Starting phenix.real_space_refine (version: dev) on Tue Apr 19 21:37:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jut_6646/04_2022/5jut_6646_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jut_6646/04_2022/5jut_6646.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jut_6646/04_2022/5jut_6646_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jut_6646/04_2022/5jut_6646_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jut_6646/04_2022/5jut_6646_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jut_6646/04_2022/5jut_6646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jut_6646/04_2022/5jut_6646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jut_6646/04_2022/5jut_6646_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jut_6646/04_2022/5jut_6646_neut_updated.pdb" } resolution = 4.0 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= -0.002 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F ASP 161": "OD1" <-> "OD2" Residue "F ARG 190": "NH1" <-> "NH2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F ARG 200": "NH1" <-> "NH2" Residue "F ASP 208": "OD1" <-> "OD2" Residue "G TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 71": "OE1" <-> "OE2" Residue "G ASP 112": "OD1" <-> "OD2" Residue "G TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 145": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G ASP 290": "OD1" <-> "OD2" Residue "G TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 316": "OE1" <-> "OE2" Residue "G ASP 320": "OD1" <-> "OD2" Residue "G PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G GLU 353": "OE1" <-> "OE2" Residue "G PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 369": "NH1" <-> "NH2" Residue "G GLU 375": "OE1" <-> "OE2" Residue "H ARG 3": "NH1" <-> "NH2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "H GLU 211": "OE1" <-> "OE2" Residue "H PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 326": "NH1" <-> "NH2" Residue "H PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 337": "OE1" <-> "OE2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I ASP 29": "OD1" <-> "OD2" Residue "I TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 136": "OE1" <-> "OE2" Residue "I ARG 140": "NH1" <-> "NH2" Residue "I PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "I ASP 191": "OD1" <-> "OD2" Residue "I TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 209": "OE1" <-> "OE2" Residue "I ASP 213": "OD1" <-> "OD2" Residue "I ASP 214": "OD1" <-> "OD2" Residue "I ASP 215": "OD1" <-> "OD2" Residue "I PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 221": "OE1" <-> "OE2" Residue "I ASP 234": "OD1" <-> "OD2" Residue "I ASP 250": "OD1" <-> "OD2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 257": "OE1" <-> "OE2" Residue "I GLU 263": "OE1" <-> "OE2" Residue "I GLU 268": "OE1" <-> "OE2" Residue "J TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 104": "OE1" <-> "OE2" Residue "J TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "J GLU 118": "OE1" <-> "OE2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "J PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 30": "NH1" <-> "NH2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 170": "OE1" <-> "OE2" Residue "K TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "K PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 234": "OE1" <-> "OE2" Residue "L GLU 54": "OE1" <-> "OE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 204": "NH1" <-> "NH2" Residue "L TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 228": "OE1" <-> "OE2" Residue "L ASP 247": "OD1" <-> "OD2" Residue "M GLU 7": "OE1" <-> "OE2" Residue "M GLU 11": "OE1" <-> "OE2" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M ARG 23": "NH1" <-> "NH2" Residue "M ASP 42": "OD1" <-> "OD2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "M ASP 107": "OD1" <-> "OD2" Residue "M ASP 120": "OD1" <-> "OD2" Residue "M GLU 135": "OE1" <-> "OE2" Residue "M ASP 142": "OD1" <-> "OD2" Residue "M ARG 168": "NH1" <-> "NH2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N GLU 45": "OE1" <-> "OE2" Residue "N GLU 56": "OE1" <-> "OE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 150": "OE1" <-> "OE2" Residue "N TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 177": "OD1" <-> "OD2" Residue "N ARG 185": "NH1" <-> "NH2" Residue "N PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 212": "OE1" <-> "OE2" Residue "N GLU 215": "OE1" <-> "OE2" Residue "O GLU 15": "OE1" <-> "OE2" Residue "O GLU 25": "OE1" <-> "OE2" Residue "O GLU 38": "OE1" <-> "OE2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ARG 55": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 108": "OE1" <-> "OE2" Residue "O TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 117": "OD1" <-> "OD2" Residue "O TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 168": "OD1" <-> "OD2" Residue "O ASP 170": "OD1" <-> "OD2" Residue "P GLU 131": "OE1" <-> "OE2" Residue "P ASP 144": "OD1" <-> "OD2" Residue "Q PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q ASP 27": "OD1" <-> "OD2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 49": "NH1" <-> "NH2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q GLU 136": "OE1" <-> "OE2" Residue "Q PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 153": "OD1" <-> "OD2" Residue "Q PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 171": "NH1" <-> "NH2" Residue "Q GLU 176": "OE1" <-> "OE2" Residue "Q GLU 194": "OE1" <-> "OE2" Residue "R ARG 19": "NH1" <-> "NH2" Residue "R ASP 47": "OD1" <-> "OD2" Residue "R ARG 108": "NH1" <-> "NH2" Residue "R PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 20": "NH1" <-> "NH2" Residue "S TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 103": "OE1" <-> "OE2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "S TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 136": "OD1" <-> "OD2" Residue "T GLU 46": "OE1" <-> "OE2" Residue "T PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 100": "OE1" <-> "OE2" Residue "T ASP 113": "OD1" <-> "OD2" Residue "T ASP 151": "OD1" <-> "OD2" Residue "U ARG 3": "NH1" <-> "NH2" Residue "U TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 31": "OE1" <-> "OE2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "U TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 56": "NH1" <-> "NH2" Residue "U PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "U PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 103": "OE1" <-> "OE2" Residue "U ASP 108": "OD1" <-> "OD2" Residue "U ARG 126": "NH1" <-> "NH2" Residue "U ARG 128": "NH1" <-> "NH2" Residue "U TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 154": "OE1" <-> "OE2" Residue "U GLU 155": "OE1" <-> "OE2" Residue "U ARG 175": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "V ARG 92": "NH1" <-> "NH2" Residue "V PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 120": "OE1" <-> "OE2" Residue "V ASP 125": "OD1" <-> "OD2" Residue "V GLU 148": "OE1" <-> "OE2" Residue "V PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 176": "NH1" <-> "NH2" Residue "V ARG 178": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 110": "NH1" <-> "NH2" Residue "W TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 126": "OE1" <-> "OE2" Residue "W ARG 162": "NH1" <-> "NH2" Residue "W ARG 163": "NH1" <-> "NH2" Residue "X GLU 6": "OE1" <-> "OE2" Residue "X ARG 28": "NH1" <-> "NH2" Residue "X TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X ARG 80": "NH1" <-> "NH2" Residue "X GLU 104": "OE1" <-> "OE2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X GLU 128": "OE1" <-> "OE2" Residue "X ARG 155": "NH1" <-> "NH2" Residue "X PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 8": "NH1" <-> "NH2" Residue "Y TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 18": "OD1" <-> "OD2" Residue "Y PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 108": "NH1" <-> "NH2" Residue "Y ARG 139": "NH1" <-> "NH2" Residue "Z TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 39": "OD1" <-> "OD2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "Z ASP 91": "OD1" <-> "OD2" Residue "Z TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ASP 27": "OD1" <-> "OD2" Residue "AA ARG 32": "NH1" <-> "NH2" Residue "AA TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ASP 97": "OD1" <-> "OD2" Residue "BA GLU 4": "OE1" <-> "OE2" Residue "BA ASP 25": "OD1" <-> "OD2" Residue "BA PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA GLU 101": "OE1" <-> "OE2" Residue "CA ASP 106": "OD1" <-> "OD2" Residue "CA ARG 125": "NH1" <-> "NH2" Residue "CA ASP 131": "OD1" <-> "OD2" Residue "CA ARG 138": "NH1" <-> "NH2" Residue "DA TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA GLU 38": "OE1" <-> "OE2" Residue "DA GLU 67": "OE1" <-> "OE2" Residue "DA ASP 112": "OD1" <-> "OD2" Residue "DA ARG 121": "NH1" <-> "NH2" Residue "EA GLU 31": "OE1" <-> "OE2" Residue "EA GLU 47": "OE1" <-> "OE2" Residue "EA TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA ARG 84": "NH1" <-> "NH2" Residue "EA TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA GLU 90": "OE1" <-> "OE2" Residue "EA GLU 108": "OE1" <-> "OE2" Residue "EA PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA ARG 135": "NH1" <-> "NH2" Residue "FA TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA GLU 97": "OE1" <-> "OE2" Residue "FA ASP 103": "OD1" <-> "OD2" Residue "FA GLU 135": "OE1" <-> "OE2" Residue "HA GLU 57": "OE1" <-> "OE2" Residue "HA GLU 76": "OE1" <-> "OE2" Residue "HA ASP 97": "OD1" <-> "OD2" Residue "HA ASP 99": "OD1" <-> "OD2" Residue "IA TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA ARG 70": "NH1" <-> "NH2" Residue "IA PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA GLU 94": "OE1" <-> "OE2" Residue "JA PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA GLU 3": "OE1" <-> "OE2" Residue "KA ARG 60": "NH1" <-> "NH2" Residue "LA ASP 46": "OD1" <-> "OD2" Residue "LA TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 107": "OE1" <-> "OE2" Residue "MA GLU 15": "OE1" <-> "OE2" Residue "MA GLU 30": "OE1" <-> "OE2" Residue "MA ARG 105": "NH1" <-> "NH2" Residue "NA TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA GLU 66": "OE1" <-> "OE2" Residue "NA GLU 89": "OE1" <-> "OE2" Residue "OA TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OA ARG 63": "NH1" <-> "NH2" Residue "RA GLU 79": "OE1" <-> "OE2" Residue "SA ARG 21": "NH1" <-> "NH2" Residue "SA ARG 23": "NH1" <-> "NH2" Residue "TA ARG 18": "NH1" <-> "NH2" Residue "TA TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA GLU 73": "OE1" <-> "OE2" Residue "TA GLU 92": "OE1" <-> "OE2" Residue "TA GLU 96": "OE1" <-> "OE2" Residue "UA GLU 30": "OE1" <-> "OE2" Residue "UA ARG 36": "NH1" <-> "NH2" Residue "UA ASP 38": "OD1" <-> "OD2" Residue "UA GLU 88": "OE1" <-> "OE2" Residue "UA GLU 91": "OE1" <-> "OE2" Residue "VA GLU 6": "OE1" <-> "OE2" Residue "VA TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA ASP 31": "OD1" <-> "OD2" Residue "VA GLU 40": "OE1" <-> "OE2" Residue "VA GLU 44": "OE1" <-> "OE2" Residue "VA GLU 74": "OE1" <-> "OE2" Residue "VA PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA GLU 91": "OE1" <-> "OE2" Residue "VA PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA GLU 169": "OE1" <-> "OE2" Residue "VA PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WA GLU 14": "OE1" <-> "OE2" Residue "WA GLU 98": "OE1" <-> "OE2" Residue "WA ASP 116": "OD1" <-> "OD2" Residue "WA ASP 164": "OD1" <-> "OD2" Residue "WA PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WA GLU 277": "OE1" <-> "OE2" Residue "WA TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "XA GLU 12": "OE1" <-> "OE2" Residue "XA ARG 41": "NH1" <-> "NH2" Residue "XA ASP 43": "OD1" <-> "OD2" Residue "XA GLU 71": "OE1" <-> "OE2" Residue "XA ASP 72": "OD1" <-> "OD2" Residue "XA PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "XA ASP 150": "OD1" <-> "OD2" Residue "XA GLU 154": "OE1" <-> "OE2" Residue "XA ASP 200": "OD1" <-> "OD2" Residue "XA TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "XA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA ASP 72": "OD1" <-> "OD2" Residue "YA GLU 77": "OE1" <-> "OE2" Residue "YA ARG 87": "NH1" <-> "NH2" Residue "YA PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA ARG 144": "NH1" <-> "NH2" Residue "YA ARG 152": "NH1" <-> "NH2" Residue "YA GLU 196": "OE1" <-> "OE2" Residue "YA ARG 213": "NH1" <-> "NH2" Residue "YA PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA ASP 224": "OD1" <-> "OD2" Residue "ZA GLU 65": "OE1" <-> "OE2" Residue "ZA GLU 79": "OE1" <-> "OE2" Residue "ZA ARG 91": "NH1" <-> "NH2" Residue "ZA ARG 141": "NH1" <-> "NH2" Residue "AB ARG 9": "NH1" <-> "NH2" Residue "AB GLU 28": "OE1" <-> "OE2" Residue "AB ARG 65": "NH1" <-> "NH2" Residue "AB GLU 89": "OE1" <-> "OE2" Residue "AB ARG 90": "NH1" <-> "NH2" Residue "AB ARG 124": "NH1" <-> "NH2" Residue "AB GLU 128": "OE1" <-> "OE2" Residue "AB GLU 135": "OE1" <-> "OE2" Residue "AB ARG 143": "NH1" <-> "NH2" Residue "AB ARG 146": "NH1" <-> "NH2" Residue "AB PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB ASP 191": "OD1" <-> "OD2" Residue "AB GLU 210": "OE1" <-> "OE2" Residue "AB GLU 213": "OE1" <-> "OE2" Residue "AB GLU 214": "OE1" <-> "OE2" Residue "BB ARG 11": "NH1" <-> "NH2" Residue "BB ASP 21": "OD1" <-> "OD2" Residue "BB GLU 40": "OE1" <-> "OE2" Residue "BB ARG 49": "NH1" <-> "NH2" Residue "BB ARG 59": "NH1" <-> "NH2" Residue "BB ARG 108": "NH1" <-> "NH2" Residue "BB GLU 118": "OE1" <-> "OE2" Residue "BB ARG 148": "NH1" <-> "NH2" Residue "BB ASP 163": "OD1" <-> "OD2" Residue "BB ASP 176": "OD1" <-> "OD2" Residue "BB TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB ARG 200": "NH1" <-> "NH2" Residue "BB ASP 202": "OD1" <-> "OD2" Residue "BB PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB ARG 252": "NH1" <-> "NH2" Residue "CB GLU 31": "OE1" <-> "OE2" Residue "CB GLU 52": "OE1" <-> "OE2" Residue "CB ARG 65": "NH1" <-> "NH2" Residue "CB ARG 76": "NH1" <-> "NH2" Residue "CB ASP 135": "OD1" <-> "OD2" Residue "CB GLU 144": "OE1" <-> "OE2" Residue "CB ASP 145": "OD1" <-> "OD2" Residue "CB ARG 148": "NH1" <-> "NH2" Residue "CB PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB GLU 196": "OE1" <-> "OE2" Residue "CB GLU 197": "OE1" <-> "OE2" Residue "CB ARG 219": "NH1" <-> "NH2" Residue "DB TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DB GLU 17": "OE1" <-> "OE2" Residue "DB ARG 23": "NH1" <-> "NH2" Residue "DB PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DB GLU 39": "OE1" <-> "OE2" Residue "DB ASP 57": "OD1" <-> "OD2" Residue "DB TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DB ARG 92": "NH1" <-> "NH2" Residue "DB ARG 98": "NH1" <-> "NH2" Residue "DB GLU 122": "OE1" <-> "OE2" Residue "DB ARG 137": "NH1" <-> "NH2" Residue "DB PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DB ASP 151": "OD1" <-> "OD2" Residue "DB GLU 161": "OE1" <-> "OE2" Residue "DB ARG 191": "NH1" <-> "NH2" Residue "DB ARG 219": "NH1" <-> "NH2" Residue "DB GLU 222": "OE1" <-> "OE2" Residue "EB GLU 28": "OE1" <-> "OE2" Residue "EB ARG 39": "NH1" <-> "NH2" Residue "EB PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB ARG 104": "NH1" <-> "NH2" Residue "EB GLU 127": "OE1" <-> "OE2" Residue "EB PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB GLU 134": "OE1" <-> "OE2" Residue "EB TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB ASP 155": "OD1" <-> "OD2" Residue "FB ASP 6": "OD1" <-> "OD2" Residue "FB ARG 8": "NH1" <-> "NH2" Residue "FB PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FB ARG 22": "NH1" <-> "NH2" Residue "FB GLU 28": "OE1" <-> "OE2" Residue "FB ARG 47": "NH1" <-> "NH2" Residue "FB ARG 59": "NH1" <-> "NH2" Residue "FB GLU 61": "OE1" <-> "OE2" Residue "FB ARG 110": "NH1" <-> "NH2" Residue "FB PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FB GLU 140": "OE1" <-> "OE2" Residue "FB GLU 157": "OE1" <-> "OE2" Residue "FB ARG 164": "NH1" <-> "NH2" Residue "FB ARG 178": "NH1" <-> "NH2" Residue "FB PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FB ARG 194": "NH1" <-> "NH2" Residue "GB ARG 3": "NH1" <-> "NH2" Residue "GB TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GB