, 228.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 285 16.00 P 1586 15.00 Mg 92 11.99 O 22981 8.00 N 18662 7.00 C 59002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 34.20 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 73 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " Number of angles added : 6 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15974 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: 270 helices and 80 sheets defined 41.2% alpha, 14.0% beta 367 base pairs and 856 stacking pairs defined. Time for finding SS restraints: 40.86 Creating SS restraints... Processing helix chain 'D' and resid 183 through 188 removed outlier: 4.239A pdb=" N LEU D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix No H-bonds generated for 'chain 'D' and resid 183 through 188' Processing helix chain 'D' and resid 259 through 267 removed outlier: 3.690A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.946A pdb=" N LYS E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.700A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.795A pdb=" N ASN E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.069A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 158' Processing helix chain 'E' and resid 159 through 169 removed outlier: 3.814A pdb=" N PHE E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 168 " --> pdb=" O PHE E 164 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY E 169 " --> pdb=" O TYR E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 304 through 309 removed outlier: 3.948A pdb=" N LYS E 308 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 304 through 309' Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.723A pdb=" N ARG E 199 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 109 removed outlier: 3.828A pdb=" N ASN F 105 " --> pdb=" O MET F 101 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 removed outlier: 3.900A pdb=" N LEU F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP F 185 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 211 removed outlier: 4.123A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU F 205 " --> pdb=" O GLN F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 4.319A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 5.245A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.928A pdb=" N LEU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 80 removed outlier: 3.945A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 80' Processing helix chain 'H' and resid 115 through 122 removed outlier: 3.510A pdb=" N ASN H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 147 removed outlier: 4.277A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE H 140 " --> pdb=" O ASN H 136 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU H 141 " --> pdb=" O LYS H 137 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLU H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.540A pdb=" N VAL I 50 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 93 removed outlier: 3.511A pdb=" N LEU I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE I 86 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA I 87 " --> pdb=" O ARG I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.978A pdb=" N LEU I 110 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU I 116 " --> pdb=" O MET I 112 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS I 118 " --> pdb=" O HIS I 114 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 139 Proline residue: I 133 - end of helix removed outlier: 4.814A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP I 137 " --> pdb=" O PRO I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 147 removed outlier: 3.514A pdb=" N LEU I 144 " --> pdb=" O TYR I 140 " (cutoff:3.500A) Proline residue: I 145 - end of helix No H-bonds generated for 'chain 'I' and resid 140 through 147' Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.696A pdb=" N MET I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 197 removed outlier: 3.742A pdb=" N ILE I 192 " --> pdb=" O ARG I 188 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR I 194 " --> pdb=" O GLY I 190 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER I 195 " --> pdb=" O PHE I 191 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU I 197 " --> pdb=" O ASN I 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 43 removed outlier: 5.758A pdb=" N GLN J 41 " --> pdb=" O PRO J 37 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.223A pdb=" N PHE J 49 " --> pdb=" O SER J 45 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS J 50 " --> pdb=" O ILE J 46 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN J 54 " --> pdb=" O CYS J 50 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU J 55 " --> pdb=" O LYS J 51 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE J 60 " --> pdb=" O ARG J 56 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LYS J 61 " --> pdb=" O THR J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 removed outlier: 4.363A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS J 92 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 3.777A pdb=" N ILE J 120 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG J 122 " --> pdb=" O TYR J 118 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 4.885A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG J 142 " --> pdb=" O SER J 138 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY J 152 " --> pdb=" O ALA J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 removed outlier: 3.595A pdb=" N GLN K 10 " --> pdb=" O ARG K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 41 removed outlier: 4.086A pdb=" N ILE K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG K 38 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN K 40 " --> pdb=" O SER K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.715A pdb=" N GLY K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET K 111 " --> pdb=" O ALA K 107 " (cutoff:3.500A) Proline residue: K 113 - end of helix Processing helix chain 'K' and resid 115 through 126 removed outlier: 4.772A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 4.976A pdb=" N ASN K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 167 removed outlier: 3.981A pdb=" N ALA K 165 " --> pdb=" O GLU K 161 " (cutoff:3.500A) Proline residue: K 167 - end of helix Processing helix chain 'L' and resid 44 through 49 Processing helix chain 'L' and resid 133 through 141 removed outlier: 4.477A pdb=" N VAL L 137 " --> pdb=" O GLU L 133 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.580A pdb=" N LEU L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS L 129 " --> pdb=" O SER L 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 20 removed outlier: 4.408A pdb=" N ASP M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG M 17 " --> pdb=" O LEU M 13 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 removed outlier: 4.400A pdb=" N ARG M 59 " --> pdb=" O GLY M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.991A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 91 removed outlier: 6.020A pdb=" N ARG M 91 " --> pdb=" O HIS M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 108 removed outlier: 3.598A pdb=" N LEU M 107 " --> pdb=" O TYR M 103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 125 removed outlier: 3.863A pdb=" N LEU M 121 " --> pdb=" O ASP M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.538A pdb=" N ILE M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY M 171 " --> pdb=" O ILE M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 190 removed outlier: 4.025A pdb=" N ASP M 185 " --> pdb=" O PRO M 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE M 186 " --> pdb=" O ARG M 182 " (cutoff:3.500A) Proline residue: M 190 - end of helix Processing helix chain 'M' and resid 191 through 197 removed outlier: 4.188A pdb=" N ARG M 196 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY M 197 " --> pdb=" O PHE M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 216 Proline residue: M 212 - end of helix removed outlier: 4.315A pdb=" N ASP M 216 " --> pdb=" O PRO M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 241 removed outlier: 4.237A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix removed outlier: 3.678A pdb=" N LEU M 234 " --> pdb=" O PRO M 230 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU M 235 " --> pdb=" O GLU M 231 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.607A pdb=" N THR M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.829A pdb=" N SER M 296 " --> pdb=" O LYS M 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 74 removed outlier: 3.675A pdb=" N ARG N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLY N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 69 through 74' Processing helix chain 'N' and resid 98 through 113 removed outlier: 3.537A pdb=" N PHE N 102 " --> pdb=" O HIS N 98 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG N 111 " --> pdb=" O LEU N 107 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER N 112 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET N 113 " --> pdb=" O ILE N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 184 removed outlier: 4.231A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN N 178 " --> pdb=" O GLY N 174 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS N 182 " --> pdb=" O GLN N 178 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU N 183 " --> pdb=" O VAL N 179 " (cutoff:3.500A) Proline residue: N 184 - end of helix Processing helix chain 'N' and resid 191 through 209 removed outlier: 3.535A pdb=" N GLU N 196 " --> pdb=" O ARG N 192 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP N 201 " --> pdb=" O LYS N 197 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN N 202 " --> pdb=" O MET N 198 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG N 207 " --> pdb=" O GLU N 203 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN N 209 " --> pdb=" O ARG N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 225 through 231 removed outlier: 4.692A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.821A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 removed outlier: 3.559A pdb=" N ILE O 26 " --> pdb=" O PRO O 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN O 31 " --> pdb=" O HIS O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 66 removed outlier: 3.584A pdb=" N GLU O 51 " --> pdb=" O ALA O 47 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET O 52 " --> pdb=" O ARG O 48 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 3.680A pdb=" N ARG O 74 " --> pdb=" O GLU O 70 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 99 removed outlier: 4.217A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.762A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Proline residue: O 95 - end of helix removed outlier: 4.014A pdb=" N LYS O 98 " --> pdb=" O ALA O 94 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP O 99 " --> pdb=" O PRO O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 160 removed outlier: 3.556A pdb=" N LEU O 156 " --> pdb=" O LEU O 152 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 109 through 117 removed outlier: 4.795A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR P 117 " --> pdb=" O LYS P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 140 removed outlier: 3.610A pdb=" N ILE P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU P 132 " --> pdb=" O ILE P 128 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU P 137 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU P 138 " --> pdb=" O GLN P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 155 removed outlier: 4.331A pdb=" N ALA P 154 " --> pdb=" O PRO P 150 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER P 155 " --> pdb=" O TRP P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 169 removed outlier: 3.589A pdb=" N SER P 163 " --> pdb=" O LYS P 159 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR P 166 " --> pdb=" O GLN P 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.293A pdb=" N ILE Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Proline residue: Q 82 - end of helix No H-bonds generated for 'chain 'Q' and resid 77 through 82' Processing helix chain 'Q' and resid 88 through 106 removed outlier: 4.083A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS Q 97 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP Q 98 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS Q 104 " --> pdb=" O LEU Q 100 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 194 removed outlier: 5.365A pdb=" N LEU Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 4.049A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 262 removed outlier: 3.722A pdb=" N MET Q 254 " --> pdb=" O THR Q 250 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS Q 255 " --> pdb=" O GLU Q 251 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA Q 257 " --> pdb=" O GLN Q 253 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.486A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 290 removed outlier: 4.677A pdb=" N GLU Q 279 " --> pdb=" O THR Q 275 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA Q 281 " --> pdb=" O LYS Q 277 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU Q 285 " --> pdb=" O ALA Q 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS Q 290 " --> pdb=" O ILE Q 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 29 removed outlier: 3.682A pdb=" N GLU R 23 " --> pdb=" O PHE R 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS R 26 " --> pdb=" O GLN R 22 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 80 removed outlier: 3.744A pdb=" N THR R 54 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG R 65 " --> pdb=" O LYS R 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY R 80 " --> pdb=" O SER R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 removed outlier: 3.961A pdb=" N ASN R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL R 91 " --> pdb=" O ILE R 87 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 109 through 134 removed outlier: 4.892A pdb=" N GLY R 133 " --> pdb=" O ALA R 129 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 59 removed outlier: 4.074A pdb=" N SER S 58 " --> pdb=" O THR S 54 " (cutoff:3.500A) Proline residue: S 59 - end of helix No H-bonds generated for 'chain 'S' and resid 54 through 59' Processing helix chain 'S' and resid 68 through 90 removed outlier: 3.829A pdb=" N ARG S 74 " --> pdb=" O VAL S 70 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS S 82 " --> pdb=" O GLU S 78 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY S 90 " --> pdb=" O MET S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.847A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 150 through 155' Processing helix chain 'T' and resid 49 through 57 removed outlier: 3.942A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE T 57 " --> pdb=" O LYS T 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 49 through 57' Processing helix chain 'T' and resid 83 through 95 removed outlier: 4.354A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE T 94 " --> pdb=" O LEU T 90 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG T 95 " --> pdb=" O ALA T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 109 removed outlier: 3.710A pdb=" N GLU T 107 " --> pdb=" O LEU T 103 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 4.403A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP T 126 " --> pdb=" O LEU T 122 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL T 129 " --> pdb=" O GLN T 125 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG T 130 " --> pdb=" O ASP T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.798A pdb=" N GLU T 198 " --> pdb=" O ALA T 194 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER T 205 " --> pdb=" O GLN T 201 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 59 removed outlier: 3.531A pdb=" N LEU U 57 " --> pdb=" O LEU U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 137 removed outlier: 3.710A pdb=" N GLU U 132 " --> pdb=" O SER U 128 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU U 133 " --> pdb=" O MET U 129 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG U 134 " --> pdb=" O LEU U 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 36 removed outlier: 3.651A pdb=" N ARG V 33 " --> pdb=" O VAL V 29 " (cutoff:3.500A) Proline residue: V 36 - end of helix Processing helix chain 'V' and resid 116 through 121 removed outlier: 3.834A pdb=" N VAL V 120 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 116 through 121' Processing helix chain 'V' and resid 178 through 184 removed outlier: 3.808A pdb=" N GLU V 184 " --> pdb=" O GLU V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 193 through 203 removed outlier: 3.927A pdb=" N GLY V 203 " --> pdb=" O MET V 199 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 120 removed outlier: 4.189A pdb=" N LEU W 116 " --> pdb=" O GLU W 112 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU W 120 " --> pdb=" O LEU W 116 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 18 removed outlier: 4.462A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU X 16 " --> pdb=" O LYS X 12 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG X 17 " --> pdb=" O ARG X 13 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 25 removed outlier: 3.615A pdb=" N ARG X 23 " --> pdb=" O GLY X 19 " (cutoff:3.500A) Proline residue: X 25 - end of helix Processing helix chain 'X' and resid 26 through 34 removed outlier: 3.706A pdb=" N SER X 31 " --> pdb=" O HIS X 27 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU X 33 " --> pdb=" O LEU X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 4.179A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 79' Processing helix chain 'X' and resid 128 through 139 removed outlier: 3.513A pdb=" N LEU X 132 " --> pdb=" O THR X 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP X 133 " --> pdb=" O MET X 129 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP X 136 " --> pdb=" O LEU X 132 " (cutoff:3.500A) 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 removed outlier: 3.659A pdb=" N MET X 159 " --> pdb=" O SER X 155 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG X 171 " --> pdb=" O LEU X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 173 through 178 removed outlier: 5.192A pdb=" N HIS X 177 " --> pdb=" O ASP X 173 " (cutoff:3.500A) Proline residue: X 178 - end of helix No H-bonds generated for 'chain 'X' and resid 173 through 178' Processing helix chain 'X' and resid 180 through 192 removed outlier: 4.134A pdb=" N ARG X 184 " --> pdb=" O ASP X 180 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR X 188 " --> pdb=" O ARG X 184 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS X 190 " --> pdb=" O ALA X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 204 removed outlier: 3.579A pdb=" N GLU X 202 " --> pdb=" O GLU X 198 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL X 204 " --> pdb=" O GLU X 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 removed outlier: 3.579A pdb=" N LYS X 214 " --> pdb=" O GLU X 210 " (cutoff:3.500A) Processing helix chain 'X' and resid 225 through 244 removed outlier: 3.759A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN X 236 " --> pdb=" O ALA X 232 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN X 237 " --> pdb=" O GLU X 233 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER X 244 " --> pdb=" O GLN X 240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 69 removed outlier: 4.670A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 64 through 69' Processing helix chain 'Y' and resid 70 through 75 removed outlier: 3.545A pdb=" N TRP Y 74 " --> pdb=" O ASP Y 70 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 70 through 75' Processing helix chain 'Y' and resid 86 through 94 removed outlier: 3.731A pdb=" N LEU Y 90 " --> pdb=" O THR Y 86 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG Y 91 " --> pdb=" O CYS Y 87 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 86 through 94' Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.517A pdb=" N LYS Y 100 " --> pdb=" O GLU Y 96 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU Y 101 " --> pdb=" O ASP Y 97 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.615A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA Y 141 " --> pdb=" O ASP Y 137 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN Y 147 " --> pdb=" O ASP Y 143 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA Y 152 " --> pdb=" O GLU Y 148 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU Y 155 " --> pdb=" O ASP Y 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 198 removed outlier: 3.709A pdb=" N ARG Y 196 " --> pdb=" O LYS Y 192 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS Y 197 " --> pdb=" O ARG Y 193 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 205 through 238 removed outlier: 3.658A pdb=" N ASN Y 225 " --> pdb=" O ALA Y 221 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG Y 228 " --> pdb=" O GLU Y 224 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE Y 233 " --> pdb=" O LYS Y 229 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU Y 234 " --> pdb=" O LYS Y 230 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU Y 235 " --> pdb=" O ALA Y 231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS Y 236 " --> pdb=" O LYS Y 232 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.488A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA Z 48 " --> pdb=" O LYS Z 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 48' Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.881A pdb=" N HIS Z 53 " --> pdb=" O SER Z 49 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU Z 54 " --> pdb=" O PRO Z 50 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLY Z 57 " --> pdb=" O HIS Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 90 removed outlier: 3.517A pdb=" N LYS Z 87 " --> pdb=" O LYS Z 83 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY Z 90 " --> pdb=" O ILE Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 114 removed outlier: 3.543A pdb=" N ALA Z 108 " --> pdb=" O PRO Z 104 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL Z 112 " --> pdb=" O ALA Z 108 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 95 removed outlier: 3.551A pdb=" N CYS 0 92 " --> pdb=" O GLU 0 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG 0 93 " --> pdb=" O VAL 0 89 " (cutoff:3.500A) Processing helix chain '0' and resid 96 through 101 removed outlier: 6.027A pdb=" N ILE 0 101 " --> pdb=" O PRO 0 97 " (cutoff:3.500A) Processing helix chain '0' and resid 123 through 146 removed outlier: 3.555A pdb=" N VAL 0 130 " --> pdb=" O CYS 0 126 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU 0 133 " --> pdb=" O LYS 0 129 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 64 removed outlier: 3.625A pdb=" N ASN 2 62 " --> pdb=" O ILE 2 58 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 72 removed outlier: 4.160A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 73 through 86 removed outlier: 3.760A pdb=" N GLN 2 77 " --> pdb=" O PRO 2 73 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL 2 78 " --> pdb=" O ALA 2 74 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 114 removed outlier: 3.748A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 3.806A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 137' Processing helix chain '3' and resid 138 through 146 removed outlier: 3.579A pdb=" N ARG 3 145 " --> pdb=" O LYS 3 141 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 3.505A pdb=" N THR 3 162 " --> pdb=" O LEU 3 158 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 4.098A pdb=" N HIS 3 181 " --> pdb=" O TYR 3 177 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP 3 182 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 177 through 182' Processing helix chain '5' and resid 35 through 40 removed outlier: 5.536A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 53 removed outlier: 4.454A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) Proline residue: 5 53 - end of helix No H-bonds generated for 'chain '5' and resid 47 through 53' Processing helix chain '5' and resid 116 through 125 removed outlier: 3.590A pdb=" N THR 5 124 " --> pdb=" O ALA 5 120 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 142 removed outlier: 3.557A pdb=" N SER 5 138 " --> pdb=" O GLU 5 134 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP 5 142 " --> pdb=" O SER 5 138 " (cutoff:3.500A) Processing helix chain '5' and resid 149 through 163 removed outlier: 4.113A pdb=" N LEU 5 155 " --> pdb=" O ASP 5 151 " (cutoff:3.500A) Processing helix chain '5' and resid 172 through 196 Proline residue: 5 178 - end of helix removed outlier: 3.650A pdb=" N VAL 5 181 " --> pdb=" O CYS 5 177 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER 5 190 " --> pdb=" O GLN 5 186 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.349A 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 251 removed outlier: 4.571A pdb=" N GLU 5 246 " --> pdb=" O ARG 5 242 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA 5 247 " --> pdb=" O GLU 5 243 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR 5 248 " --> pdb=" O GLU 5 244 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 3.587A pdb=" N ARG 5 303 " --> pdb=" O LEU 5 299 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU 5 304 " --> pdb=" O ARG 5 300 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 299 through 304' Processing helix chain '5' and resid 305 through 329 removed outlier: 3.535A pdb=" N GLN 5 324 " --> pdb=" O SER 5 320 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU 5 327 " --> pdb=" O ALA 5 323 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 5 328 " --> pdb=" O GLN 5 324 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR 5 329 " --> pdb=" O ALA 5 325 " (cutoff:3.500A) Processing helix chain '5' and resid 407 through 420 removed outlier: 4.319A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS 5 413 " --> pdb=" O GLU 5 409 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS 5 420 " --> pdb=" O ALA 5 416 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 removed outlier: 4.167A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG 6 60 " --> pdb=" O ARG 6 56 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU 6 64 " --> pdb=" O ARG 6 60 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN 6 66 " --> pdb=" O GLU 6 62 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 6 67 " --> pdb=" O GLN 6 63 " (cutoff:3.500A) Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 73 through 79 removed outlier: 4.125A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 117 removed outlier: 3.842A pdb=" N LEU 6 103 " --> pdb=" O ARG 6 99 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU 6 104 " --> pdb=" O THR 6 100 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN 6 108 " --> pdb=" O LEU 6 104 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA 6 109 " --> pdb=" O GLU 6 105 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG 6 114 " --> pdb=" O ILE 6 110 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) Processing helix chain '6' and resid 118 through 126 removed outlier: 4.027A pdb=" N ALA 6 122 " --> pdb=" O GLU 6 118 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA 6 123 " --> pdb=" O GLU 6 119 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG 6 124 " --> pdb=" O GLU 6 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU 6 125 " --> pdb=" O ARG 6 121 " (cutoff:3.500A) Processing helix chain '6' and resid 131 through 143 removed outlier: 3.551A pdb=" N ALA 6 137 " --> pdb=" O ASP 6 133 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG 6 141 " --> pdb=" O ALA 6 137 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR 6 142 " --> pdb=" O GLU 6 138 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 156 removed outlier: 3.893A pdb=" N ARG 6 150 " --> pdb=" O TYR 6 146 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY 6 156 " --> pdb=" O ALA 6 152 " (cutoff:3.500A) Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 292 through 297 removed outlier: 4.731A pdb=" N THR 6 297 " --> pdb=" O LEU 6 293 " (cutoff:3.500A) Processing helix chain '6' and resid 299 through 308 removed outlier: 3.502A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 333 removed outlier: 4.299A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR 6 329 " --> pdb=" O ASP 6 325 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE 6 330 " --> pdb=" O SER 6 326 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 371 removed outlier: 3.640A pdb=" N ARG 6 368 " --> pdb=" O ARG 6 364 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG 6 370 " --> pdb=" O LEU 6 366 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 364 through 371' Processing helix chain '6' and resid 157 through 163 removed outlier: 3.857A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 59 removed outlier: 3.581A pdb=" N LEU 7 40 " --> pdb=" O SER 7 36 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG 7 44 " --> pdb=" O LEU 7 40 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE 7 48 " --> pdb=" O ARG 7 44 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU 7 51 " --> pdb=" O LEU 7 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA 7 53 " --> pdb=" O ASN 7 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU 7 58 " --> pdb=" O ARG 7 54 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR 7 59 " --> pdb=" O GLN 7 55 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 96 removed outlier: 3.660A pdb=" N HIS 7 94 " --> pdb=" O SER 7 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU 7 95 " --> pdb=" O CYS 7 91 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER 7 96 " --> pdb=" O ALA 7 92 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 103 removed outlier: 3.971A pdb=" N SER 7 103 " --> pdb=" O TYR 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 135 through 158 removed outlier: 3.587A pdb=" N ASN 7 139 " --> pdb=" O PRO 7 135 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER 7 145 " --> pdb=" O ALA 7 141 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG 7 156 " --> pdb=" O CYS 7 152 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 195 through 213 removed outlier: 3.697A pdb=" N LEU 7 199 " --> pdb=" O THR 7 195 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA 7 208 " --> pdb=" O LYS 7 204 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS 7 212 " --> pdb=" O ALA 7 208 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP 7 213 " --> pdb=" O LEU 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 222 through 231 Processing helix chain '7' and resid 233 through 248 removed outlier: 3.904A pdb=" N ASP 7 238 " --> pdb=" O LYS 7 234 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE 7 239 " --> pdb=" O TYR 7 235 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER 7 245 " --> pdb=" O GLU 7 241 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN 7 246 " --> pdb=" O GLU 7 242 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN 7 247 " --> pdb=" O LYS 7 243 " (cutoff:3.500A) Proline residue: 7 248 - end of helix Processing helix chain '7' and resid 309 through 322 removed outlier: 3.525A pdb=" N LYS 7 315 " --> pdb=" O THR 7 311 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER 7 320 " --> pdb=" O LEU 7 316 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG 7 321 " --> pdb=" O LEU 7 317 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 3.800A pdb=" N CYS 7 275 " --> pdb=" O THR 7 272 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 107 through 154 removed outlier: 3.628A pdb=" N GLU 8 112 " --> pdb=" O PHE 8 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG 8 113 " --> pdb=" O GLU 8 109 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN 8 126 " --> pdb=" O SER 8 122 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN 8 127 " --> pdb=" O LEU 8 123 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU 8 132 " --> pdb=" O GLU 8 128 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG 8 137 " --> pdb=" O ARG 8 133 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU 8 140 " --> pdb=" O ILE 8 136 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA 8 142 " --> pdb=" O ALA 8 138 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN 8 143 " --> pdb=" O MET 8 139 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU 8 153 " --> pdb=" O GLU 8 149 " (cutoff:3.500A) Processing helix chain '8' and resid 155 through 164 removed outlier: 5.181A pdb=" N ALA 8 159 " --> pdb=" O PRO 8 155 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA 8 161 " --> pdb=" O LEU 8 157 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE 8 162 " --> pdb=" O HIS 8 158 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 155 through 164' Processing helix chain '9' and resid 27 through 35 removed outlier: 4.035A pdb=" N ARG 9 33 " --> pdb=" O SER 9 29 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 removed outlier: 3.630A pdb=" N VAL 9 57 " --> pdb=" O ILE 9 53 " (cutoff:3.500A) Proline residue: 9 58 - end of helix No H-bonds generated for 'chain '9' and resid 53 through 58' Processing helix chain '9' and resid 87 through 95 removed outlier: 3.552A pdb=" N PHE 9 92 " --> pdb=" O ALA 9 88 " (cutoff:3.500A) Processing helix chain '9' and resid 96 through 106 removed outlier: 3.776A pdb=" N LYS 9 105 " --> pdb=" O GLU 9 101 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP 9 106 " --> pdb=" O LYS 9 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 117 removed outlier: 3.596A pdb=" N MET a 108 " --> pdb=" O GLU a 104 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET a 115 " --> pdb=" O GLN a 111 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 134 removed outlier: 3.585A pdb=" N ARG a 133 " --> pdb=" O TYR a 129 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS a 134 " --> pdb=" O HIS a 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 7 Proline residue: b 7 - end of helix Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.667A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ARG b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 37 through 49 removed outlier: 3.998A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU b 45 " --> pdb=" O ARG b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 59 removed outlier: 3.522A pdb=" N ARG b 56 " --> pdb=" O ILE b 52 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG b 57 " --> pdb=" O ASP b 53 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN b 58 " --> pdb=" O PHE b 54 " (cutoff:3.500A) Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 108 removed outlier: 3.725A pdb=" N ILE b 97 " --> pdb=" O SER b 93 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER b 108 " --> pdb=" O LEU b 104 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 53 removed outlier: 5.033A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN c 48 " --> pdb=" O GLU c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 59 through 64 removed outlier: 3.990A pdb=" N LYS c 63 " --> pdb=" O ARG c 59 " (cutoff:3.500A) Proline residue: c 64 - end of helix No H-bonds generated for 'chain 'c' and resid 59 through 64' Processing helix chain 'c' and resid 67 through 80 removed outlier: 3.647A pdb=" N GLN c 73 " --> pdb=" O HIS c 69 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY c 76 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS c 77 " --> pdb=" O GLN c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 94 removed outlier: 3.588A pdb=" N THR c 90 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA c 91 " --> pdb=" O LEU c 87 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE c 92 " --> pdb=" O LEU c 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 107 removed outlier: 3.589A pdb=" N SER c 100 " --> pdb=" O CYS c 96 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA c 103 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN c 106 " --> pdb=" O GLU c 102 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN c 107 " --> pdb=" O ALA c 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 146 removed outlier: 3.693A pdb=" N GLN c 128 " --> pdb=" O GLU c 124 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR c 130 " --> pdb=" O SER c 126 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU c 137 " --> pdb=" O SER c 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR c 138 " --> pdb=" O GLN c 134 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE c 140 " --> pdb=" O CYS c 136 " (cutoff:3.500A) 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 removed outlier: 3.831A pdb=" N HIS c 168 " --> pdb=" O GLU c 164 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG c 171 " --> pdb=" O CYS c 167 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN c 172 " --> pdb=" O HIS c 168 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA c 174 " --> pdb=" O ALA c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 206 removed outlier: 3.523A pdb=" N GLN c 193 " --> pdb=" O ALA c 189 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE c 196 " --> pdb=" O GLN c 192 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN c 204 " --> pdb=" O GLY c 200 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 224 removed outlier: 5.075A pdb=" N LEU c 213 " --> pdb=" O GLU c 209 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG c 216 " --> pdb=" O ALA c 212 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE c 218 " --> pdb=" O PHE c 214 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 4.015A pdb=" N MET c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS c 233 " --> pdb=" O PHE c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 removed outlier: 3.607A pdb=" N GLU c 243 " --> pdb=" O GLY c 239 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU c 244 " --> pdb=" O LEU c 240 " (cutoff:3.500A) Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 52 through 64 removed outlier: 3.848A pdb=" N PHE d 56 " --> pdb=" O THR d 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET d 57 " --> pdb=" O GLU d 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 130 removed outlier: 3.936A pdb=" N ILE d 122 " --> pdb=" O SER d 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG d 123 " --> pdb=" O GLN d 119 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP d 127 " --> pdb=" O ARG d 123 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 155 removed outlier: 3.772A pdb=" N PHE d 137 " --> pdb=" O LYS d 133 " (cutoff:3.500A) Proline residue: d 138 - end of helix removed outlier: 3.927A pdb=" N ASP d 143 " --> pdb=" O GLU d 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU d 147 " --> pdb=" O ASP d 143 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N CYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU d 152 " --> pdb=" O ALA d 148 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN d 153 " --> pdb=" O HIS d 149 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.988A pdb=" N HIS d 161 " --> pdb=" O HIS d 157 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 177 Proline residue: d 170 - end of helix removed outlier: 5.658A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE d 176 " --> pdb=" O MET d 172 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 82 removed outlier: 3.941A pdb=" N MET e 70 " --> pdb=" O LEU e 66 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN e 75 " --> pdb=" O ALA e 71 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN e 76 " --> pdb=" O SER e 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE e 77 " --> pdb=" O LEU e 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU e 78 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG e 81 " --> pdb=" O ILE e 77 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER e 82 " --> pdb=" O GLU e 78 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 104 removed outlier: 3.653A pdb=" N ARG e 90 " --> pdb=" O ASP e 86 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP e 93 " --> pdb=" O LEU e 89 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLU e 94 " --> pdb=" O ARG e 90 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN e 95 " --> pdb=" O ALA e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 132 removed outlier: 3.820A pdb=" N LEU e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU e 125 " --> pdb=" O GLU e 121 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN e 126 " --> pdb=" O ASP e 122 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS e 127 " --> pdb=" O MET e 123 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE e 128 " --> pdb=" O TRP e 124 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN e 130 " --> pdb=" O GLN e 126 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 137 through 143 removed outlier: 5.846A pdb=" N ASP e 141 " --> pdb=" O ILE e 137 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 194 removed outlier: 3.926A pdb=" N LEU e 192 " --> pdb=" O ALA e 188 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR e 194 " --> pdb=" O ARG e 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 264 removed outlier: 6.715A pdb=" N LEU e 260 " --> pdb=" O THR e 256 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 4.176A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG e 273 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL e 276 " --> pdb=" O VAL e 272 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.931A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 59 through 64' Processing helix chain 'f' and resid 99 through 118 removed outlier: 3.609A pdb=" N GLU f 104 " --> pdb=" O MET f 100 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR f 106 " --> pdb=" O LEU f 102 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA f 107 " --> pdb=" O ALA f 103 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS f 111 " --> pdb=" O ALA f 107 " (cutoff:3.500A) Processing helix chain 'f' and resid 163 through 178 removed outlier: 3.754A pdb=" N ALA f 167 " --> pdb=" O SER f 163 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE f 169 " --> pdb=" O THR f 165 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU f 171 " --> pdb=" O ALA f 167 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE f 173 " --> pdb=" O ILE f 169 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN f 175 " --> pdb=" O LEU f 171 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU f 178 " --> pdb=" O ILE f 174 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 53 removed outlier: 3.597A pdb=" N ARG g 50 " --> pdb=" O GLN g 46 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) Proline residue: g 53 - end of helix Processing helix chain 'g' and resid 116 through 132 removed outlier: 3.845A pdb=" N SER g 129 " --> pdb=" O GLU g 125 " (cutoff:3.500A) Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 removed outlier: 3.957A pdb=" N GLU g 163 " --> pdb=" O ALA g 159 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY g 165 " --> pdb=" O LEU g 161 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 78 removed outlier: 3.814A pdb=" N GLU h 71 " --> pdb=" O GLN h 67 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS h 75 " --> pdb=" O GLU h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 109 removed outlier: 3.744A pdb=" N LEU h 100 " --> pdb=" O LEU h 96 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA h 105 " --> pdb=" O LEU h 101 " (cutoff:3.500A) Processing helix chain 'h' and resid 113 through 118 removed outlier: 4.603A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 132 removed outlier: 3.835A pdb=" N PHE h 129 " --> pdb=" O ASP h 125 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR h 130 " --> pdb=" O VAL h 126 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 147 removed outlier: 3.953A pdb=" N SER h 146 " --> pdb=" O GLU h 142 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 54 Processing helix chain 'i' and resid 59 through 64 removed outlier: 3.535A pdb=" N LEU i 63 " --> pdb=" O ASN i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 75 removed outlier: 4.426A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 75' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 removed outlier: 3.796A pdb=" N ASN i 109 " --> pdb=" O ASP i 105 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS i 119 " --> pdb=" O ARG i 115 " (cutoff:3.500A) Processing helix chain 'j' and resid 25 through 32 removed outlier: 3.825A pdb=" N LEU j 29 " --> pdb=" O GLY j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 60 through 107 removed outlier: 3.613A pdb=" N VAL j 78 " --> pdb=" O ALA j 74 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP j 85 " --> pdb=" O SER j 81 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU j 93 " --> pdb=" O GLN j 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU j 100 " --> pdb=" O GLN j 96 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN j 105 " --> pdb=" O GLU j 101 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN j 107 " --> pdb=" O ARG j 103 " (cutoff:3.500A) Processing helix chain 'j' and resid 41 through 46 removed outlier: 4.293A pdb=" N LEU j 46 " --> pdb=" O GLY j 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 41 through 46' Processing helix chain 'k' and resid 27 through 38 removed outlier: 4.816A pdb=" N ARG k 31 " --> pdb=" O VAL k 27 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR k 36 " --> pdb=" O THR k 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 47 removed outlier: 4.353A pdb=" N SER k 44 " --> pdb=" O GLU k 40 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR k 45 " --> pdb=" O LYS k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 96 removed outlier: 4.379A pdb=" N ALA k 89 " --> pdb=" O GLU k 85 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG k 95 " --> pdb=" O ALA k 91 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA k 96 " --> pdb=" O SER k 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 134 removed outlier: 5.126A pdb=" N TRP l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER l 133 " --> pdb=" O HIS l 129 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS l 134 " --> pdb=" O ASN l 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 40 removed outlier: 5.242A pdb=" N ALA m 38 " --> pdb=" O ASP m 34 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER m 39 " --> pdb=" O SER m 35 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU m 40 " --> pdb=" O SER m 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 34 through 40' Processing helix chain 'o' and resid 28 through 51 removed outlier: 3.563A pdb=" N MET o 35 " --> pdb=" O ALA o 31 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 removed outlier: 3.568A pdb=" N ARG o 60 " --> pdb=" O ARG o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 81 removed outlier: 3.889A pdb=" N SER o 80 " --> pdb=" O ALA o 76 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 4.087A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS o 100 " --> pdb=" O ASN o 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 49 removed outlier: 3.844A pdb=" N TYR p 49 " --> pdb=" O LEU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 77 removed outlier: 3.806A pdb=" N LEU p 76 " --> pdb=" O PRO p 72 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 72 through 77' Processing helix chain 'p' and resid 112 through 123 removed outlier: 3.695A pdb=" N LYS p 118 " --> pdb=" O PRO p 114 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA p 120 " --> pdb=" O ARG p 116 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE p 121 " --> pdb=" O GLN p 117 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 163 removed outlier: 4.207A pdb=" N ILE p 154 " --> pdb=" O CYS p 150 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU p 160 " --> pdb=" O ASP p 156 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN p 163 " --> pdb=" O THR p 159 " (cutoff:3.500A) Processing helix chain 'p' and resid 174 through 190 removed outlier: 3.684A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE p 180 " --> pdb=" O HIS p 176 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET p 183 " --> pdb=" O ARG p 179 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG p 185 " --> pdb=" O GLU p 181 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 4.179A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 48 through 53' Processing helix chain 'q' and resid 54 through 64 removed outlier: 4.126A pdb=" N LYS q 59 " --> pdb=" O ARG q 55 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 93 removed outlier: 3.848A pdb=" N GLU q 84 " --> pdb=" O GLU q 80 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU q 91 " --> pdb=" O ALA q 87 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 152 removed outlier: 3.617A pdb=" N GLN q 107 " --> pdb=" O LEU q 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG q 117 " --> pdb=" O LYS q 113 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS q 127 " --> pdb=" O GLU q 123 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET q 128 " --> pdb=" O CYS q 124 " (cutoff:3.500A) Proline residue: q 129 - end of helix removed outlier: 3.768A pdb=" N VAL q 133 " --> pdb=" O PRO q 129 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN q 138 " --> pdb=" O ASN q 134 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU q 144 " --> pdb=" O ARG q 140 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA q 146 " --> pdb=" O ASN q 142 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG q 152 " --> pdb=" O ALA q 148 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 76 removed outlier: 3.502A pdb=" N SER q 74 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TRP q 76 " --> pdb=" O GLY q 73 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 76 removed outlier: 3.944A pdb=" N TRP r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN r 76 " --> pdb=" O ILE r 72 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 3.662A pdb=" N LEU r 89 " --> pdb=" O ASP r 85 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 126 removed outlier: 3.501A pdb=" N ARG r 113 " --> pdb=" O GLN r 109 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS r 120 " --> pdb=" O GLU r 116 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY r 126 " --> pdb=" O ALA r 122 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 73 removed outlier: 3.864A pdb=" N THR s 69 " --> pdb=" O ARG s 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL s 70 " --> pdb=" O TRP s 66 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 removed outlier: 3.553A pdb=" N LEU s 83 " --> pdb=" O LYS s 79 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 111 removed outlier: 3.793A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR s 108 " --> pdb=" O ARG s 104 " (cutoff:3.500A) Processing helix chain 's' and resid 140 through 155 removed outlier: 3.511A pdb=" N ALA s 144 " --> pdb=" O ALA s 140 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL s 145 " --> pdb=" O ALA s 141 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS s 147 " --> pdb=" O ARG s 143 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN s 152 " --> pdb=" O ASP s 148 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 193 removed outlier: 5.410A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU s 170 " --> pdb=" O TYR s 166 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER s 173 " --> pdb=" O SER s 169 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU s 174 " --> pdb=" O GLU s 170 " (cutoff:3.500A) Proline residue: s 175 - end of helix removed outlier: 3.533A pdb=" N VAL s 181 " --> pdb=" O LEU s 177 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER s 182 " --> pdb=" O ASP s 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL s 185 " --> pdb=" O VAL s 181 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY s 186 " --> pdb=" O SER s 182 " (cutoff:3.500A) 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: 4.392A 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 removed outlier: 4.903A pdb=" N ASN s 315 " --> pdb=" O LEU s 311 " (cutoff:3.500A) Processing helix chain 's' and resid 319 through 344 removed outlier: 3.978A pdb=" N ALA s 328 " --> pdb=" O PHE s 324 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY s 344 " --> pdb=" O ALA s 340 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 3.802A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN s 420 " --> pdb=" O ASP s 416 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN s 427 " --> pdb=" O HIS s 423 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 105 removed outlier: 3.624A pdb=" N SER u 99 " --> pdb=" O ASP u 95 " (cutoff:3.500A) Processing helix chain 'u' and resid 131 through 150 removed outlier: 3.735A pdb=" N PHE u 140 " --> pdb=" O HIS u 136 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS u 150 " --> pdb=" O TYR u 146 " (cutoff:3.500A) Processing helix chain 'u' and resid 181 through 189 removed outlier: 3.887A pdb=" N ILE u 187 " --> pdb=" O GLU u 183 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR u 188 " --> pdb=" O THR u 184 " (cutoff:3.500A) Processing helix chain 'u' and resid 190 through 196 removed outlier: 3.751A pdb=" N THR u 195 " --> pdb=" O GLU u 191 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU u 196 " --> pdb=" O LYS u 192 " (cutoff:3.500A) Processing helix chain 'v' and resid 5 through 23 removed outlier: 4.468A pdb=" N VAL v 9 " --> pdb=" O SER v 5 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA v 15 " --> pdb=" O SER v 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU v 17 " --> pdb=" O TYR v 13 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 42 removed outlier: 3.865A pdb=" N ALA v 33 " --> pdb=" O ASP v 29 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LYS v 41 " --> pdb=" O ARG v 37 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASN v 42 " --> pdb=" O GLU v 38 " (cutoff:3.500A) Processing helix chain 'v' and resid 47 through 64 removed outlier: 4.379A pdb=" N ARG v 51 " --> pdb=" O ASP v 47 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU v 52 " --> pdb=" O ALA v 48 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARG v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN v 54 " --> pdb=" O ALA v 50 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU v 56 " --> pdb=" O GLU v 52 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE v 61 " --> pdb=" O LYS v 57 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY v 64 " --> pdb=" O VAL v 60 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.638A pdb=" N ILE w 79 " --> pdb=" O THR w 75 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN w 80 " --> pdb=" O LEU w 76 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP w 81 " --> pdb=" O GLU w 77 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG w 82 " --> pdb=" O GLY w 78 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL w 83 " --> pdb=" O ILE w 79 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS w 88 " --> pdb=" O LEU w 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU w 89 " --> pdb=" O TYR w 85 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 124 removed outlier: 4.392A pdb=" N ASP w 124 " --> pdb=" O MET w 120 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 138 removed outlier: 3.806A pdb=" N GLU w 136 " --> pdb=" O ASP w 132 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU w 138 " --> pdb=" O ASP w 134 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 152 removed outlier: 3.509A pdb=" N ILE w 144 " --> pdb=" O CYS w 140 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL w 145 " --> pdb=" O PRO w 141 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP w 146 " --> pdb=" O GLN w 142 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP w 150 " --> pdb=" O ASP w 146 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS w 152 " --> pdb=" O ILE w 148 " (cutoff:3.500A) Processing helix chain 'w' and resid 104 through 109 Processing helix chain 'C' and resid 72 through 78 removed outlier: 5.482A pdb=" N ASN C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 77 " --> pdb=" O MEQ C 73 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 78' Processing helix chain 'C' and resid 100 through 121 removed outlier: 4.693A pdb=" N LYS C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 162 removed outlier: 4.186A pdb=" N GLU C 130 " --> pdb=" O PRO C 126 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LYS C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 148 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU C 160 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 153 removed outlier: 5.306A pdb=" N LEU G 148 " --> pdb=" O TYR G 144 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR G 150 " --> pdb=" O VAL G 146 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY G 151 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 166 removed outlier: 4.404A pdb=" N VAL G 159 " --> pdb=" O GLY G 155 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP G 161 " --> pdb=" O ASN G 157 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 165 " --> pdb=" O ASP G 161 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY G 166 " --> pdb=" O ALA G 162 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.597A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 190 through 194 removed outlier: 4.585A pdb=" N THR D 191 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 215 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU D 237 " --> pdb=" O TYR D 295 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 139 through 143 Processing sheet with id= 4, first strand: chain 'E' and resid 98 through 101 removed outlier: 7.324A pdb=" N TYR E 203 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 105 through 111 removed outlier: 3.776A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 176 through 181 removed outlier: 6.413A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 202 through 205 removed outlier: 4.511A pdb=" N GLN E 202 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 62 through 67 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 10, first strand: chain 'H' and resid 53 through 56 removed outlier: 5.661A pdb=" N THR H 53 " --> pdb=" O THR H 86 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 94 through 98 removed outlier: 4.118A pdb=" N ASP H 110 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'I' and resid 94 through 100 removed outlier: 3.831A pdb=" N MET I 95 " --> pdb=" O SER I 156 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA I 97 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET I 152 " --> pdb=" O CYS I 99 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'J' and resid 19 through 24 removed outlier: 3.715A pdb=" N ILE J 20 " --> pdb=" O ILE J 70 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE J 70 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL J 24 " --> pdb=" O LEU J 66 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY J 83 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS J 81 " --> pdb=" O LYS J 69 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'K' and resid 55 through 60 removed outlier: 3.568A pdb=" N MET K 60 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU K 143 " --> pdb=" O TRP K 18 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'K' and resid 77 through 81 removed outlier: 3.612A pdb=" N VAL K 90 " --> pdb=" O TYR K 77 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY K 86 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'L' and resid 38 through 41 Processing sheet with id= 17, first strand: chain 'L' and resid 72 through 75 Processing sheet with id= 18, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 19, first strand: chain 'M' and resid 273 through 276 Processing sheet with id= 20, first strand: chain 'N' and resid 94 through 97 Processing sheet with id= 21, first strand: chain 'N' and resid 118 through 123 removed outlier: 4.299A pdb=" N PHE N 119 " --> pdb=" O GLY N 164 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE N 87 " --> pdb=" O MET N 163 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.301A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG O 106 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'P' and resid 79 through 85 Processing sheet with id= 24, first strand: chain 'Q' and resid 129 through 135 removed outlier: 4.501A pdb=" N LYS Q 129 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Q' and resid 139 through 142 removed outlier: 3.539A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER Q 141 " --> pdb=" O THR Q 148 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'S' and resid 105 through 109 removed outlier: 3.566A pdb=" N LEU S 135 " --> pdb=" O VAL S 98 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE S 141 " --> pdb=" O ALA S 138 