ARG 17": "NH1" <-> "NH2" Residue "GB ARG 53": "NH1" <-> "NH2" Residue "GB ARG 54": "NH1" <-> "NH2" Residue "GB ARG 62": "NH1" <-> "NH2" Residue "GB PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GB ARG 78": "NH1" <-> "NH2" Residue "GB GLU 88": "OE1" <-> "OE2" Residue "GB TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GB GLU 102": "OE1" <-> "OE2" Residue "GB ASP 103": "OD1" <-> "OD2" Residue "GB GLU 153": "OE1" <-> "OE2" Residue "GB ARG 168": "NH1" <-> "NH2" Residue "GB ARG 171": "NH1" <-> "NH2" Residue "HB GLU 6": "OE1" <-> "OE2" Residue "HB ASP 26": "OD1" <-> "OD2" Residue "HB TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB GLU 71": "OE1" <-> "OE2" Residue "HB GLU 74": "OE1" <-> "OE2" Residue "HB GLU 78": "OE1" <-> "OE2" Residue "HB ARG 95": "NH1" <-> "NH2" Residue "IB PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IB PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IB ARG 30": "NH1" <-> "NH2" Residue "IB ARG 33": "NH1" <-> "NH2" Residue "IB TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IB TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IB GLU 101": "OE1" <-> "OE2" Residue "IB ARG 116": "NH1" <-> "NH2" Residue "IB PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KB GLU 31": "OE1" <-> "OE2" Residue "KB ASP 87": "OD1" <-> "OD2" Residue "KB ARG 104": "NH1" <-> "NH2" Residue "KB ARG 106": "NH1" <-> "NH2" Residue "KB ASP 108": "OD1" <-> "OD2" Residue "KB GLU 119": "OE1" <-> "OE2" Residue "KB GLU 142": "OE1" <-> "OE2" Residue "LB ASP 66": "OD1" <-> "OD2" Residue "LB GLU 73": "OE1" <-> "OE2" Residue "LB ARG 90": "NH1" <-> "NH2" Residue "LB ARG 103": "NH1" <-> "NH2" Residue "LB ARG 107": "NH1" <-> "NH2" Residue "LB ASP 124": "OD1" <-> "OD2" Residue "MB ARG 10": "NH1" <-> "NH2" Residue "MB PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB GLU 23": "OE1" <-> "OE2" Residue "MB GLU 31": "OE1" <-> "OE2" Residue "MB ARG 47": "NH1" <-> "NH2" Residue "MB GLU 71": "OE1" <-> "OE2" Residue "MB ARG 77": "NH1" <-> "NH2" Residue "MB GLU 88": "OE1" <-> "OE2" Residue "MB TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB GLU 110": "OE1" <-> "OE2" Residue "MB TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB ARG 127": "NH1" <-> "NH2" Residue "NB GLU 40": "OE1" <-> "OE2" Residue "NB GLU 50": "OE1" <-> "OE2" Residue "NB ASP 58": "OD1" <-> "OD2" Residue "NB ASP 64": "OD1" <-> "OD2" Residue "NB TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NB ASP 113": "OD1" <-> "OD2" Residue "NB ARG 114": "NH1" <-> "NH2" Residue "NB ARG 143": "NH1" <-> "NH2" Residue "OB ARG 3": "NH1" <-> "NH2" Residue "OB TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB ARG 33": "NH1" <-> "NH2" Residue "OB ASP 36": "OD1" <-> "OD2" Residue "OB GLU 37": "OE1" <-> "OE2" Residue "OB TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB ARG 67": "NH1" <-> "NH2" Residue "PB ASP 53": "OD1" <-> "OD2" Residue "PB GLU 60": "OE1" <-> "OE2" Residue "PB ARG 88": "NH1" <-> "NH2" Residue "PB ASP 94": "OD1" <-> "OD2" Residue "PB ASP 97": "OD1" <-> "OD2" Residue "PB ARG 115": "NH1" <-> "NH2" Residue "PB ARG 120": "NH1" <-> "NH2" Residue "PB ARG 144": "NH1" <-> "NH2" Residue "PB ARG 145": "NH1" <-> "NH2" Residue "QB ASP 8": "OD1" <-> "OD2" Residue "QB TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QB GLU 109": "OE1" <-> "OE2" Residue "QB GLU 126": "OE1" <-> "OE2" Residue "QB ASP 133": "OD1" <-> "OD2" Residue "QB GLU 142": "OE1" <-> "OE2" Residue "QB GLU 144": "OE1" <-> "OE2" Residue "RB ARG 57": "NH1" <-> "NH2" Residue "RB GLU 74": "OE1" <-> "OE2" Residue "RB TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RB ARG 89": "NH1" <-> "NH2" Residue "SB ASP 4": "OD1" <-> "OD2" Residue "SB GLU 10": "OE1" <-> "OE2" Residue "SB ASP 27": "OD1" <-> "OD2" Residue "SB ASP 28": "OD1" <-> "OD2" Residue "SB GLU 42": "OE1" <-> "OE2" Residue "SB GLU 49": "OE1" <-> "OE2" Residue "SB TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB ARG 60": "NH1" <-> "NH2" Residue "SB ARG 71": "NH1" <-> "NH2" Residue "SB ASP 76": "OD1" <-> "OD2" Residue "SB TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TB GLU 115": "OE1" <-> "OE2" Residue "UB ARG 16": "NH1" <-> "NH2" Residue "UB ARG 19": "NH1" <-> "NH2" Residue "UB GLU 60": "OE1" <-> "OE2" Residue "UB ASP 90": "OD1" <-> "OD2" Residue "UB ASP 100": "OD1" <-> "OD2" Residue "UB ASP 116": "OD1" <-> "OD2" Residue "UB GLU 138": "OE1" <-> "OE2" Residue "UB ARG 144": "NH1" <-> "NH2" Residue "VB ARG 20": "NH1" <-> "NH2" Residue "VB ARG 32": "NH1" <-> "NH2" Residue "VB GLU 39": "OE1" <-> "OE2" Residue "VB ASP 53": "OD1" <-> "OD2" Residue "VB PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VB GLU 101": "OE1" <-> "OE2" Residue "VB ARG 131": "NH1" <-> "NH2" Residue "WB ARG 49": "NH1" <-> "NH2" Residue "WB TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WB TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WB GLU 86": "OE1" <-> "OE2" Residue "WB ARG 103": "NH1" <-> "NH2" Residue "XB ARG 10": "NH1" <-> "NH2" Residue "XB GLU 46": "OE1" <-> "OE2" Residue "XB ARG 51": "NH1" <-> "NH2" Residue "XB TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YB ASP 6": "OD1" <-> "OD2" Residue "YB PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YB PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YB GLU 75": "OE1" <-> "OE2" Residue "YB PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZB PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZB GLU 34": "OE1" <-> "OE2" Residue "ZB ARG 65": "NH1" <-> "NH2" Residue "AC PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ARG 54": "NH1" <-> "NH2" Residue "DC ASP 85": "OD1" <-> "OD2" Residue "DC PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC GLU 114": "OE1" <-> "OE2" Residue "DC ASP 161": "OD1" <-> "OD2" Residue "DC GLU 166": "OE1" <-> "OE2" Residue "DC GLU 195": "OE1" <-> "OE2" Residue "DC PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC ASP 236": "OD1" <-> "OD2" Residue "DC PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC GLU 315": "OE1" <-> "OE2" Residue "DC TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC ASP 447": "OD1" <-> "OD2" Residue "DC ASP 460": "OD1" <-> "OD2" Residue "DC GLU 473": "OE1" <-> "OE2" Residue "DC GLU 591": "OE1" <-> "OE2" Residue "DC GLU 602": "OE1" <-> "OE2" Residue "DC PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC ASP 622": "OD1" <-> "OD2" Residue "DC PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC GLU 679": "OE1" <-> "OE2" Residue "DC ASP 696": "OD1" <-> "OD2" Residue "DC TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC ASP 799": "OD1" <-> "OD2" Residue "DC ASP 807": "OD1" <-> "OD2" Residue "DC GLU 830": "OE1" <-> "OE2" Residue "DC TYR 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 215222 Number of models: 1 Model: "" Number of chains: 84 Chain: "A" Number of atoms: 37658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1781, 37658 Classifications: {'RNA': 1764, 'DNA': 17} Modifications used: {'rna3p_pyr': 673, 'p5*END': 1, 'rna2p_pur': 153, 'rna2p_pyr': 158, 'rna3p_pur': 773} Link IDs: {'rna3p': 1470, 'rna2p': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 534 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {' G:plan2': 7, ' A:plan': 3, ' C:plan': 7, ' U:plan': 7, ' G:plan': 7, ' C:plan2': 7, ' A:plan2': 3} Unresolved non-hydrogen planarities: 277 Chain: "B" Number of atoms: 70288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3309, 70288 Classifications: {'RNA': 3282, 'DNA': 27} Modifications used: {'rna3p_pyr': 1250, 'rna2p_pur': 322, 'rna3p_pur': 1485, 'rna2p_pyr': 213} Link IDs: {'rna3p': 2773, 'rna2p': 535} Chain breaks: 3 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {' G:plan2': 12, ' A:plan': 6, ' C:plan': 9, ' U:plan': 12, ' G:plan': 12, ' C:plan2': 9, ' A:plan2': 6} Unresolved non-hydrogen planarities: 453 Chain: "C" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3354 Classifications: {'RNA': 158} Modifications used: {'rna2p_pyr': 14, 'rna3p_pyr': 66, 'p5*END': 1, 'rna3p_pur': 63, 'rna2p_pur': 15} Link IDs: {'rna3p': 129, 'rna2p': 28} Chain: "D" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2580 Classifications: {'RNA': 121} Modifications used: {'rna3p_pyr': 51, 'p5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 57, 'rna2p_pyr': 7} Link IDs: {'rna3p': 108, 'rna2p': 12} Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1359 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain breaks: 2 Chain: "F" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1918 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 240, 'PCIS': 1} Chain: "G" Number of atoms: 3082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3082 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 371, 'PCIS': 2} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2750 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 343, 'PCIS': 1} Chain: "I" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2376 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain: "J" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1401 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165, 'PCIS': 2} Chain: "K" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1785 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "L" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1818 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "M" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1519 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1718 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Chain: "O" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1354 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "P" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 723 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "Q" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "R" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1054 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "S" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1721 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "T" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1556 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "U" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1443 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain: "V" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1442 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "W" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1522 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain: "X" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1446 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "Y" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1277 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "Z" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "AA" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1004 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "BA" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 509 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "CA" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "DA" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "EA" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1093 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "FA" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1174 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "GA" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 463 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "HA" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "IA" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 890 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "JA" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "KA" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 101, 'PCIS': 1} Chain: "LA" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "MA" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 970 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "NA" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 772 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "OA" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 682 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84, 'PCIS': 1} Chain: "PA" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 613 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "QA" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 437 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "RA" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 418 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "SA" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 234 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "TA" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 848 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "UA" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 695 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "VA" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1473 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "WA" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2445 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 309, 'PCIS': 1} Chain: "XA" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 15, 'TRANS': 189, 'PCIS': 1} Chain: "YA" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "ZA" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1635 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain: "AB" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1734 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "BB" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "CB" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1610 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain: "DB" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1820 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "EB" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "FB" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1490 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "GB" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "HB" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 817 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "IB" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1245 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "JB" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 496 Classifications: {'peptide': 124} Incomplete info: {'backbone_only': 114} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 447 Unresolved non-hydrogen angles: 655 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 158 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 173 Chain: "KB" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1193 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 142, 'PCIS': 1} Chain: "LB" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 942 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "MB" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} Chain: "NB" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1106 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134, 'PCIS': 1} Chain: "OB" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 836 Classifications: {'peptide': 117} Incomplete info: {'backbone_only': 25} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "PB" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1193 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "QB" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1113 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "RB" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "SB" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 685 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "TB" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1022 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 125, 'PCIS': 2} Chain: "UB" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 137, 'PCIS': 1} Chain: "VB" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1074 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "WB" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 563 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "XB" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "YB" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 611 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "ZB" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 498 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "AC" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "BC" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 475 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain: "CC" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 284 Classifications: {'peptide': 71} Incomplete info: {'backbone_only': 67} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 114 Chain: "DC" Number of atoms: 6419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6419 Classifications: {'peptide': 824} Link IDs: {'PTRANS': 39, 'TRANS': 783, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DDE:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EC" Number of atoms: 4105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 4105 Classifications: {'RNA': 193, 'DNA': 5} Modifications used: {'rna3p_pyr': 87, 'p5*END': 1, 'rna2p_pur': 8, 'rna3p_pur': 90, 'rna2p_pyr': 4} Link IDs: {'rna3p': 185, 'rna2p': 12} Chain breaks: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {' G:plan2': 1, ' A:plan': 3, ' C:plan': 1, ' U:plan': 4, ' G:plan': 1, ' C:plan2': 1, ' A:plan2': 3} Unresolved non-hydrogen planarities: 100 Chain: "DC" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'GDP': 1, 'SO1': 1, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A A1756 " occ=0.45 ... (20 atoms not shown) pdb=" C4 A A1756 " occ=0.45 Time building chain proxies: 77.04, per 1000 atoms: 0.36 Number of scatterers: 215222 At special positions: 0 Unit cell: (294.38, 280.44, 261.