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'S' and resid 111 through 117 removed outlier: 3.671A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'S' and resid 162 through 166 removed outlier: 3.796A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR S 188 " --> pdb=" O SER S 166 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 168 through 175 removed outlier: 4.197A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 71 through 78 removed outlier: 4.629A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'T' and resid 144 through 150 removed outlier: 3.938A pdb=" N GLY T 148 " --> pdb=" O HIS T 173 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR T 171 " --> pdb=" O GLY T 150 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'T' and resid 152 through 159 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'U' and resid 26 through 29 removed outlier: 3.572A pdb=" N GLN U 27 " --> pdb=" O ARG U 43 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'V' and resid 60 through 65 removed outlier: 4.416A pdb=" N ASP V 60 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS V 72 " --> pdb=" O ILE V 64 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'V' and resid 78 through 81 removed outlier: 3.835A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'V' and resid 93 through 97 Processing sheet with id= 37, first strand: chain 'W' and resid 81 through 84 removed outlier: 4.809A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 98 through 101 Processing sheet with id= 39, first strand: chain 'X' and resid 49 through 52 removed outlier: 5.213A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU X 60 " --> pdb=" O LYS X 51 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 85 through 91 Processing sheet with id= 41, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 42, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.004A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '0' and resid 108 through 111 removed outlier: 4.606A pdb=" N HIS 0 115 " --> pdb=" O CYS 0 110 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '0' and resid 155 through 160 Processing sheet with id= 45, first strand: chain '1' and resid 16 through 22 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain '1' and resid 41 through 45 removed outlier: 6.184A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '3' and resid 122 through 125 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain '5' and resid 126 through 130 removed outlier: 3.531A pdb=" N PHE 5 354 " --> pdb=" O ASP 5 377 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR 5 347 " --> pdb=" O LEU 5 293 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '5' and resid 201 through 205 removed outlier: 6.534A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '5' and resid 206 through 214 removed outlier: 5.574A pdb=" N SER 5 207 " --> pdb=" O GLY 5 226 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY 5 226 " --> pdb=" O SER 5 207 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE 5 209 " --> pdb=" O GLY 5 224 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '5' and resid 389 through 392 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain '6' and resid 183 through 187 removed outlier: 3.920A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL 6 179 " --> pdb=" O ASP 6 183 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain '6' and resid 190 through 193 removed outlier: 3.665A pdb=" N ASN 6 191 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG 6 322 " --> pdb=" O VAL 6 193 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY 6 315 " --> pdb=" O LEU 6 272 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA 6 269 " --> pdb=" O THR 6 219 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU 6 218 " --> pdb=" O TRP 6 235 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP 6 235 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain '6' and resid 273 through 276 removed outlier: 8.865A pdb=" N THR 6 310 " --> pdb=" O ASP 6 276 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain '7' and resid 77 through 82 removed outlier: 4.121A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU 7 105 " --> pdb=" O LEU 7 128 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain '7' and resid 178 through 184 removed outlier: 7.006A pdb=" N GLN 7 298 " --> pdb=" O SER 7 281 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain '7' and resid 217 through 221 Processing sheet with id= 58, first strand: chain '7' and resid 282 through 286 removed outlier: 3.694A pdb=" N ALA 7 282 " --> pdb=" O GLN 7 298 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE 7 294 " --> pdb=" O LEU 7 286 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain '9' and resid 42 through 45 removed outlier: 3.964A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'a' and resid 45 through 52 removed outlier: 6.222A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'b' and resid 61 through 68 removed outlier: 6.070A pdb=" N VAL b 33 " --> pdb=" O ASN b 66 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG b 68 " --> pdb=" O VAL b 33 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG b 74 " --> pdb=" O SER b 32 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL b 75 " --> pdb=" O GLU b 86 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU b 86 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA b 77 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL b 84 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR b 79 " --> pdb=" O GLY b 82 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'c' and resid 254 through 257 removed outlier: 3.527A pdb=" N ARG c 259 " --> pdb=" O PHE c 271 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'c' and resid 269 through 274 removed outlier: 3.965A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'd' and resid 212 through 219 removed outlier: 3.612A pdb=" N ILE d 212 " --> pdb=" O PHE d 248 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL d 247 " --> pdb=" O THR d 263 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR d 263 " --> pdb=" O VAL d 247 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'e' and resid 174 through 178 removed outlier: 5.928A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU e 159 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU e 157 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG e 162 " --> pdb=" O HIS e 251 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N HIS e 251 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'e' and resid 211 through 214 removed outlier: 4.305A pdb=" N GLY e 211 " --> pdb=" O PHE e 233 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE e 233 " --> pdb=" O GLY e 211 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU e 201 " --> pdb=" O LEU e 239 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'e' and resid 48 through 55 removed outlier: 3.987A pdb=" N PHE e 232 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE e 234 " --> pdb=" O ALA e 50 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'f' and resid 123 through 127 removed outlier: 4.480A pdb=" N GLU f 123 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET f 127 " --> pdb=" O GLU f 154 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA f 97 " --> pdb=" O HIS f 153 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS f 187 " --> pdb=" O ASN f 92 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS f 94 " --> pdb=" O SER f 185 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER f 185 " --> pdb=" O HIS f 94 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR f 96 " --> pdb=" O ARG f 183 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG f 183 " --> pdb=" O THR f 96 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.397A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'h' and resid 58 through 61 removed outlier: 6.034A pdb=" N ARG h 58 " --> pdb=" O ASP h 136 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP h 136 " --> pdb=" O ARG h 58 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'k' and resid 49 through 56 removed outlier: 3.577A pdb=" N GLN k 15 " --> pdb=" O LEU k 67 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'm' and resid 63 through 67 Processing sheet with id= 73, first strand: chain 'p' and resid 78 through 82 removed outlier: 3.524A pdb=" N ALA p 99 " --> pdb=" O SER p 137 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER p 137 " --> pdb=" O ALA p 99 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'r' and resid 35 through 41 removed outlier: 3.602A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG r 52 " --> pdb=" O GLU r 37 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU r 50 " --> pdb=" O VAL r 39 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE r 48 " --> pdb=" O THR r 41 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 's' and resid 112 through 116 removed outlier: 6.478A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR s 362 " --> pdb=" O HIS s 300 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR s 297 " --> pdb=" O ILE s 241 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 's' and resid 206 through 216 removed outlier: 7.231A pdb=" N MET s 89 " --> pdb=" O ASP s 228 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG s 230 " --> pdb=" O MET s 89 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE s 274 " --> pdb=" O MET s 92 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 's' and resid 241 through 244 removed outlier: 6.682A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'u' and resid 107 through 114 removed outlier: 4.227A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'C' and resid 60 through 66 removed outlier: 3.701A pdb=" N GLU C 61 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN C 63 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE C 91 " --> pdb=" O HIS C 86 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'G' and resid 135 through 138 removed outlier: 3.986A pdb=" N LEU G 135 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU G 225 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL G 224 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS G 209 " --> pdb=" O VAL G 224 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU G 207 " --> pdb=" O ARG G 226 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ARG G 205 " --> pdb=" O TRP G 228 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER G 230 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL G 203 " --> pdb=" O SER G 230 " (cutoff:3.500A) 2144 hydrogen bonds defined for protein. 6330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 888 hydrogen bonds 1524 hydrogen bond angles 0 basepair planarities 367 basepair parallelities 856 stacking parallelities Total time for adding SS restraints: 69.34 Time building geometry restraints manager: 37.