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 219 16.00 P 5569 15.00 Mg 1 11.99 O 56112 8.00 N 39311 7.00 C 114010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYSOA 19 " - pdb=" SG CYSOA 37 " distance=2.99 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=0, symmetry=0 Time building additional restraints: 69.68 Conformation dependent library (CDL) restraints added in 10.2 seconds 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22648 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: 407 helices and 118 sheets defined 39.6% alpha, 13.5% beta 1378 base pairs and 2568 stacking pairs defined. Time for finding SS restraints: 81.43 Creating SS restraints... Processing helix chain 'E' and resid 5 through 20 removed outlier: 3.570A pdb=" N VAL E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG E 10 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS E 12 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 17 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 81 removed outlier: 6.543A pdb=" N ASP E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS E 80 " --> pdb=" O ARG E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 97 removed outlier: 4.440A pdb=" N LEU E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 107 Processing helix chain 'E' and resid 116 through 128 Proline residue: E 121 - end of helix removed outlier: 3.683A pdb=" N GLY E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 146 through 152 removed outlier: 3.567A pdb=" N VAL E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 193 removed outlier: 3.589A pdb=" N VAL E 180 " --> pdb=" O GLU E 176 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 184 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE E 189 " --> pdb=" O MET E 185 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE E 190 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 202 removed outlier: 4.450A pdb=" N VAL E 201 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY E 202 " --> pdb=" O TRP E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 197 through 202' Processing helix chain 'F' and resid 5 through 13 removed outlier: 3.581A pdb=" N ARG F 9 " --> pdb=" O ILE F 5 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY F 11 " --> pdb=" O ASN F 7 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 5 through 13' Processing helix chain 'F' and resid 33 through 38 removed outlier: 3.506A pdb=" N HIS F 38 " --> pdb=" O TYR F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 4.446A pdb=" N VAL F 107 " --> pdb=" O PRO F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix No H-bonds generated for 'chain 'F' and resid 103 through 108' Processing helix chain 'F' and resid 181 through 193 removed outlier: 3.572A pdb=" N TYR F 189 " --> pdb=" O ALA F 185 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU F 191 " --> pdb=" O HIS F 187 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 205 removed outlier: 3.666A pdb=" N MET F 204 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASN F 205 " --> pdb=" O GLY F 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 200 through 205' Processing helix chain 'G' and resid 13 through 18 removed outlier: 4.667A pdb=" N LEU G 17 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Proline residue: G 18 - end of helix No H-bonds generated for 'chain 'G' and resid 13 through 18' Processing helix chain 'G' and resid 111 through 120 removed outlier: 4.228A pdb=" N PHE G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR G 119 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LYS G 120 " --> pdb=" O ARG G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 139 removed outlier: 3.748A pdb=" N ALA G 135 " --> pdb=" O THR G 131 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN G 139 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.548A pdb=" N ARG G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 170 removed outlier: 3.950A pdb=" N THR G 169 " --> pdb=" O GLN G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix No H-bonds generated for 'chain 'G' and resid 165 through 170' Processing helix chain 'G' and resid 187 through 199 removed outlier: 3.501A pdb=" N VAL G 192 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE G 199 " --> pdb=" O ALA G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 234 Processing helix chain 'G' and resid 347 through 352 removed outlier: 6.501A pdb=" N LEU G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 381 removed outlier: 3.507A pdb=" N HIS G 377 " --> pdb=" O PRO G 373 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA G 378 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE G 379 " --> pdb=" O GLU G 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 28 removed outlier: 6.222A pdb=" N SER H 27 " --> pdb=" O PRO H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 48 removed outlier: 3.504A pdb=" N VAL H 35 " --> pdb=" O ARG H 31 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS H 36 " --> pdb=" O PRO H 32 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS H 46 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 4.729A pdb=" N GLN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLY H 88 " --> pdb=" O ARG H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 88' Processing helix chain 'H' and resid 114 through 132 removed outlier: 3.551A pdb=" N ALA H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR H 129 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA H 130 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA H 132 " --> pdb=" O ALA H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 139 removed outlier: 3.571A pdb=" N ALA H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 159 removed outlier: 4.580A pdb=" N GLU H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER H 158 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 153 through 159' Processing helix chain 'H' and resid 161 through 173 removed outlier: 3.611A pdb=" N ALA H 165 " --> pdb=" O LYS H 161 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL H 172 " --> pdb=" O ALA H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 185 removed outlier: 4.239A pdb=" N LEU H 182 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS H 183 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER H 184 " --> pdb=" O LYS H 180 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS H 185 " --> pdb=" O VAL H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.933A pdb=" N ARG H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 191 through 196' Processing helix chain 'H' and resid 214 through 223 removed outlier: 3.575A pdb=" N ALA H 218 " --> pdb=" O GLY H 214 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN H 221 " --> pdb=" O LYS H 217 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL H 222 " --> pdb=" O ALA H 218 " (cutoff:3.500A) Proline residue: H 223 - end of helix Processing helix chain 'H' and resid 234 through 240 Proline residue: H 240 - end of helix Processing helix chain 'H' and resid 251 through 263 removed outlier: 3.905A pdb=" N ASP H 259 " --> pdb=" O PHE H 255 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN H 260 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP H 262 " --> pdb=" O LEU H 258 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY H 263 " --> pdb=" O ASP H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 293 removed outlier: 3.857A pdb=" N ILE H 289 " --> pdb=" O ASP H 285 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER H 292 " --> pdb=" O ARG H 288 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N SER H 293 " --> pdb=" O ILE H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.878A pdb=" N ALA H 298 " --> pdb=" O GLU H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 328 removed outlier: 3.529A pdb=" N LEU H 327 " --> pdb=" O VAL H 323 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 338 removed outlier: 4.690A pdb=" N VAL H 333 " --> pdb=" O PRO H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 361 removed outlier: 3.537A pdb=" N THR H 356 " --> pdb=" O ALA H 352 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU H 357 " --> pdb=" O ALA H 353 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU H 359 " --> pdb=" O PHE H 355 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 16 removed outlier: 4.745A pdb=" N ARG I 15 " --> pdb=" O ALA I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 26 removed outlier: 5.191A pdb=" N ARG I 24 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 79 through 87 removed outlier: 4.317A pdb=" N LEU I 83 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Proline residue: I 84 - end of helix Processing helix chain 'I' and resid 94 through 114 removed outlier: 3.539A pdb=" N ARG I 108 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU I 110 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN I 111 " --> pdb=" O ARG I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 120 removed outlier: 4.766A pdb=" N TYR I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS I 120 " --> pdb=" O ASP I 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 115 through 120' Processing helix chain 'I' and resid 157 through 170 removed outlier: 3.620A pdb=" N ALA I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU I 163 " --> pdb=" O VAL I 159 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS I 164 " --> pdb=" O PHE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 201 Processing helix chain 'I' and resid 202 through 213 removed outlier: 3.588A pdb=" N GLN I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR I 207 " --> pdb=" O HIS I 203 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU I 210 " --> pdb=" O GLN I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 222 removed outlier: 4.395A pdb=" N PHE I 219 " --> pdb=" O ASP I 215 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU I 221 " --> pdb=" O GLU I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 230 removed outlier: 3.824A pdb=" N LEU I 227 " --> pdb=" O PHE I 223 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP I 229 " --> pdb=" O GLY I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 250 removed outlier: 4.015A pdb=" N GLU I 237 " --> pdb=" O ALA I 233 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP I 238 " --> pdb=" O ASP I 234 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR I 240 " --> pdb=" O LEU I 236 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR I 241 " --> pdb=" O GLU I 237 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA I 243 " --> pdb=" O ILE I 239 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU I 245 " --> pdb=" O THR I 241 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA I 249 " --> pdb=" O GLU I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 273 removed outlier: 3.557A pdb=" N ALA I 266 " --> pdb=" O LYS I 262 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU I 268 " --> pdb=" O GLN I 264 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER I 269 " --> pdb=" O TYR I 265 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS I 271 " --> pdb=" O ALA I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 293 removed outlier: 3.524A pdb=" N LYS I 289 " --> pdb=" O ARG I 285 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA I 292 " --> pdb=" O ALA I 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 107 removed outlier: 4.214A pdb=" N PHE J 106 " --> pdb=" O ASN J 102 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ALA J 107 " --> pdb=" O VAL J 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 102 through 107' Processing helix chain 'J' and resid 110 through 122 removed outlier: 3.719A pdb=" N LYS J 114 " --> pdb=" O LYS J 110 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU J 115 " --> pdb=" O LEU J 111 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS J 116 " --> pdb=" O THR J 112 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA J 119 " --> pdb=" O GLU J 115 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASN J 120 " --> pdb=" O LYS J 116 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 153 removed outlier: 4.034A pdb=" N VAL J 135 " --> pdb=" O LYS J 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS J 139 " --> pdb=" O VAL J 135 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL J 141 " --> pdb=" O ASP J 137 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS J 143 " --> pdb=" O LYS J 139 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA J 144 " --> pdb=" O VAL J 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA J 147 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE J 149 " --> pdb=" O LEU J 145 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS J 151 " --> pdb=" O ALA J 147 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR J 152 " --> pdb=" O GLU J 148 " (cutoff:3.500A) Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 154 through 162 removed outlier: 3.568A pdb=" N ALA J 161 " --> pdb=" O GLN J 157 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER J 162 " --> pdb=" O TYR J 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 73 removed outlier: 5.289A pdb=" N ARG K 30 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 42 " --> pdb=" O LYS K 38 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS K 66 " --> pdb=" O ILE K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 107 removed outlier: 3.516A pdb=" N ARG K 107 " --> pdb=" O LEU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 131 removed outlier: 3.551A pdb=" N GLU K 125 " --> pdb=" O LYS K 121 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU K 126 " --> pdb=" O ALA K 122 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU K 127 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.504A pdb=" N ARG K 151 " --> pdb=" O LEU K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 173 removed outlier: 3.595A pdb=" N ILE K 169 " --> pdb=" O ASP K 165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU K 170 " --> pdb=" O ASN K 166 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN K 172 " --> pdb=" O ILE K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 190 removed outlier: 3.500A pdb=" N ILE K 188 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR K 190 " --> pdb=" O HIS K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 203 removed outlier: 4.684A pdb=" N TRP K 203 " --> pdb=" O ASN K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 244 removed outlier: 4.123A pdb=" N LEU K 239 " --> pdb=" O PHE K 235 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET K 243 " --> pdb=" O LEU K 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 69 removed outlier: 3.540A pdb=" N GLN L 61 " --> pdb=" O ARG L 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS L 63 " --> pdb=" O GLN L 59 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE L 67 " --> pdb=" O LYS L 63 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU L 69 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 77 removed outlier: 4.042A pdb=" N ALA L 76 " --> pdb=" O PRO L 72 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN L 77 " --> pdb=" O PRO L 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 72 through 77' Processing helix chain 'L' and resid 84 through 98 removed outlier: 3.669A pdb=" N GLU L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR L 97 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG L 98 " --> pdb=" O PHE L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 116 removed outlier: 3.512A pdb=" N ARG L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU L 109 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS L 111 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU L 112 " --> pdb=" O ARG L 108 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA L 114 " --> pdb=" O THR L 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA L 115 " --> pdb=" O LYS L 111 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL L 116 " --> pdb=" O GLU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 146 removed outlier: 3.523A pdb=" N ILE L 143 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU L 144 " --> pdb=" O VAL L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 174 removed outlier: 5.046A pdb=" N VAL L 163 " --> pdb=" O PRO L 159 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE L 165 " --> pdb=" O GLU L 161 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU L 166 " --> pdb=" O LEU L 162 " (cutoff:3.500A) Proline residue: L 167 - end of helix removed outlier: 3.529A pdb=" N CYS L 170 " --> pdb=" O LEU L 166 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS L 171 " --> pdb=" O PRO L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 191 removed outlier: 3.670A pdb=" N GLY L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 189 " --> pdb=" O ARG L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 226 removed outlier: 5.931A pdb=" N ALA L 209 " --> pdb=" O ALA L 205 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ALA L 210 " --> pdb=" O GLU L 206 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU L 211 " --> pdb=" O ASP L 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA L 212 " --> pdb=" O GLU L 208 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU L 214 " --> pdb=" O ALA L 210 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER L 216 " --> pdb=" O ALA L 212 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP L 219 " --> pdb=" O VAL L 215 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA L 220 " --> pdb=" O SER L 216 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN L 221 " --> pdb=" O THR L 217 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP L 224 " --> pdb=" O ALA L 220 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS L 225 " --> pdb=" O ASN L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 233 removed outlier: 4.528A pdb=" N LYS L 231 " --> pdb=" O ASP L 227 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HIS L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TRP L 233 " --> pdb=" O VAL L 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 227 through 233' Processing helix chain 'L' and resid 239 through 255 removed outlier: 4.543A pdb=" N LYS L 251 " --> pdb=" O ASP L 247 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN L 252 " --> pdb=" O LYS L 248 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER L 253 " --> pdb=" O ARG L 249 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP L 254 " --> pdb=" O ALA L 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 84 removed outlier: 3.623A pdb=" N ALA M 67 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU M 68 " --> pdb=" O HIS M 64 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG M 69 " --> pdb=" O VAL M 65 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU M 74 " --> pdb=" O THR M 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP M 76 " --> pdb=" O LYS M 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET M 78 " --> pdb=" O LEU M 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY M 81 " --> pdb=" O ASN M 77 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL M 82 " --> pdb=" O MET M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 164 removed outlier: 3.553A pdb=" N GLN M 156 " --> pdb=" O GLU M 152 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN M 157 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 176 removed outlier: 4.405A pdb=" N LEU M 176 " --> pdb=" O ILE M 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 80 removed outlier: 3.520A pdb=" N THR N 78 " --> pdb=" O LYS N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 160 removed outlier: 3.586A pdb=" N VAL N 148 " --> pdb=" O ASN N 144 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA N 155 " --> pdb=" O GLY N 151 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR N 157 " --> pdb=" O ARG N 153 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS N 158 " --> pdb=" O ARG N 154 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE N 159 " --> pdb=" O ALA N 155 " (cutoff:3.500A) Proline residue: N 160 - end of helix Processing helix chain 'N' and resid 177 through 188 removed outlier: 3.504A pdb=" N LEU N 182 " --> pdb=" O ARG N 178 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 214 removed outlier: 3.512A pdb=" N ARG N 211 " --> pdb=" O GLU N 207 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE N 213 " --> pdb=" O ASN N 209 " (cutoff:3.500A) Proline residue: N 214 - end of helix Processing helix chain 'O' and resid 28 through 42 removed outlier: 3.508A pdb=" N ALA O 33 " --> pdb=" O ARG O 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS O 35 " --> pdb=" O THR O 31 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL O 36 " --> pdb=" O ARG O 32 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN O 39 " --> pdb=" O LYS O 35 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU O 40 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 88 removed outlier: 3.771A pdb=" N GLU O 77 " --> pdb=" O GLY O 73 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU O 78 " --> pdb=" O PRO O 74 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE O 79 " --> pdb=" O LYS O 75 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL O 86 " --> pdb=" O ARG O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 141 Processing helix chain 'O' and resid 155 through 167 removed outlier: 3.595A pdb=" N GLN O 165 " --> pdb=" O SER O 161 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR O 167 " --> pdb=" O PHE O 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 87 removed outlier: 3.507A pdb=" N VAL P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR P 83 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU P 85 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS P 86 " --> pdb=" O ILE P 82 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU P 87 " --> pdb=" O THR P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 118 removed outlier: 4.453A pdb=" N GLU P 111 " --> pdb=" O ASP P 107 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE P 112 " --> pdb=" O GLU P 108 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN P 115 " --> pdb=" O GLU P 111 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP P 118 " --> pdb=" O ARG P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 133 removed outlier: 3.668A pdb=" N LYS P 130 " --> pdb=" O ALA P 126 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU P 131 " --> pdb=" O SER P 127 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU P 133 " --> pdb=" O THR P 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 22 removed outlier: 4.229A pdb=" N ARG Q 21 " --> pdb=" O HIS Q 17 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL Q 22 " --> pdb=" O TRP Q 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 17 through 22' Processing helix chain 'Q' and resid 27 through 47 removed outlier: 3.529A pdb=" N ARG Q 36 " --> pdb=" O LYS Q 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 40 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA Q 47 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 84 removed outlier: 3.532A pdb=" N VAL Q 80 " --> pdb=" O THR Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 94 removed outlier: 3.692A pdb=" N THR Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE Q 93 " --> pdb=" O TYR Q 89 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 123 removed outlier: 3.596A pdb=" N ARG Q 115 " --> pdb=" O ALA Q 111 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS Q 122 " --> pdb=" O GLU Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 146 removed outlier: 3.821A pdb=" N THR Q 144 " --> pdb=" O SER Q 140 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE Q 145 " --> pdb=" O ALA Q 141 " (cutoff:3.500A) Proline residue: Q 146 - end of helix No H-bonds generated for 'chain 'Q' and resid 140 through 146' Processing helix chain 'Q' and resid 165 through 180 removed outlier: 5.677A pdb=" N THR Q 169 " --> pdb=" O SER Q 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER Q 175 " --> pdb=" O ARG Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 193 removed outlier: 3.603A pdb=" N LYS Q 190 " --> pdb=" O ARG Q 186 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU Q 192 " --> pdb=" O ARG Q 188 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA Q 193 " --> pdb=" O GLU Q 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.713A pdb=" N VAL R 63 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 59 through 64' Processing helix chain 'R' and resid 77 through 89 removed outlier: 3.554A pdb=" N VAL R 81 " --> pdb=" O ARG R 77 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA R 88 " --> pdb=" O LYS R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 98 removed outlier: 4.024A pdb=" N SER R 97 " --> pdb=" O LYS R 93 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER R 98 " --> pdb=" O TRP R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 112 removed outlier: 3.501A pdb=" N ARG R 109 " --> pdb=" O GLN R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 136 removed outlier: 3.517A pdb=" N LYS R 125 " --> pdb=" O MET R 121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS R 127 " --> pdb=" O LEU R 123 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR R 130 " --> pdb=" O GLN R 126 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA R 136 " --> pdb=" O LYS R 132 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 14 removed outlier: 3.609A pdb=" N LEU S 7 " --> pdb=" O ALA S 3 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG S 12 " --> pdb=" O GLU S 8 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS S 13 " --> pdb=" O GLU S 9 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS S 14 " --> pdb=" O LEU S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 34 removed outlier: 3.567A pdb=" N PHE S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL S 25 " --> pdb=" O PHE S 21 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N TRP S 28 " --> pdb=" O ARG S 24 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN S 34 " --> pdb=" O TYR S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 52 removed outlier: 3.652A pdb=" N ARG S 49 " --> pdb=" O PRO S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 111 removed outlier: 3.556A pdb=" N GLU S 103 " --> pdb=" O ARG S 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG S 105 " --> pdb=" O THR S 101 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL S 106 " --> pdb=" O ALA S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 145 removed outlier: 5.151A pdb=" N ASP S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 153 removed outlier: 4.845A pdb=" N TRP S 150 " --> pdb=" O ALA S 146 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS S 152 " --> pdb=" O TYR S 148 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP S 153 " --> pdb=" O ASN S 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 146 through 153' Processing helix chain 'S' and resid 158 through 163 removed outlier: 4.857A pdb=" N ARG S 162 " --> pdb=" O HIS S 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 173 removed outlier: 3.515A pdb=" N GLY S 173 " --> pdb=" O LYS S 169 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 182 removed outlier: 4.250A pdb=" N ASN S 181 " --> pdb=" O GLY S 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASN S 182 " --> pdb=" O HIS S 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 177 through 182' Processing helix chain 'S' and resid 186 through 196 Processing helix chain 'T' and resid 15 through 30 removed outlier: 3.556A pdb=" N LEU T 19 " --> pdb=" O LEU T 15 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL T 22 " --> pdb=" O ARG T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 42 removed outlier: 3.786A pdb=" N LEU T 41 " --> pdb=" O ARG T 37 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASN T 42 " --> pdb=" O ALA T 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 37 through 42' Processing helix chain 'T' and resid 46 through 61 removed outlier: 3.672A pdb=" N ASN T 50 " --> pdb=" O GLU T 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE T 57 " --> pdb=" O LYS T 53 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA T 61 " --> pdb=" O PHE T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 70 removed outlier: 3.946A pdb=" N GLY T 69 " --> pdb=" O ASN T 65 " (cutoff:3.500A) Proline residue: T 70 - end of helix No H-bonds generated for 'chain 'T' and resid 65 through 70' Processing helix chain 'T' and resid 75 through 89 removed outlier: 3.537A pdb=" N LYS T 82 " --> pdb=" O ARG T 78 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA T 83 " --> pdb=" O ILE T 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU T 84 " --> pdb=" O PHE T 80 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N MET T 87 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER T 89 " --> pdb=" O ARG T 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 103 removed outlier: 3.518A pdb=" N GLU T 100 " --> pdb=" O LYS T 96 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG T 101 " --> pdb=" O ALA T 97 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU T 102 " --> pdb=" O ALA T 98 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS T 103 " --> pdb=" O LEU T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 116 removed outlier: 3.755A pdb=" N LYS T 114 " --> pdb=" O PRO T 110 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS T 115 " --> pdb=" O PRO T 111 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS T 116 " --> pdb=" O TYR T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 129 Processing helix chain 'T' and resid 137 through 146 removed outlier: 3.600A pdb=" N LEU T 141 " --> pdb=" O THR T 137 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY T 146 " --> pdb=" O SER T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 186 removed outlier: 3.522A pdb=" N ALA T 158 " --> pdb=" O ALA T 154 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU T 166 " --> pdb=" O VAL T 162 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR T 167 " --> pdb=" O SER T 163 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR T 168 " --> pdb=" O SER T 164 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA T 169 " --> pdb=" O ALA T 165 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA T 179 " --> pdb=" O THR T 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER T 180 " --> pdb=" O LYS T 176 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA T 186 " --> pdb=" O