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 12436 1.28 - 1.42: 37384 1.42 - 1.55: 54666 1.55 - 1.69: 3189 1.69 - 1.83: 453 Bond restraints: 108128 Sorted by residual: bond pdb=" C ARG 6 28 " pdb=" N THR 6 29 " ideal model delta sigma weight residual 1.335 1.177 0.158 1.43e-02 4.89e+03 1.21e+02 bond pdb=" C VAL T 58 " pdb=" N TYR T 59 " ideal model delta sigma weight residual 1.329 1.145 0.184 3.03e-02 1.09e+03 3.69e+01 bond pdb=" CA ASN Y 195 " pdb=" C ASN Y 195 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.39e-02 5.18e+03 3.30e+01 bond pdb=" C LEU s 301 " pdb=" N LEU s 302 " ideal model delta sigma weight residual 1.331 1.206 0.125 2.83e-02 1.25e+03 1.94e+01 bond pdb=" CA GLU U 132 " pdb=" C GLU U 132 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.41e-02 5.03e+03 1.75e+01 ... (remaining 108123 not shown) Histogram of bond angle deviations from ideal: 96.44 - 104.72: 8653 104.72 - 112.99: 60419 112.99 - 121.27: 56184 121.27 - 129.55: 26810 129.55 - 137.83: 1679 Bond angle restraints: 153745 Sorted by residual: angle pdb=" N VAL I 102 " pdb=" CA VAL I 102 " pdb=" C VAL I 102 " ideal model delta sigma weight residual 113.20 103.98 9.22 9.60e-01 1.09e+00 9.22e+01 angle pdb=" N ASP G 145 " pdb=" CA ASP G 145 " pdb=" C ASP G 145 " ideal model delta sigma weight residual 114.62 104.83 9.79 1.14e+00 7.69e-01 7.37e+01 angle pdb=" C ASP G 189 " pdb=" N LEU G 190 " pdb=" CA LEU G 190 " ideal model delta sigma weight residual 121.54 137.36 -15.82 1.91e+00 2.74e-01 6.86e+01 angle pdb=" N PRO U 118 " pdb=" CA PRO U 118 " pdb=" CB PRO U 118 " ideal model delta sigma weight residual 103.25 111.76 -8.51 1.05e+00 9.07e-01 6.56e+01 angle pdb=" N PRO 8 183 " pdb=" CA PRO 8 183 " pdb=" CB PRO 8 183 " ideal model delta sigma weight residual 103.25 111.25 -8.00 1.05e+00 9.07e-01 5.80e+01 ... (remaining 153740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 58680 35.96 - 71.92: 3177 71.92 - 107.88: 188 107.88 - 143.84: 17 143.84 - 179.80: 32 Dihedral angle restraints: 62094 sinusoidal: 37441 harmonic: 24653 Sorted by residual: dihedral pdb=" CA VAL G 211 " pdb=" C VAL G 211 " pdb=" N PHE G 212 " pdb=" CA PHE G 212 " ideal model delta harmonic sigma weight residual -180.00 -128.29 -51.71 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" O4' C A3170 " pdb=" C1' C A3170 " pdb=" N1 C A3170 " pdb=" C2 C A3170 " ideal model delta sinusoidal sigma weight residual 200.00 20.20 179.80 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A2493 " pdb=" C1' C A2493 " pdb=" N1 C A2493 " pdb=" C2 C A2493 " ideal model delta sinusoidal sigma weight residual 200.00 20.24 179.76 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 62091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 16345 0.106 - 0.212: 1675 0.212 - 0.319: 76 0.319 - 0.425: 14 0.425 - 0.531: 10 Chirality restraints: 18120 Sorted by residual: chirality pdb=" CB ILE e 137 " pdb=" CA ILE e 137 " pdb=" CG1 ILE e 137 " pdb=" CG2 ILE e 137 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" C3' U A3092 " pdb=" C4' U A3092 " pdb=" O3' U A3092 " pdb=" C2' U A3092 " both_signs ideal model delta sigma weight residual False -2.48 -1.96 -0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" C3' A A2530 " pdb=" C4' A A2530 " pdb=" O3' A A2530 " pdb=" C2' A A2530 " both_signs ideal model delta sigma weight residual False -2.74 -2.27 -0.48 2.00e-01 2.50e+01 5.72e+00 ... (remaining 18117 not shown) Planarity restraints: 13853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1671 " -0.050 2.00e-02 2.50e+03 2.16e-02 1.40e+01 pdb=" N9 G A1671 " 0.049 2.00e-02 2.50e+03 pdb=" C8 G A1671 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G A1671 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A1671 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A1671 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G A1671 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G A1671 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A1671 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G A1671 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A1671 " 0.014 2.00e-02 2.50e+03 pdb=" C4 G A1671 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1703 " 0.046 2.00e-02 2.50e+03 2.49e-02 1.40e+01 pdb=" N1 C A1703 " -0.054 2.00e-02 2.50e+03 pdb=" C2 C A1703 " -0.008 2.00e-02 2.50e+03 pdb=" O2 C A1703 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C A1703 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C A1703 " 0.014 2.00e-02 2.50e+03 pdb=" N4 C A1703 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C A1703 " 0.007 2.00e-02 2.50e+03 pdb=" C6 C A1703 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 83 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C VAL C 83 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL C 83 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU C 84 " -0.022 2.00e-02 2.50e+03 ... (remaining 13850 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 14 2.03 - 2.75: 17698 2.75 - 3.46: 126482 3.46 - 4.18: 295290 4.18 - 4.90: 451920 Nonbonded interactions: 891404 Sorted by model distance: nonbonded pdb=" O3' A24 73 " pdb=" C LYSY2 29 " model vdw 1.312 3.270 nonbonded pdb=" O3' A24 73 " pdb=" O LYSY2 29 " model vdw 1.540 3.040 nonbonded pdb=" OP1 C A2915 " pdb="MG MG A3359 " model vdw 1.977 2.170 nonbonded pdb=" OP1 U A2035 " pdb="MG MG A3359 " model vdw 1.982 2.170 nonbonded pdb=" OP1 A A2430 " pdb="MG MG A3316 " model vdw 1.985 2.170 ... (remaining 891399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'Y2' and (resid 1 through 25 or resid 28)) selection = (chain 't' and (resid 1 through 25 or resid 28)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 31.580 Check model and map are aligned: 1.120 Set scattering table: 0.680 Process input model: 270.280 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 316.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 0.184 108128 Z= 0.863 Angle : 1.247 16.243 153745 Z= 0.653 Chirality : 0.066 0.531 18120 Planarity : 0.009 0.086 13853 Dihedral : 18.974 179.802 46120 Min Nonbonded Distance : 1.312 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.54 % Favored : 93.30 % Rotamer Outliers : 10.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.14 % 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: -4.57 (0.07), residues: 8247 helix: -4.48 (0.05), residues: 2598 sheet: -2.43 (0.13), residues: 1108 loop : -2.26 (0.08), residues: 4541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2331 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 763 poor density : 1568 time to evaluate : 6.771 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 outliers start: 763 outliers final: 500 residues processed: 2159 average time/residue: 1.0109 time to fit residues: 3653.5160 Evaluate side-chains 1856 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 500 poor density : 1356 time to evaluate : 6.822 Switching outliers to nearest non-outliers outliers start: 500 outliers final: 0 residues processed: 500 average time/residue: 0.7882 time to fit residues: 742.7398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 823 optimal weight: 0.6980 chunk 739 optimal weight: 0.9980 chunk 410 optimal weight: 0.8980 chunk 252 optimal weight: 0.8980 chunk 498 optimal weight: 0.0020 chunk 394 optimal weight: 0.8980 chunk 764 optimal weight: 0.7980 chunk 295 optimal weight: 4.9990 chunk 464 optimal weight: 4.9990 chunk 568 optimal weight: 0.0570 chunk 885 optimal weight: 1.9990 overall best weight: 0.4906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN D 235 GLN D 252 HIS E 57 ASN E 139 ASN E 231 HIS F 58 HIS ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN H 104 ASN H 121 ASN H 126 GLN I 61 HIS ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS I 128 ASN J 116 HIS J 133 GLN K 89 GLN K 140 ASN L 43 ASN ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN N 98 HIS N 178 GLN O 147 GLN O 150 GLN P 87 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN Q 139 GLN Q 172 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 252 GLN R 22 GLN R 30 HIS ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 ASN R 125 HIS S 118 ASN S 140 ASN T 62 GLN U 4 ASN U 55 ASN U 62 ASN U 82 HIS V 92 ASN X 215 GLN X 241 GLN Y 147 GLN Y 195 ASN Z 107 ASN 3 151 ASN 5 96 HIS 5 353 HIS 6 320 GLN 6 359 HIS 7 55 GLN 7 69 HIS 7 84 ASN 7 94 HIS 7 207 HIS 7 232 HIS 7 247 ASN 7 255 HIS 7 287 GLN ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 177 HIS ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 24 GLN b 27 GLN b 66 ASN b 123 ASN b 129 GLN c 42 GLN c 65 ASN c 128 GLN c 155 ASN c 172 ASN d 161 HIS d 167 HIS d 220 GLN e 54 GLN e 75 GLN e 95 ASN e 198 ASN e 207 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 248 ASN ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN f 94 HIS f 153 HIS f 189 HIS g 63 HIS h 67 GLN j 31 GLN o 46 HIS p 163 GLN r 112 HIS r 146 GLN r 184 ASN s 246 GLN s 281 HIS ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 343 GLN s 427 ASN u 156 HIS v 42 ASN w 115 GLN C 63 GLN C 86 HIS C 97 GLN C 139 GLN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.003 0.055 108128 Z= 0.178 Angle : 0.660 14.809 153745 Z= 0.338 Chirality : 0.040 0.289 18120 Planarity : 0.006 0.065 13853 Dihedral : 15.527 179.353 28405 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.14 (0.08), residues: 8247 helix: -2.71 (0.08), residues: 2720 sheet: -1.86 (0.14), residues: 1086 loop : -1.66 (0.09), residues: 4441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1780 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1573 time to evaluate : 6.889 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 outliers start: 207 outliers final: 84 residues processed: 1714 average time/residue: 1.0110 time to fit residues: 2912.0718 Evaluate side-chains 1434 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1350 time to evaluate : 7.071 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 0.8248 time to fit residues: 134.6653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 492 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 736 optimal weight: 0.7980 chunk 602 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 887 optimal weight: 5.9990 chunk 958 optimal weight: 9.9990 chunk 789 optimal weight: 8.9990 chunk 879 optimal weight: 5.9990 chunk 302 optimal weight: 1.9990 chunk 711 optimal weight: 0.0030 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN D 205 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN H 104 ASN I 45 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN N 98 HIS P 87 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 172 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN T 195 HIS 3 154 GLN 5 150 GLN ** 5 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 343 GLN 6 361 GLN 8 144 GLN ** 8 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 65 ASN c 94 ASN d 220 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 251 HIS ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN g 65 HIS h 87 GLN ** h 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 ASN r 65 ASN s 107 GLN s 246 GLN ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 108128 Z= 0.242 Angle : 0.624 12.731 153745 Z= 0.318 Chirality : 0.041 0.351 18120 Planarity : 0.005 0.058 13853 Dihedral : 15.226 179.408 28405 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.24 % Favored : 94.66 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.09), residues: 8247 helix: -1.62 (0.09), residues: 2732 sheet: -1.64 (0.14), residues: 1097 loop : -1.39 (0.09), residues: 4418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1637 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1372 time to evaluate : 8.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 265 outliers final: 144 residues processed: 1551 average time/residue: 1.0431 time to fit residues: 2749.3962 Evaluate side-chains 1454 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1310 time to evaluate : 6.823 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 0 residues processed: 144 average time/residue: 0.7805 time to fit residues: 223.5225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 876 optimal weight: 4.9990 chunk 666 optimal weight: 2.9990 chunk 460 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 423 optimal weight: 0.0170 chunk 595 optimal weight: 1.9990 chunk 890 optimal weight: 4.9990 chunk 942 optimal weight: 5.9990 chunk 465 optimal weight: 1.9990 chunk 843 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 HIS E 174 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 HIS ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN M 102 GLN N 138 HIS P 87 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** Z 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 106 ASN 0 118 GLN ** 5 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 275 GLN 8 158 HIS ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 ASN b 66 ASN c 65 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 252 HIS f 158 GLN g 65 HIS h 87 GLN r 65 ASN r 146 GLN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 108128 Z= 0.163 Angle : 0.564 13.365 153745 Z= 0.286 Chirality : 0.038 0.276 18120 Planarity : 0.004 0.056 13853 Dihedral : 14.985 179.773 28405 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.57 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.09), residues: 8247 helix: -0.87 (0.10), residues: 2747 sheet: -1.49 (0.14), residues: 1108 loop : -1.11 (0.09), residues: 4392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1397 time to evaluate : 6.