ASN T 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 198 removed outlier: 3.533A pdb=" N LEU T 194 " --> pdb=" O VAL T 190 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA T 196 " --> pdb=" O LYS T 192 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY T 198 " --> pdb=" O LEU T 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 15 removed outlier: 3.654A pdb=" N SER U 14 " --> pdb=" O ASN U 10 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA U 15 " --> pdb=" O PRO U 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 10 through 15' Processing helix chain 'U' and resid 25 through 37 removed outlier: 3.568A pdb=" N GLU U 31 " --> pdb=" O LYS U 27 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA U 33 " --> pdb=" O THR U 29 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA U 35 " --> pdb=" O GLU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 54 removed outlier: 3.506A pdb=" N LYS U 46 " --> pdb=" O THR U 42 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU U 49 " --> pdb=" O GLN U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 75 removed outlier: 4.625A pdb=" N LYS U 74 " --> pdb=" O THR U 70 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU U 75 " --> pdb=" O ALA U 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 70 through 75' Processing helix chain 'U' and resid 84 through 106 removed outlier: 3.503A pdb=" N VAL U 88 " --> pdb=" O PRO U 84 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE U 90 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY U 93 " --> pdb=" O LYS U 89 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN U 97 " --> pdb=" O GLY U 93 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS U 105 " --> pdb=" O ASN U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 183 removed outlier: 4.324A pdb=" N ARG U 175 " --> pdb=" O ARG U 171 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE U 176 " --> pdb=" O GLN U 172 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA U 177 " --> pdb=" O ARG U 173 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN U 179 " --> pdb=" O ARG U 175 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS U 180 " --> pdb=" O ILE U 176 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG U 181 " --> pdb=" O ALA U 177 " (cutoff:3.500A) Processing helix chain 'V' and resid 23 through 40 Processing helix chain 'V' and resid 42 through 54 removed outlier: 4.179A pdb=" N LYS V 46 " --> pdb=" O ALA V 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL V 47 " --> pdb=" O PRO V 43 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE V 53 " --> pdb=" O LEU V 49 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU V 54 " --> pdb=" O LYS V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 60 Proline residue: V 60 - end of helix Processing helix chain 'V' and resid 63 through 73 removed outlier: 3.504A pdb=" N ALA V 70 " --> pdb=" O ARG V 66 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS V 72 " --> pdb=" O ALA V 68 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN V 73 " --> pdb=" O ARG V 69 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 118 removed outlier: 3.586A pdb=" N VAL V 115 " --> pdb=" O ARG V 111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY V 118 " --> pdb=" O ILE V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 132 removed outlier: 3.582A pdb=" N LEU V 127 " --> pdb=" O THR V 123 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL V 129 " --> pdb=" O ASP V 125 " (cutoff:3.500A) Proline residue: V 132 - end of helix Processing helix chain 'V' and resid 147 through 153 removed outlier: 4.229A pdb=" N ARG V 151 " --> pdb=" O ARG V 147 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS V 152 " --> pdb=" O GLU V 148 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE V 153 " --> pdb=" O ALA V 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 147 through 153' Processing helix chain 'W' and resid 4 through 16 removed outlier: 3.589A pdb=" N ALA W 12 " --> pdb=" O LYS W 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL W 14 " --> pdb=" O LEU W 10 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL W 15 " --> pdb=" O ALA W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 36 removed outlier: 5.204A pdb=" N ASN W 36 " --> pdb=" O ILE W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 48 removed outlier: 3.577A pdb=" N LYS W 43 " --> pdb=" O ASN W 39 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS W 46 " --> pdb=" O ARG W 42 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN W 47 " --> pdb=" O LYS W 43 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY W 48 " --> pdb=" O LEU W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 73 removed outlier: 4.863A pdb=" N THR W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA W 65 " --> pdb=" O SER W 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS W 66 " --> pdb=" O ARG W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 113 Proline residue: W 90 - end of helix removed outlier: 6.705A pdb=" N VAL W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL W 94 " --> pdb=" O PRO W 90 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG W 104 " --> pdb=" O ARG W 100 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG W 110 " --> pdb=" O LEU W 106 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP W 111 " --> pdb=" O ALA W 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA W 112 " --> pdb=" O LYS W 108 " (cutoff:3.500A) Processing helix chain 'W' and resid 116 through 130 removed outlier: 3.542A pdb=" N VAL W 122 " --> pdb=" O HIS W 118 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS W 125 " --> pdb=" O HIS W 121 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN W 130 " --> pdb=" O GLU W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 134 through 187 removed outlier: 4.247A pdb=" N GLN W 150 " --> pdb=" O LYS W 146 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU W 155 " --> pdb=" O ARG W 151 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN W 156 " --> pdb=" O GLU W 152 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU W 160 " --> pdb=" O ASN W 156 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA W 161 " --> pdb=" O GLU W 157 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG W 162 " --> pdb=" O GLU W 158 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ARG W 163 " --> pdb=" O ALA W 159 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU W 164 " --> pdb=" O GLU W 160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN W 166 " --> pdb=" O ARG W 162 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA W 169 " --> pdb=" O LYS W 165 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN W 175 " --> pdb=" O ASP W 171 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS W 180 " --> pdb=" O ARG W 176 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG W 181 " --> pdb=" O VAL W 177 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASP W 182 " --> pdb=" O ALA W 178 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA W 183 " --> pdb=" O GLU W 179 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU W 184 " --> pdb=" O LYS W 180 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU W 185 " --> pdb=" O ARG W 181 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS W 186 " --> pdb=" O ASP W 182 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLU W 187 " --> pdb=" O ALA W 183 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 49 removed outlier: 3.555A pdb=" N HIS X 49 " --> pdb=" O LEU X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 98 through 113 removed outlier: 3.605A pdb=" N ALA X 111 " --> pdb=" O TYR X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 122 removed outlier: 3.887A pdb=" N ILE X 121 " --> pdb=" O ARG X 117 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N HIS X 122 " --> pdb=" O PHE X 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 117 through 122' Processing helix chain 'X' and resid 137 through 145 removed outlier: 5.859A pdb=" N PHE X 143 " --> pdb=" O TYR X 139 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU X 144 " --> pdb=" O VAL X 140 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR X 145 " --> pdb=" O LYS X 141 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 32 removed outlier: 4.647A pdb=" N TYR Y 30 " --> pdb=" O HIS Y 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU Y 31 " --> pdb=" O LEU Y 27 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS Y 32 " --> pdb=" O SER Y 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 26 through 32' Processing helix chain 'Y' and resid 92 through 97 removed outlier: 5.355A pdb=" N LYS Y 97 " --> pdb=" O VAL Y 93 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 123 removed outlier: 4.248A pdb=" N GLN Y 103 " --> pdb=" O SER Y 99 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU Y 104 " --> pdb=" O LYS Y 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU Y 106 " --> pdb=" O ARG Y 102 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU Y 107 " --> pdb=" O GLN Y 103 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA Y 117 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA Y 119 " --> pdb=" O LYS Y 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 19 through 26 removed outlier: 4.386A pdb=" N ASN Z 25 " --> pdb=" O SER Z 21 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY Z 26 " --> pdb=" O PRO Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 40 removed outlier: 3.513A pdb=" N ILE Z 38 " --> pdb=" O ALA Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 88 Processing helix chain 'AA' and resid 66 through 71 removed outlier: 4.891A pdb=" N LYSAA 71 " --> pdb=" O PROAA 67 " (cutoff:3.500A) Processing helix chain 'AA' and resid 119 through 127 removed outlier: 3.566A pdb=" N ALAAA 123 " --> pdb=" O GLYAA 119 " (cutoff:3.500A) Proline residue: AA 127 - end of helix Processing helix chain 'AA' and resid 128 through 133 removed outlier: 4.127A pdb=" N ASNAA 132 " --> pdb=" O ARGAA 128 " (cutoff:3.500A) Processing helix chain 'BA' and resid 33 through 43 Processing helix chain 'BA' and resid 45 through 50 removed outlier: 3.796A pdb=" N ILEBA 49 " --> pdb=" O ASNBA 45 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALABA 50 " --> pdb=" O PROBA 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'BA' and resid 45 through 50' Processing helix chain 'BA' and resid 52 through 60 removed outlier: 3.521A pdb=" N ARGBA 56 " --> pdb=" O THRBA 52 " (cutoff:3.500A) Processing helix chain 'CA' and resid 58 through 63 removed outlier: 3.505A pdb=" N ILECA 63 " --> pdb=" O SERCA 59 " (cutoff:3.500A) Processing helix chain 'CA' and resid 69 through 79 removed outlier: 6.302A pdb=" N LYSCA 75 " --> pdb=" O THRCA 71 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLUCA 77 " --> pdb=" O METCA 73 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASPCA 78 " --> pdb=" O LYSCA 74 " (cutoff:3.500A) Processing helix chain 'CA' and resid 92 through 104 removed outlier: 3.638A pdb=" N LYSCA 97 " --> pdb=" O TYRCA 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYRCA 103 " --> pdb=" O VALCA 99 " (cutoff:3.500A) Processing helix chain 'CA' and resid 131 through 140 removed outlier: 3.613A pdb=" N ILECA 135 " --> pdb=" O ASPCA 131 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLYCA 140 " --> pdb=" O ALACA 136 " (cutoff:3.500A) Processing helix chain 'DA' and resid 11 through 22 removed outlier: 3.522A pdb=" N LYSDA 17 " --> pdb=" O ARGDA 13 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEDA 20 " --> pdb=" O ARGDA 16 " (cutoff:3.500A) Processing helix chain 'DA' and resid 23 through 31 removed outlier: 4.339A pdb=" N VALDA 29 " --> pdb=" O SERDA 25 " (cutoff:3.500A) Processing helix chain 'DA' and resid 36 through 44 removed outlier: 3.543A pdb=" N ALADA 41 " --> pdb=" O LYSDA 37 " (cutoff:3.500A) Processing helix chain 'DA' and resid 100 through 105 removed outlier: 4.649A pdb=" N LEUDA 104 " --> pdb=" O HISDA 100 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VALDA 105 " --> pdb=" O PRODA 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'DA' and resid 100 through 105' Processing helix chain 'DA' and resid 112 through 123 removed outlier: 3.573A pdb=" N GLNDA 120 " --> pdb=" O LYSDA 116 " (cutoff:3.500A) Processing helix chain 'EA' and resid 60 through 67 removed outlier: 3.523A pdb=" N ARGEA 65 " --> pdb=" O LYSEA 61 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THREA 66 " --> pdb=" O VALEA 62 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LYSEA 67 " --> pdb=" O ALAEA 63 " (cutoff:3.500A) Processing helix chain 'EA' and resid 76 through 81 removed outlier: 5.361A pdb=" N LEUEA 81 " --> pdb=" O TYREA 77 " (cutoff:3.500A) Processing helix chain 'EA' and resid 92 through 98 removed outlier: 4.370A pdb=" N SEREA 97 " --> pdb=" O LYSEA 93 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N THREA 98 " --> pdb=" O SEREA 94 " (cutoff:3.500A) Processing helix chain 'EA' and resid 105 through 123 removed outlier: 3.521A pdb=" N GLUEA 109 " --> pdb=" O SEREA 105 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VALEA 114 " --> pdb=" O ALAEA 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLUEA 120 " --> pdb=" O LYSEA 116 " (cutoff:3.500A) Processing helix chain 'EA' and resid 127 through 132 removed outlier: 4.552A pdb=" N PHEEA 131 " --> pdb=" O ASNEA 127 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SEREA 132 " --> pdb=" O GLNEA 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'EA' and resid 127 through 132' Processing helix chain 'FA' and resid 2 through 7 removed outlier: 3.943A pdb=" N THRFA 6 " --> pdb=" O PROFA 2 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYSFA 7 " --> pdb=" O SERFA 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'FA' and resid 2 through 7' Processing helix chain 'FA' and resid 41 through 48 removed outlier: 5.434A pdb=" N TYRFA 48 " --> pdb=" O ASNFA 44 " (cutoff:3.500A) Processing helix chain 'FA' and resid 64 through 69 removed outlier: 4.073A pdb=" N PHEFA 68 " --> pdb=" O GLNFA 64 " (cutoff:3.500A) Processing helix chain 'FA' and resid 77 through 83 removed outlier: 6.371A pdb=" N LEUFA 81 " --> pdb=" O LYSFA 77 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILEFA 82 " --> pdb=" O LEUFA 78 " (cutoff:3.500A) Proline residue: FA 83 - end of helix No H-bonds generated for 'chain 'FA' and resid 77 through 83' Processing helix chain 'FA' and resid 84 through 94 removed outlier: 3.603A pdb=" N ASPFA 88 " --> pdb=" O GLUFA 84 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLNFA 89 " --> pdb=" O ASPFA 85 " (cutoff:3.500A) Processing helix chain 'FA' and resid 103 through 108 Processing helix chain 'FA' and resid 131 through 142 removed outlier: 3.542A pdb=" N LYSFA 137 " --> pdb=" O LEUFA 133 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARGFA 139 " --> pdb=" O GLUFA 135 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLYFA 142 " --> pdb=" O ILEFA 138 " (cutoff:3.500A) Processing helix chain 'GA' and resid 11 through 20 removed outlier: 3.968A pdb=" N ASNGA 19 " --> pdb=" O LYSGA 15 " (cutoff:3.500A) Processing helix chain 'GA' and resid 36 through 59 removed outlier: 3.549A pdb=" N HISGA 48 " --> pdb=" O LYSGA 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALAGA 57 " --> pdb=" O ALAGA 53 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYSGA 58 " --> pdb=" O LEUGA 54 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYSGA 59 " --> pdb=" O ALAGA 55 " (cutoff:3.500A) Processing helix chain 'HA' and resid 9 through 21 removed outlier: 3.581A pdb=" N LEUHA 14 " --> pdb=" O ILEHA 10 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALAHA 15 " --> pdb=" O ASNHA 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VALHA 17 " --> pdb=" O LYSHA 13 " (cutoff:3.500A) Processing helix chain 'HA' and resid 26 through 37 Processing helix chain 'HA' and resid 49 through 64 removed outlier: 3.531A pdb=" N METHA 61 " --> pdb=" O GLUHA 57 " (cutoff:3.500A) Processing helix chain 'HA' and resid 74 through 82 removed outlier: 4.622A pdb=" N THRHA 79 " --> pdb=" O ASNHA 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALAHA 80 " --> pdb=" O GLUHA 76 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLYHA 82 " --> pdb=" O GLYHA 78 " (cutoff:3.500A) Processing helix chain 'HA' and resid 99 through 104 removed outlier: 4.179A pdb=" N THRHA 103 " --> pdb=" O ASPHA 99 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEUHA 104 " --> pdb=" O ILEHA 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'HA' and resid 99 through 104' Processing helix chain 'IA' and resid 15 through 21 removed outlier: 3.509A pdb=" N HISIA 21 " --> pdb=" O HISIA 17 " (cutoff:3.500A) Processing helix chain 'IA' and resid 27 through 44 removed outlier: 3.515A pdb=" N VALIA 33 " --> pdb=" O ALAIA 29 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYSIA 37 " --> pdb=" O VALIA 33 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYSIA 41 " --> pdb=" O LYSIA 37 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEUIA 42 " --> pdb=" O LYSIA 38 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HISIA 43 " --> pdb=" O PHEIA 39 " (cutoff:3.500A) Processing helix chain 'IA' and resid 52 through 61 removed outlier: 3.585A pdb=" N GLNIA 57 " --> pdb=" O PROIA 53 " (cutoff:3.500A) Processing helix chain 'JA' and resid 21 through 26 removed outlier: 4.771A pdb=" N HISJA 26 " --> pdb=" O SERJA 22 " (cutoff:3.500A) Processing helix chain 'JA' and resid 40 through 45 Processing helix chain 'JA' and resid 78 through 87 removed outlier: 3.508A pdb=" N GLUJA 83 " --> pdb=" O VALJA 79 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THRJA 84 " --> pdb=" O LYSJA 80 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEUJA 85 " --> pdb=" O ASPJA 81 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THRJA 86 " --> pdb=" O LEUJA 82 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N METJA 87 " --> pdb=" O GLUJA 83 " (cutoff:3.500A) Processing helix chain 'JA' and resid 101 through 116 removed outlier: 3.694A pdb=" N VALJA 107 " --> pdb=" O LYSJA 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEUJA 109 " --> pdb=" O ARGJA 105 " (cutoff:3.500A) Processing helix chain 'KA' and resid 37 through 46 removed outlier: 3.564A pdb=" N GLNKA 42 " --> pdb=" O PROKA 38 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHEKA 43 " --> pdb=" O GLNKA 39 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N TYRKA 44 " --> pdb=" O ASPKA 40 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEUKA 45 " --> pdb=" O ALAKA 41 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLYKA 46 " --> pdb=" O GLNKA 42 " (cutoff:3.500A) Processing helix chain 'LA' and resid 66 through 72 removed outlier: 3.862A pdb=" N LYSLA 70 " --> pdb=" O SERLA 66 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THRLA 71 " --> pdb=" O LYSLA 67 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VALLA 72 " --> pdb=" O THRLA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 66 through 72' Processing helix chain 'LA' and resid 81 through 113 removed outlier: 5.363A pdb=" N VALLA 85 " --> pdb=" O CYSLA 81 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLULA 87 " --> pdb=" O ASNLA 83 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARGLA 88 " --> pdb=" O CYSLA 84 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILELA 100 " --> pdb=" O GLULA 96 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYSLA 103 " --> pdb=" O LYSLA 99 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VALLA 105 " --> pdb=" O VALLA 101 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYSLA 106 " --> pdb=" O LYSLA 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLULA 107 " --> pdb=" O LYSLA 103 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLNLA 108 " --> pdb=" O VALLA 104 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THRLA 109 " --> pdb=" O VALLA 105 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALALA 111 " --> pdb=" O GLULA 107 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALALA 112 " --> pdb=" O GLNLA 108 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYSLA 113 " --> pdb=" O THRLA 109 " (cutoff:3.500A) Processing helix chain 'LA' and resid 59 through 64 removed outlier: 3.534A pdb=" N THRLA 64 " --> pdb=" O GLNLA 61 " (cutoff:3.500A) Processing helix chain 'MA' and resid 5 through 13 removed outlier: 3.504A pdb=" N LEUMA 9 " --> pdb=" O LYSMA 5 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THRMA 11 " --> pdb=" O TYRMA 7 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYSMA 12 " --> pdb=" O GLUMA 8 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SERMA 13 " --> pdb=" O LEUMA 9 " (cutoff:3.500A) Processing helix chain 'MA' and resid 14 through 39 removed outlier: 3.513A pdb=" N GLUMA 27 " --> pdb=" O ASPMA 23 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLNMA 34 " --> pdb=" O GLUMA 30 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYSMA 35 " --> pdb=" O LEUMA 31 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEUMA 36 " --> pdb=" O LYSMA 32 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SERMA 37 " --> pdb=" O VALMA 33 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARGMA 38 " --> pdb=" O GLNMA 34 " (cutoff:3.500A) Proline residue: MA 39 - end of helix Processing helix chain 'MA' and resid 42 through 71 removed outlier: 4.244A pdb=" N THRMA 46 " --> pdb=" O PROMA 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VALMA 47 " --> pdb=" O LYSMA 43 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SERMA 50 " --> pdb=" O THRMA 46 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEUMA 55 " --> pdb=" O ILEMA 51 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VALMA 66 " --> pdb=" O GLNMA 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLNMA 68 " --> pdb=" O GLUMA 64 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEUMA 69 " --> pdb=" O ALAMA 65 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYSMA 71 " --> pdb=" O ARGMA 67 " (cutoff:3.500A) Processing helix chain 'MA' and resid 85 through 91 removed outlier: 3.668A pdb=" N ARGMA 90 " --> pdb=" O ARGMA 86 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALAMA 91 " --> pdb=" O ALAMA 87 " (cutoff:3.500A) Processing helix chain 'MA' and resid 93 through 99 removed outlier: 5.110A pdb=" N ALAMA 97 " --> pdb=" O THRMA 93 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SERMA 98 " --> pdb=" O LYSMA 94 " (cutoff:3.500A) Processing helix chain 'MA' and resid 101 through 112 removed outlier: 5.564A pdb=" N LYSMA 106 " --> pdb=" O GLUMA 102 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYSMA 107 " --> pdb=" O LYSMA 103 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILEMA 109 " --> pdb=" O ARGMA 105 " (cutoff:3.500A) Proline residue: MA 112 - end of helix Processing helix chain 'NA' and resid 34 through 49 removed outlier: 3.558A pdb=" N PHENA 39 " --> pdb=" O ASNNA 35 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VALNA 40 " --> pdb=" O ARGNA 36 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARGNA 45 " --> pdb=" O ARGNA 41 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLUNA 46 " --> pdb=" O SERNA 42 " (cutoff:3.500A) Processing helix chain 'NA' and resid 51 through 64 removed outlier: 3.500A pdb=" N ILENA 58 " --> pdb=" O GLUNA 54 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASPNA 59 " --> pdb=" O ARGNA 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARGNA 62 " --> pdb=" O ILENA 58 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SERNA 64 " --> pdb=" O LEUNA 60 " (cutoff:3.500A) Processing helix chain 'NA' and resid 65 through 77 removed outlier: 3.516A pdb=" N ALANA 69 " --> pdb=" O GLYNA 65 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VALNA 72 " --> pdb=" O ARGNA 68 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYSNA 75 " --> pdb=" O LYSNA 71 " (cutoff:3.500A) Processing helix chain 'NA' and resid 79 through 96 removed outlier: 3.520A pdb=" N ALANA 85 " --> pdb=" O THRNA 81 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILENA 93 " --> pdb=" O GLUNA 89 " (cutoff:3.500A) Processing helix chain 'OA' and resid 4 through 12 removed outlier: 4.021A pdb=" N GLYOA 9 " --> pdb=" O THROA 5 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYSOA 10 " --> pdb=" O PROOA 6 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARGOA 11 " --> pdb=" O SEROA 7 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N HISOA 12 " --> pdb=" O PHEOA 8 " (cutoff:3.500A) Processing helix chain 'OA' and resid 50 through 58 removed outlier: 3.555A pdb=" N LYSOA 54 " --> pdb=" O GLYOA 50 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARGOA 55 " --> pdb=" O ALAOA 51 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HISOA 57 " --> pdb=" O ALAOA 53 " (cutoff:3.500A) Processing helix chain 'OA' and resid 64 through 77 removed outlier: 3.526A pdb=" N LYSOA 68 " --> pdb=" O METOA 64 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HISOA 69 " --> pdb=" O ARGOA 65 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALOA 70 " --> pdb=" O TYROA 66 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SEROA 71 " --> pdb=" O LEUOA 67 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARGOA 72 " --> pdb=" O LYSOA 68 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYSOA 75 " --> pdb=" O SEROA 71 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASNOA 76 " --> pdb=" O ARGOA 72 " (cutoff:3.500A) Processing helix chain 'PA' and resid 7 through 17 removed outlier: 3.527A pdb=" N LEUPA 12 " --> pdb=" O ILEPA 8 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARGPA 16 " --> pdb=" O LEUPA 12 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARGPA 17 " --> pdb=" O GLUPA 13 " (cutoff:3.500A) Processing helix chain 'PA' and resid 58 through 69 removed outlier: 3.661A pdb=" N LEUPA 65 " --> pdb=" O LYSPA 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILEPA 66 " --> pdb=" O ALAPA 62 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLNPA 67 " --> pdb=" O LYSPA 63 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SERPA 68 " --> pdb=" O LYSPA 64 " (cutoff:3.500A) Processing helix chain 'QA' and resid 6 through 21 removed outlier: 3.536A pdb=" N LYSQA 12 " --> pdb=" O ARGQA 8 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYSQA 18 " --> pdb=" O ALAQA 14 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARGQA 21 " --> pdb=" O LYSQA 17 " (cutoff:3.500A) Processing helix chain 'QA' and resid 24 through 31 removed outlier: 4.089A pdb=" N ARGQA 28 " --> pdb=" O PROQA 24 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEUQA 29 " --> pdb=" O GLNQA 25 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N THRQA 31 " --> pdb=" O ILEQA 27 " (cutoff:3.500A) Processing helix chain 'RA' and resid 80 through 91 removed outlier: 3.596A pdb=" N TYRRA 89 " --> pdb=" O LEURA 85 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASNRA 90 " --> pdb=" O ALARA 86 " (cutoff:3.500A) Processing helix chain 'SA' and resid 2 through 25 removed outlier: 3.531A pdb=" N LYSSA 8 " --> pdb=" O LYSSA 4 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARGSA 21 " --> pdb=" O ARGSA 17 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SERSA 24 " --> pdb=" O VALSA 20 " (cutoff:3.500A) Processing helix chain 'TA' and resid 38 through 48 removed outlier: 3.550A pdb=" N ASPTA 44 " --> pdb=" O LYSTA 40 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARGTA 45 " --> pdb=" O ARGTA 41 " (cutoff:3.500A) Processing helix chain 'UA' and resid 19 through 35 removed outlier: 3.506A pdb=" N ARGUA 23 " --> pdb=" O GLYUA 19 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSUA 28 " --> pdb=" O ARGUA 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEUUA 29 " --> pdb=" O GLNUA 25 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALAUA 35 " --> pdb=" O ILEUA 31 " (cutoff:3.500A) Processing helix chain 'UA' and resid 73 through 92 removed outlier: 3.550A pdb=" N THRUA 78 " --> pdb=" O ALAUA 74 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLUUA 88 " --> pdb=" O ARGUA 84 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N METUA 89 " --> pdb=" O ARGUA 85 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLUUA 91 " --> pdb=" O ARGUA 87 " (cutoff:3.500A) Processing helix chain 'VA' and resid 5 through 22 removed outlier: 3.536A pdb=" N GLUVA 10 " --> pdb=" O GLUVA 6 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALAVA 13 " --> pdb=" O ALAVA 9 " (cutoff:3.500A) Processing helix chain 'VA' and resid 34 through 46 removed outlier: 3.561A pdb=" N LEUVA 45 " --> pdb=" O VALVA 41 " (cutoff:3.500A) Processing helix chain 'VA' and resid 55 through 68 removed outlier: 3.695A pdb=" N VALVA 59 " --> pdb=" O LYSVA 55 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARGVA 61 " --> pdb=" O THRVA 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILEVA 63 " --> pdb=" O VALVA 59 " (cutoff:3.500A) Processing helix chain 'VA' and resid 72 through 77 removed outlier: 4.878A pdb=" N LEUVA 76 " --> pdb=" O ASPVA 72 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEUVA 77 " --> pdb=" O PHEVA 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'VA' and resid 72 through 77' Processing helix chain 'VA' and resid 92 through 104 removed outlier: 3.527A pdb=" N VALVA 99 " --> pdb=" O GLUVA 95 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARGVA 104 " --> pdb=" O ILEVA 100 " (cutoff:3.500A) Processing helix chain 'VA' and resid 132 through 140 removed outlier: 3.614A pdb=" N PHEVA 136 " --> pdb=" O LYSVA 132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALAVA 138 " --> pdb=" O SERVA 134 " (cutoff:3.500A) Processing helix chain 'VA' and resid 166 through 177 removed outlier: 3.545A pdb=" N LEUVA 172 " --> pdb=" O SERVA 168 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEUVA 175 " --> pdb=" O SERVA 171 " (cutoff:3.500A) Processing helix chain 'XA' and resid 10 through 21 removed outlier: 3.532A pdb=" N GLNXA 15 " --> pdb=" O PROXA 11 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEUXA 16 " --> pdb=" O GLUXA 12 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALAXA 20 " --> pdb=" O LEUXA 16 " (cutoff:3.500A) Processing helix chain 'XA' and resid 49 through 67 removed outlier: 3.558A pdb=" N THRXA 53 " --> pdb=" O ASNXA 49 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRPXA 54 " --> pdb=" O VALXA 50 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VALXA 58 " --> pdb=" O TRPXA 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEUXA 59 " --> pdb=" O GLUXA 55 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALAXA 61 " --> pdb=" O LEUXA 57 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEXA 63 " --> pdb=" O LEUXA 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILEXA 64 " --> pdb=" O ALAXA 60 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILEXA 67 " --> pdb=" O ILEXA 63 " (cutoff:3.500A) Processing helix chain 'XA' and resid 80 through 93 removed outlier: 4.664A pdb=" N ARGXA 84 " --> pdb=" O THRXA 80 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALAXA 85 " --> pdb=" O PHEXA 81 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEUXA 87 " --> pdb=" O GLNXA 83 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYSXA 88 " --> pdb=" O ARGXA 84 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALAXA 91 " --> pdb=" O LEUXA 87 " (cutoff:3.500A) Processing helix chain 'XA' and resid 125 through 130 Processing helix chain 'XA' and resid 131 through 140 removed outlier: 3.533A pdb=" N TYRXA 138 " --> pdb=" O LYSXA 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VALXA 139 " --> pdb=" O GLUXA 135 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASNXA 140 " --> pdb=" O ALAXA 136 " (cutoff:3.500A) Processing helix chain 'XA' and resid 168 through 185 removed outlier: 3.535A pdb=" N ARGXA 183 " --> pdb=" O ARGXA 179 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARGXA 185 " --> pdb=" O VALXA 181 " (cutoff:3.500A) Processing helix chain 'XA' and resid 198 through 204 removed outlier: 4.477A pdb=" N TYRXA 202 " --> pdb=" O METXA 198 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHEXA 203 " --> pdb=" O PROXA 199 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYRXA 204 " --> pdb=" O ASPXA 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'XA' and resid 198 through 