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 171 outliers final: 79 residues processed: 1511 average time/residue: 1.0139 time to fit residues: 2579.1995 Evaluate side-chains 1383 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1304 time to evaluate : 6.709 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 0 residues processed: 79 average time/residue: 0.8386 time to fit residues: 134.6376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 784 optimal weight: 7.9990 chunk 534 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 701 optimal weight: 6.9990 chunk 388 optimal weight: 0.7980 chunk 804 optimal weight: 4.9990 chunk 651 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 481 optimal weight: 1.9990 chunk 845 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 HIS ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN P 87 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN U 74 HIS W 41 ASN 3 170 ASN ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 65 ASN c 172 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 175 GLN g 65 HIS h 87 GLN ** h 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 GLN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 139 GLN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.107 108128 Z= 0.338 Angle : 0.661 15.193 153745 Z= 0.332 Chirality : 0.043 0.311 18120 Planarity : 0.005 0.078 13853 Dihedral : 15.058 179.838 28405 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.09), residues: 8247 helix: -0.81 (0.10), residues: 2748 sheet: -1.47 (0.14), residues: 1133 loop : -1.10 (0.09), residues: 4366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1309 time to evaluate : 7.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 235 outliers final: 157 residues processed: 1460 average time/residue: 1.0056 time to fit residues: 2479.9365 Evaluate side-chains 1425 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1268 time to evaluate : 6.912 Switching outliers to nearest non-outliers outliers start: 157 outliers final: 0 residues processed: 157 average time/residue: 0.7679 time to fit residues: 237.9171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 317 optimal weight: 0.6980 chunk 848 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 553 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 943 optimal weight: 10.0000 chunk 783 optimal weight: 7.9990 chunk 436 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 312 optimal weight: 0.6980 chunk 495 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN F 97 HIS ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN M 102 GLN N 138 HIS N 209 ASN ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 170 ASN ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 360 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 65 ASN c 172 ASN d 154 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 GLN q 136 GLN r 65 ASN r 146 GLN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.064 108128 Z= 0.155 Angle : 0.558 15.128 153745 Z= 0.282 Chirality : 0.038 0.269 18120 Planarity : 0.004 0.058 13853 Dihedral : 14.868 179.969 28405 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.58 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.09), residues: 8247 helix: -0.29 (0.10), residues: 2738 sheet: -1.32 (0.14), residues: 1129 loop : -0.95 (0.09), residues: 4380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1358 time to evaluate : 6.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 48 residues processed: 1419 average time/residue: 1.0159 time to fit residues: 2429.7932 Evaluate side-chains 1338 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1290 time to evaluate : 6.739 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 48 outliers final: 1 residues processed: 48 average time/residue: 0.7682 time to fit residues: 79.3809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 909 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 537 optimal weight: 2.9990 chunk 688 optimal weight: 2.9990 chunk 533 optimal weight: 0.0170 chunk 794 optimal weight: 10.0000 chunk 526 optimal weight: 4.9990 chunk 939 optimal weight: 5.9990 chunk 588 optimal weight: 1.9990 chunk 572 optimal weight: 2.9990 chunk 433 optimal weight: 0.5980 overall best weight: 1.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN L 143 ASN M 26 ASN M 102 GLN P 87 GLN P 97 GLN ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN W 41 ASN Z 47 GLN 0 106 ASN 1 35 ASN 3 170 ASN ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 285 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 65 ASN c 172 ASN d 154 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** h 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 65 ASN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 156 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 108128 Z= 0.243 Angle : 0.595 15.804 153745 Z= 0.299 Chirality : 0.040 0.292 18120 Planarity : 0.005 0.058 13853 Dihedral : 14.844 179.679 28405 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.24 % Favored : 94.66 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.09), residues: 8247 helix: -0.24 (0.10), residues: 2745 sheet: -1.29 (0.14), residues: 1143 loop : -0.91 (0.09), residues: 4359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1325 time to evaluate : 6.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 73 residues processed: 1410 average time/residue: 1.0208 time to fit residues: 2433.4596 Evaluate side-chains 1365 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1292 time to evaluate : 6.796 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.7476 time to fit residues: 114.0644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 581 optimal weight: 0.9980 chunk 375 optimal weight: 3.9990 chunk 561 optimal weight: 0.7980 chunk 283 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 597 optimal weight: 4.9990 chunk 640 optimal weight: 0.6980 chunk 464 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 738 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN N 209 ASN ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN Z 47 GLN 1 35 ASN 3 170 ASN 5 360 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 ASN c 172 ASN d 154 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN r 146 GLN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 156 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 108128 Z= 0.165 Angle : 0.557 16.017 153745 Z= 0.282 Chirality : 0.038 0.278 18120 Planarity : 0.004 0.058 13853 Dihedral : 14.768 179.469 28405 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.09), residues: 8247 helix: 0.01 (0.10), residues: 2736 sheet: -1.16 (0.15), residues: 1096 loop : -0.82 (0.09), residues: 4415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1415 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1346 time to evaluate : 6.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 47 residues processed: 1384 average time/residue: 1.0249 time to fit residues: 2397.9122 Evaluate side-chains 1353 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1306 time to evaluate : 6.809 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 47 outliers final: 1 residues processed: 47 average time/residue: 0.7696 time to fit residues: 77.5552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 854 optimal weight: 4.9990 chunk 900 optimal weight: 5.9990 chunk 821 optimal weight: 5.9990 chunk 875 optimal weight: 4.9990 chunk 527 optimal weight: 5.9990 chunk 381 optimal weight: 2.9990 chunk 687 optimal weight: 7.9990 chunk 268 optimal weight: 0.8980 chunk 791 optimal weight: 3.9990 chunk 828 optimal weight: 4.9990 chunk 872 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN N 86 ASN ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN W 41 ASN 3 170 ASN 7 285 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 ASN c 172 ASN d 154 ASN ** f 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN i 120 HIS k 80 HIS r 65 ASN s 164 HIS ** s 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.141 108128 Z= 0.479 Angle : 0.749 14.919 153745 Z= 0.374 Chirality : 0.048 0.347 18120 Planarity : 0.006 0.090 13853 Dihedral : 15.122 179.547 28405 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.17 % Favored : 93.73 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.09), residues: 8247 helix: -0.55 (0.10), residues: 2732 sheet: -1.32 (0.14), residues: 1125 loop : -1.05 (0.09), residues: 4390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1410 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1296 time to evaluate : 7.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 85 residues processed: 1357 average time/residue: 1.0332 time to fit residues: 2367.4016 Evaluate side-chains 1357 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1272 time to evaluate : 7.034 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 85 outliers final: 1 residues processed: 85 average time/residue: 0.7932 time to fit residues: 136.4870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 575 optimal weight: 0.9980 chunk 926 optimal weight: 4.9990 chunk 565 optimal weight: 0.9980 chunk 439 optimal weight: 0.9990 chunk 643 optimal weight: 0.9980 chunk 971 optimal weight: 1.9990 chunk 894 optimal weight: 2.9990 chunk 773 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 597 optimal weight: 6.9990 chunk 474 optimal weight: 0.0870 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN H 104 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 HIS N 209 ASN ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 170 ASN 5 360 ASN 7 285 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 65 ASN c 172 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN r 146 GLN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 156 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 108128 Z= 0.180 Angle : 0.586 15.522 153745 Z= 0.296 Chirality : 0.039 0.277 18120 Planarity : 0.004 0.057 13853 Dihedral : 14.881 179.914 28405 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.04 (0.09), residues: 8247 helix: -0.09 (0.10), residues: 2737 sheet: -1.21 (0.14), residues: 1114 loop : -0.86 (0.09), residues: 4396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16494 Ramachandran restraints generated. 8247 Oldfield, 0 Emsley, 8247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1326 time to evaluate : 6.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 1342 average time/residue: 1.0446 time to fit residues: 2364.6526 Evaluate side-chains 1310 residues out of total 7430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1287 time to evaluate : 6.991 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.8198 time to fit residues: 44.7562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 614 optimal weight: 2.9990 chunk 823 optimal weight: 5.9990 chunk 236 optimal weight: 0.0570 chunk 713 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 774 optimal weight: 0.8980 chunk 324 optimal weight: 2.9990 chunk 795 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN K 147 GLN N 138 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN 3 170 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 65 ASN c 172 ASN d 154 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 92 ASN h 67 GLN k 93 HIS ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 156 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.145758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.116418 restraints weight = 140661.920| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.20 r_work: 0.3009 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 108128 Z= 0.156 Angle : 0.557 15.339 153745 Z= 0.281 Chirality : 0.037 0.266 18120 Planarity : 0.004 0.060 13853 Dihedral : 14.679 179.572 28405 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.84 % Favored : 95.10 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.74 (0.09), residues: 8247 helix: 0.24 (0.10), residues: 2732 sheet: -1.08 (0.15), residues: 1102 loop : -0.74 (0.10), residues: 4413 =============================================================================== Job complete usr+sys time: 36884.63 seconds wall clock time: 642 minutes 28.10 seconds (38548.10 seconds total)