204' Processing helix chain 'YA' and resid 22 through 28 removed outlier: 4.739A pdb=" N ARGYA 26 " --> pdb=" O ASPYA 22 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLUYA 28 " --> pdb=" O PHEYA 24 " (cutoff:3.500A) Processing helix chain 'YA' and resid 57 through 62 removed outlier: 4.048A pdb=" N LEUYA 61 " --> pdb=" O ALAYA 57 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYSYA 62 " --> pdb=" O SERYA 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'YA' and resid 57 through 62' Processing helix chain 'YA' and resid 69 through 75 Processing helix chain 'YA' and resid 106 through 115 removed outlier: 3.523A pdb=" N SERYA 112 " --> pdb=" O ASPYA 108 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARGYA 115 " --> pdb=" O ARGYA 111 " (cutoff:3.500A) Processing helix chain 'YA' and resid 157 through 177 removed outlier: 5.327A pdb=" N ILEYA 161 " --> pdb=" O GLNYA 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VALYA 167 " --> pdb=" O ALAYA 163 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SERYA 169 " --> pdb=" O ARGYA 165 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLUYA 175 " --> pdb=" O ILEYA 171 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VALYA 176 " --> pdb=" O LEUYA 172 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLNYA 177 " --> pdb=" O THRYA 173 " (cutoff:3.500A) Processing helix chain 'YA' and resid 180 through 189 removed outlier: 3.588A pdb=" N LEUYA 184 " --> pdb=" O THRYA 180 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SERYA 186 " --> pdb=" O ALAYA 182 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYSYA 187 " --> pdb=" O GLNYA 183 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILEYA 189 " --> pdb=" O THRYA 185 " (cutoff:3.500A) Processing helix chain 'YA' and resid 191 through 202 removed outlier: 4.174A pdb=" N LYSYA 195 " --> pdb=" O GLUYA 191 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLUYA 196 " --> pdb=" O VALYA 192 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASNYA 199 " --> pdb=" O LYSYA 195 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALAYA 200 " --> pdb=" O GLUYA 196 " (cutoff:3.500A) Processing helix chain 'YA' and resid 224 through 233 removed outlier: 3.701A pdb=" N LEUYA 228 " --> pdb=" O ASPYA 224 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALAYA 230 " --> pdb=" O GLYYA 226 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEUYA 231 " --> pdb=" O ALAYA 227 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLYYA 233 " --> pdb=" O METYA 229 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 39 through 48 removed outlier: 3.558A pdb=" N LYSZA 46 " --> pdb=" O GLYZA 42 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLYZA 48 " --> pdb=" O LEUZA 44 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 52 through 60 removed outlier: 3.925A pdb=" N ILEZA 56 " --> pdb=" O THRZA 52 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 65 through 74 removed outlier: 4.683A pdb=" N ILEZA 69 " --> pdb=" O GLUZA 65 " (cutoff:3.500A) Proline residue: ZA 74 - end of helix Processing helix chain 'ZA' and resid 120 through 136 removed outlier: 3.550A pdb=" N ILEZA 125 " --> pdb=" O VALZA 121 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLYZA 128 " --> pdb=" O ALAZA 124 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILEZA 130 " --> pdb=" O ARGZA 126 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILEZA 131 " --> pdb=" O ALAZA 127 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VALZA 136 " --> pdb=" O ALAZA 132 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 181 through 192 removed outlier: 3.595A pdb=" N LYSZA 186 " --> pdb=" O PROZA 182 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEUZA 187 " --> pdb=" O ALAZA 183 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALAZA 191 " --> pdb=" O LEUZA 187 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 206 through 224 removed outlier: 3.565A pdb=" N THRZA 210 " --> pdb=" O THRZA 206 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEUZA 211 " --> pdb=" O LEUZA 207 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THRZA 221 " --> pdb=" O ALAZA 217 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYRZA 222 " --> pdb=" O ILEZA 218 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLYZA 223 " --> pdb=" O GLYZA 219 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHEZA 224 " --> pdb=" O ASNZA 220 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 226 through 231 removed outlier: 3.764A pdb=" N TRPZA 230 " --> pdb=" O THRZA 226 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ALAZA 231 " --> pdb=" O PROZA 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'ZA' and resid 226 through 231' Processing helix chain 'ZA' and resid 238 through 244 removed outlier: 3.549A pdb=" N ILEZA 242 " --> pdb=" O SERZA 238 " (cutoff:3.500A) Processing helix chain 'AB' and resid 7 through 29 removed outlier: 3.509A pdb=" N LEUAB 11 " --> pdb=" O LYSAB 7 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VALAB 12 " --> pdb=" O LYSAB 8 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALAAB 13 " --> pdb=" O ARGAB 9 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEUAB 21 " --> pdb=" O PHEAB 17 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLUAB 23 " --> pdb=" O ALAAB 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THRAB 26 " --> pdb=" O ASNAB 22 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARGAB 27 " --> pdb=" O GLUAB 23 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLUAB 28 " --> pdb=" O PHEAB 24 " (cutoff:3.500A) Processing helix chain 'AB' and resid 54 through 59 removed outlier: 4.322A pdb=" N VALAB 58 " --> pdb=" O ARGAB 54 " (cutoff:3.500A) Processing helix chain 'AB' and resid 64 through 78 removed outlier: 3.536A pdb=" N VALAB 73 " --> pdb=" O LEUAB 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARGAB 76 " --> pdb=" O LEUAB 72 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHEAB 77 " --> pdb=" O VALAB 73 " (cutoff:3.500A) Processing helix chain 'AB' and resid 80 through 85 removed outlier: 3.630A pdb=" N ILEAB 84 " --> pdb=" O ALAAB 80 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VALAB 85 " --> pdb=" O PROAB 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'AB' and resid 80 through 85' Processing helix chain 'AB' and resid 93 through 98 removed outlier: 4.607A pdb=" N ALAAB 98 " --> pdb=" O ARGAB 94 " (cutoff:3.500A) Processing helix chain 'AB' and resid 99 through 112 removed outlier: 3.513A pdb=" N GLUAB 103 " --> pdb=" O VALAB 99 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SERAB 104 " --> pdb=" O ALAAB 100 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N METAB 105 " --> pdb=" O GLNAB 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYSAB 106 " --> pdb=" O ALAAB 102 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHEAB 107 " --> pdb=" O GLUAB 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYSAB 108 " --> pdb=" O SERAB 104 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEUAB 109 " --> pdb=" O METAB 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEUAB 110 " --> pdb=" O LYSAB 106 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASNAB 111 " --> pdb=" O PHEAB 107 " (cutoff:3.500A) Processing helix chain 'AB' and resid 114 through 130 removed outlier: 3.554A pdb=" N ALAAB 118 " --> pdb=" O ALAAB 114 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALAAB 119 " --> pdb=" O ILEAB 115 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLYAB 121 " --> pdb=" O ARGAB 117 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLUAB 128 " --> pdb=" O ARGAB 124 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SERAB 129 " --> pdb=" O TYRAB 125 " (cutoff:3.500A) Processing helix chain 'AB' and resid 161 through 167 removed outlier: 4.780A pdb=" N ASNAB 165 " --> pdb=" O GLYAB 161 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASPAB 166 " --> pdb=" O GLNAB 162 " (cutoff:3.500A) Processing helix chain 'AB' and resid 191 through 196 removed outlier: 3.824A pdb=" N SERAB 195 " --> pdb=" O ASPAB 191 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARGAB 196 " --> pdb=" O PROAB 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'AB' and resid 191 through 196' Processing helix chain 'BB' and resid 43 through 49 removed outlier: 3.531A pdb=" N ARGBB 49 " --> pdb=" O ILEBB 45 " (cutoff:3.500A) Processing helix chain 'BB' and resid 57 through 68 removed outlier: 3.574A pdb=" N ALABB 63 " --> pdb=" O ARGBB 59 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEBB 64 " --> pdb=" O GLUBB 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEUBB 65 " --> pdb=" O VALBB 61 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLNBB 67 " --> pdb=" O ALABB 63 " (cutoff:3.500A) Processing helix chain 'BB' and resid 115 through 122 removed outlier: 4.437A pdb=" N SERBB 120 " --> pdb=" O ASPBB 116 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYRBB 121 " --> pdb=" O GLUBB 117 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYSBB 122 " --> pdb=" O GLUBB 118 " (cutoff:3.500A) Processing helix chain 'BB' and resid 221 through 226 removed outlier: 3.562A pdb=" N VALBB 225 " --> pdb=" O ARGBB 221 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHEBB 226 " --> pdb=" O LEUBB 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 221 through 226' Processing helix chain 'BB' and resid 247 through 259 removed outlier: 3.506A pdb=" N ARGBB 254 " --> pdb=" O GLUBB 250 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLNBB 258 " --> pdb=" O ARGBB 254 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLNBB 259 " --> pdb=" O ARGBB 255 " (cutoff:3.500A) Processing helix chain 'CB' and resid 30 through 37 removed outlier: 3.502A pdb=" N GLNCB 34 " --> pdb=" O PROCB 30 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALACB 36 " --> pdb=" O GLUCB 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLNCB 37 " --> pdb=" O VALCB 33 " (cutoff:3.500A) Processing helix chain 'CB' and resid 58 through 63 removed outlier: 3.557A pdb=" N VALCB 62 " --> pdb=" O LEUCB 58 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLNCB 63 " --> pdb=" O VALCB 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 58 through 63' Processing helix chain 'CB' and resid 82 through 88 removed outlier: 3.921A pdb=" N GLNCB 86 " --> pdb=" O PHECB 82 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYSCB 87 " --> pdb=" O ARGCB 83 " (cutoff:3.500A) Proline residue: CB 88 - end of helix No H-bonds generated for 'chain 'CB' and resid 82 through 88' Processing helix chain 'CB' and resid 89 through 99 removed outlier: 3.590A pdb=" N THRCB 94 " --> pdb=" O ILECB 90 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASNCB 95 " --> pdb=" O GLUCB 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SERCB 96 " --> pdb=" O ARGCB 92 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N METCB 99 " --> pdb=" O ASNCB 95 " (cutoff:3.500A) Processing helix chain 'CB' and resid 106 through 126 removed outlier: 3.877A pdb=" N ALACB 110 " --> pdb=" O LYSCB 106 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THRCB 125 " --> pdb=" O ILECB 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASPCB 126 " --> pdb=" O ASNCB 122 " (cutoff:3.500A) Processing helix chain 'CB' and resid 128 through 141 removed outlier: 3.623A pdb=" N VALCB 132 " --> pdb=" O ASNCB 128 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VALCB 134 " --> pdb=" O ILECB 130 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASPCB 135 " --> pdb=" O GLNCB 131 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALACB 136 " --> pdb=" O VALCB 132 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILECB 137 " --> pdb=" O VALCB 133 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THRCB 140 " --> pdb=" O ALACB 136 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLYCB 141 " --> pdb=" O ILECB 137 " (cutoff:3.500A) Processing helix chain 'CB' and resid 163 through 185 removed outlier: 3.536A pdb=" N ALACB 171 " --> pdb=" O ARGCB 167 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALACB 173 " --> pdb=" O ASNCB 169 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRCB 176 " --> pdb=" O ILECB 172 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALACB 182 " --> pdb=" O GLYCB 178 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALACB 183 " --> pdb=" O ALACB 179 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ARGCB 185 " --> pdb=" O GLUCB 181 " (cutoff:3.500A) Processing helix chain 'CB' and resid 189 through 204 removed outlier: 3.569A pdb=" N ALACB 195 " --> pdb=" O ALACB 191 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEUCB 198 " --> pdb=" O LEUCB 194 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALACB 202 " --> pdb=" O LEUCB 198 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYSCB 203 " --> pdb=" O ILECB 199 " (cutoff:3.500A) Processing helix chain 'CB' and resid 208 through 225 removed outlier: 3.598A pdb=" N LYSCB 213 " --> pdb=" O TYRCB 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VALCB 220 " --> pdb=" O GLUCB 216 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARGCB 225 " --> pdb=" O ALACB 221 " (cutoff:3.500A) Processing helix chain 'DB' and resid 20 through 25 removed outlier: 3.661A pdb=" N ILEDB 24 " --> pdb=" O ASPDB 20 " (cutoff:3.500A) Processing helix chain 'DB' and resid 137 through 146 removed outlier: 3.571A pdb=" N LYSDB 143 " --> pdb=" O ASNDB 139 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHEDB 144 " --> pdb=" O ASNDB 140 " (cutoff:3.500A) Processing helix chain 'DB' and resid 180 through 226 removed outlier: 3.660A pdb=" N LEUDB 184 " --> pdb=" O THRDB 180 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSDB 187 " --> pdb=" O ARGDB 183 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALADB 200 " --> pdb=" O ARGDB 196 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLUDB 222 " --> pdb=" O GLUDB 218 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALADB 224 " --> pdb=" O LYSDB 220 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILEDB 226 " --> pdb=" O GLUDB 222 " (cutoff:3.500A) Processing helix chain 'DB' and resid 121 through 127 removed outlier: 3.858A pdb=" N THRDB 127 " --> pdb=" O GLUDB 122 " (cutoff:3.500A) Processing helix chain 'EB' and resid 14 through 30 removed outlier: 3.857A pdb=" N LEUEB 18 " --> pdb=" O THREB 14 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALAEB 21 " --> pdb=" O GLUEB 17 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEUEB 27 " --> pdb=" O ALAEB 23 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLUEB 28 " --> pdb=" O PHEEB 24 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SEREB 30 " --> pdb=" O GLUEB 26 " (cutoff:3.500A) Processing helix chain 'EB' and resid 32 through 38 removed outlier: 3.753A pdb=" N ALAEB 36 " --> pdb=" O PROEB 32 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLUEB 37 " --> pdb=" O GLUEB 33 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEUEB 38 " --> pdb=" O LEUEB 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'EB' and resid 32 through 38' Processing helix chain 'EB' and resid 63 through 74 removed outlier: 6.585A pdb=" N LEUEB 67 " --> pdb=" O PROEB 63 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALAEB 68 " --> pdb=" O VALEB 64 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLYEB 69 " --> pdb=" O PROEB 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHEEB 70 " --> pdb=" O SEREB 66 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYSEB 72 " --> pdb=" O ALAEB 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VALEB 73 " --> pdb=" O GLYEB 69 " (cutoff:3.500A) Processing helix chain 'EB' and resid 75 through 86 removed outlier: 3.575A pdb=" N ARGEB 79 " --> pdb=" O THREB 75 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYSEB 84 " --> pdb=" O GLUEB 80 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHEEB 85 " --> pdb=" O LEUEB 81 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLNEB 86 " --> pdb=" O GLUEB 82 " (cutoff:3.500A) Processing helix chain 'EB' and resid 117 through 131 removed outlier: 3.530A pdb=" N HISEB 122 " --> pdb=" O LEUEB 118 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLUEB 127 " --> pdb=" O ASPEB 123 " (cutoff:3.500A) Processing helix chain 'EB' and resid 165 through 177 removed outlier: 3.626A pdb=" N GLNEB 170 " --> pdb=" O LEUEB 166 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALAEB 171 " --> pdb=" O GLUEB 167 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASNEB 174 " --> pdb=" O GLNEB 170 " (cutoff:3.500A) Processing helix chain 'FB' and resid 6 through 11 removed outlier: 4.032A pdb=" N LYSFB 10 " --> pdb=" O ASPFB 6 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARGFB 11 " --> pdb=" O SERFB 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'FB' and resid 6 through 11' Processing helix chain 'FB' and resid 88 through 94 removed outlier: 3.666A pdb=" N ARGFB 92 " --> pdb=" O ASNFB 88 " (cutoff:3.500A) Processing helix chain 'FB' and resid 106 through 117 removed outlier: 3.551A pdb=" N TRPFB 112 " --> pdb=" O PROFB 108 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYRFB 117 " --> pdb=" O PHEFB 113 " (cutoff:3.500A) Processing helix chain 'FB' and resid 136 through 150 removed outlier: 3.542A pdb=" N ARGFB 141 " --> pdb=" O LYSFB 137 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALAFB 144 " --> pdb=" O GLUFB 140 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALAFB 148 " --> pdb=" O ALAFB 144 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SERFB 149 " --> pdb=" O ALAFB 145 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALAFB 150 " --> pdb=" O ARGFB 146 " (cutoff:3.500A) Processing helix chain 'FB' and resid 153 through 162 removed outlier: 3.524A pdb=" N GLNFB 159 " --> pdb=" O SERFB 155 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SERFB 161 " --> pdb=" O GLUFB 157 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALAFB 162 " --> pdb=" O SERFB 158 " (cutoff:3.500A) Processing helix chain 'FB' and resid 186 through 198 removed outlier: 3.519A pdb=" N ALAFB 190 " --> pdb=" O GLYFB 186 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEUFB 196 " --> pdb=" O TYRFB 192 " (cutoff:3.500A) Processing helix chain 'GB' and resid 21 through 34 removed outlier: 3.560A pdb=" N ASPGB 25 " --> pdb=" O SERGB 21 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALAGB 26 " --> pdb=" O SERGB 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLUGB 27 " --> pdb=" O ARGGB 23 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEUGB 28 " --> pdb=" O LEUGB 24 " (cutoff:3.500A) Processing helix chain 'GB' and resid 38 through 63 removed outlier: 3.833A pdb=" N ILEGB 42 " --> pdb=" O ASNGB 38 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILEGB 45 " --> pdb=" O GLUGB 41 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARGGB 62 " --> pdb=" O ASPGB 58 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASPGB 63 " --> pdb=" O LEUGB 59 " (cutoff:3.500A) Processing helix chain 'GB' and resid 66 through 84 removed outlier: 3.506A pdb=" N ARGGB 82 " --> pdb=" O ARGGB 78 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLYGB 84 " --> pdb=" O LEUGB 80 " (cutoff:3.500A) Processing helix chain 'GB' and resid 93 through 99 removed outlier: 3.557A pdb=" N LEUGB 97 " --> pdb=" O LEUGB 93 " (cutoff:3.500A) Processing helix chain 'GB' and resid 100 through 108 removed outlier: 3.955A pdb=" N PHEGB 104 " --> pdb=" O LYSGB 100 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEUGB 105 " --> pdb=" O VALGB 101 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARGGB 107 " --> pdb=" O ASPGB 103 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARGGB 108 " --> pdb=" O PHEGB 104 " (cutoff:3.500A) Processing helix chain 'GB' and resid 109 through 117 removed outlier: 3.706A pdb=" N TYRGB 114 " --> pdb=" O GLNGB 110 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEUGB 116 " --> pdb=" O GLNGB 112 " (cutoff:3.500A) Processing helix chain 'GB' and resid 121 through 132 removed outlier: 3.926A pdb=" N ARGGB 132 " --> pdb=" O LEUGB 128 " (cutoff:3.500A) Processing helix chain 'GB' and resid 149 through 154 removed outlier: 6.166A pdb=" N GLUGB 153 " --> pdb=" O ARGGB 149 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYSGB 154 " --> pdb=" O LEUGB 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'GB' and resid 149 through 154' Processing helix chain 'GB' and resid 170 through 184 removed outlier: 3.564A pdb=" N ARGGB 175 " --> pdb=" O ARGGB 171 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLUGB 182 " --> pdb=" O ALAGB 178 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALAGB 183 " --> pdb=" O ARGGB 179 " (cutoff:3.500A) Processing helix chain 'HB' and resid 6 through 18 removed outlier: 3.519A pdb=" N ILEHB 11 " --> pdb=" O ASPHB 7 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEUHB 15 " --> pdb=" O ILEHB 11 " (cutoff:3.500A) Processing helix chain 'HB' and resid 38 through 53 removed outlier: 3.583A pdb=" N VALHB 42 " --> pdb=" O LYSHB 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLNHB 47 " --> pdb=" O ILEHB 43 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEUHB 49 " --> pdb=" O ALAHB 45 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYSHB 52 " --> pdb=" O SERHB 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLYHB 53 " --> pdb=" O LEUHB 49 " (cutoff:3.500A) Processing helix chain 'HB' and resid 69 through 81 removed outlier: 3.547A pdb=" N GLUHB 74 " --> pdb=" O GLUHB 70 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYRHB 75 " --> pdb=" O GLUHB 71 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEUHB 76 " --> pdb=" O GLYHB 72 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLUHB 78 " --> pdb=" O GLUHB 74 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYRHB 79 " --> pdb=" O TYRHB 75 " (cutoff:3.500A) Processing helix chain 'IB' and resid 45 through 51 removed outlier: 4.052A pdb=" N ILEIB 49 " --> pdb=" O PROIB 45 " (cutoff:3.500A) Processing helix chain 'IB' and resid 148 through 153 removed outlier: 4.429A pdb=" N PHEIB 153 " --> pdb=" O ALAIB 149 " (cutoff:3.500A) Processing helix chain 'JB' and resid 28 through 39 removed outlier: 3.583A pdb=" N ARGJB 33 " --> pdb=" O LYSJB 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THRJB 34 " --> pdb=" O VALJB 30 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEUJB 36 " --> pdb=" O LEUJB 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALJB 37 " --> pdb=" O ARGJB 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASPJB 39 " --> pdb=" O ALAJB 35 " (cutoff:3.500A) Processing helix chain 'JB' and resid 44 through 55 removed outlier: 3.545A pdb=" N THRJB 49 " --> pdb=" O LEUJB 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYSJB 50 " --> pdb=" O ARGJB 46 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALAJB 51 " --> pdb=" O GLUJB 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEUJB 52 " --> pdb=" O SERJB 48 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THRJB 53 " --> pdb=" O THRJB 49 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARGJB 54 " --> pdb=" O LYSJB 50 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLYJB 55 " --> pdb=" O ALAJB 51 " (cutoff:3.500A) Processing helix chain 'JB' and resid 69 through 81 removed outlier: 3.546A pdb=" N LEUJB 74 " --> pdb=" O ASNJB 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VALJB 75 " --> pdb=" O ILEJB 71 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEUJB 78 " --> pdb=" O LEUJB 74 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASNJB 80 " --> pdb=" O GLUJB 76 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASPJB 81 " --> pdb=" O GLYJB 77 " (cutoff:3.500A) Processing helix chain 'JB' and resid 93 through 102 removed outlier: 3.706A pdb=" N LEUJB 97 " --> pdb=" O ASPJB 93 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRPJB 100 " --> pdb=" O GLNJB 96 " (cutoff:3.500A) Processing helix chain 'JB' and resid 131 through 143 removed outlier: 3.594A pdb=" N METJB 135 " --> pdb=" O ASPJB 131 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILEJB 136 " --> pdb=" O GLUJB 132 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLUJB 138 " --> pdb=" O SERJB 134 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHEJB 140 " --> pdb=" O ILEJB 136 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SERJB 141 " --> pdb=" O METJB 137 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLNJB 142 " --> pdb=" O GLUJB 138 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLNJB 143 " --> pdb=" O HISJB 139 " (cutoff:3.500A) Processing helix chain 'KB' and resid 29 through 44 removed outlier: 3.591A pdb=" N VALKB 33 " --> pdb=" O SERKB 29 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILEKB 34 " --> pdb=" O SERKB 30 " (cutoff:3.500A) Processing helix chain 'KB' and resid 46 through 57 removed outlier: 3.520A pdb=" N ARGKB 55 " --> pdb=" O GLYKB 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALAKB 57 " --> pdb=" O LEUKB 53 " (cutoff:3.500A) Processing helix chain 'KB' and resid 62 through 67 Processing helix chain 'KB' and resid 70 through 79 removed outlier: 3.553A pdb=" N LYSKB 76 " --> pdb=" O METKB 72 " (cutoff:3.500A) Processing helix chain 'KB' and resid 85 through 106 removed outlier: 3.575A pdb=" N TYRKB 90 " --> pdb=" O GLUKB 86 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SERKB 97 " --> pdb=" O LYSKB 93 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARGKB 99 " --> pdb=" O ALAKB 95 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARGKB 104 " --> pdb=" O LYSKB 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARGKB 106 " --> pdb=" O LEUKB 102 " (cutoff:3.500A) Processing helix chain 'KB' and resid 108 through 133 removed outlier: 3.605A pdb=" N THRKB 131 " --> pdb=" O ARGKB 127 " (cutoff:3.500A) Processing helix chain 'KB' and resid 142 through 147 removed outlier: 3.573A pdb=" N ALAKB 146 " --> pdb=" O GLUKB 142 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SERKB 147 " --> pdb=" O SERKB 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'KB' and resid 142 through 147' Processing helix chain 'LB' and resid 43 through 49 removed outlier: 4.342A pdb=" N LYSLB 47 " --> pdb=" O THRLB 43 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VALLB 48 " --> pdb=" O GLYLB 44 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYSLB 49 " --> pdb=" O GLYLB 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 43 through 49' Processing helix chain 'LB' and resid 56 through 75 removed outlier: 3.535A pdb=" N ALALB 69 " --> pdb=" O GLNLB 65 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLULB 73 " --> pdb=" O ALALB 69 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VALLB 74 " --> pdb=" O LYSLB 70 " (cutoff:3.500A) Processing helix chain 'LB' and resid 95 through 109 removed outlier: 4.483A pdb=" N GLNLB 99 " --> pdb=" O GLYLB 95 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALALB 100 " --> pdb=" O PROLB 96 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEULB 102 " --> pdb=" O GLYLB 98 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARGLB 103 " --> pdb=" O GLNLB 99 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARGLB 107 " --> pdb=" O ARGLB 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLYLB 109 " --> pdb=" O LEULB 105 " (cutoff:3.500A) Processing helix chain 'MB' and resid 21 through 28 removed outlier: 3.539A pdb=" N LEUMB 26 " --> pdb=" O LEUMB 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLUMB 27 " --> pdb=" O GLUMB 23 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N METMB 28 " --> pdb=" O LYSMB 24 " (cutoff:3.500A) Processing helix chain 'MB' and resid 29 through 37 Processing helix chain 'MB' and resid 38 through 49 removed outlier: 3.515A pdb=" N ARGMB 43 " --> pdb=" O ALAMB 39 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALAMB 46 " --> pdb=" O ARGMB 42 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARGMB 47 " --> pdb=" O ARGMB 43 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLYMB 48 " --> pdb=" O ARGMB 44 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N METMB 49 " --> pdb=" O PHEMB 45 " (cutoff:3.500A) Processing helix chain 'MB' and resid 53 through 67 removed outlier: 5.052A pdb=" N METMB 57 " --> pdb=" O PROMB 53 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYSMB 58 " --> pdb=" O ALAMB 54 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYSMB 59 " --> pdb=" O GLYMB 55 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYSMB 64 " --> pdb=" O LEUMB 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEUMB 65 " --> pdb=" O ARGMB 61 " (cutoff:3.500A) Processing helix chain 'MB' and resid 115 through 120 removed outlier: 4.303A pdb=" N PHEMB 119 " --> pdb=" O TYRMB 115 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SERMB 120 " --> pdb=" O LEUMB 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'MB' and resid 115 through 120' Processing helix chain 'NB' and resid 41 through 56 removed outlier: 6.939A pdb=" N ARGNB 45 " --> pdb=" O PRONB 41 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHENB 46 " --> pdb=" O GLUNB 42 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYSNB 47 " --> pdb=" O ILENB 43 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLUNB 50 " --> pdb=" O PHENB 46 " (cutoff:3.500A) Proline residue: NB 51 - end of helix removed outlier: 3.664A pdb=" N VALNB 55 " --> pdb=" O PRONB 51 " (cutoff:3.500A) Processing helix chain 'NB' and resid 57 through 62 removed outlier: 4.112A pdb=" N SERNB 61 " --> pdb=" O LEUNB 57 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASNNB 62 " --> pdb=" O ASPNB 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'NB' and resid 57 through 62' Processing helix chain 'NB' and resid 73 through 96 removed outlier: 3.601A pdb=" N GLNNB 77 " --> pdb=" O GLYNB 73 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYRNB 79 " --> pdb=" O VALNB 75 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILENB 81 " --> pdb=" O GLNNB 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARGNB 82 " --> pdb=" O VALNB 78 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLYNB 88 " --> pdb=" O ALANB 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYSNB 95 " --> pdb=" O ALANB 91 " (cutoff:3.500A) Processing helix chain 'NB' and resid 98 through 113 removed outlier: 3.587A pdb=" N LYSNB 102 " --> pdb=" O ASPNB 98 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYSNB 106 " --> pdb=" O LYSNB 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALANB 108 " --> pdb=" O GLUNB 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SERNB 111 " --> pdb=" O LYSNB 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYRNB 112 " --> pdb=" O ALANB 108 " (cutoff:3.500A) Processing helix chain 'NB' and resid 114 through 119 removed outlier: 6.201A pdb=" N ILENB 118 " --> pdb=" O ARGNB 114 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALANB 119 " --> pdb=" O THRNB 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'NB' and resid 114 through 119' Processing helix chain 'OB' and resid 6 through 20 removed outlier: 3.629A pdb=" N LYSOB 10 " --> pdb=" O THROB 6 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALAOB 12 " --> pdb=" O THROB 8 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALAOB 15 " --> pdb=" O ARGOB 11 " (cutoff:3.500A) Processing helix chain 'OB' and resid 27 through 39 removed outlier: 3.531A pdb=" N ASNOB 31 " --> pdb=" O ASPOB 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLUOB 37 " --> pdb=" O ARGOB 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALAOB 39 " --> pdb=" O CYSOB 35 " (cutoff:3.500A) Processing helix chain 'OB' and resid 43 through 65 removed outlier: 3.597A pdb=" N ARGOB 47 " --> pdb=" O SEROB 43 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYROB 53 " --> pdb=" O LYSOB 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THROB 55 " --> pdb=" O ALAOB 51 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HISOB 56 " --> pdb=" O GLYOB 52 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N METOB 58 " --> pdb=" O THROB 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLNOB 62 " --> pdb=" O METOB 58 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LYSOB 63 " --> pdb=" O LYSOB 59 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLYOB 64 " --> pdb=" O ARGOB 60 " (cutoff:3.500A) Proline residue: OB 65 - end of helix Processing helix chain 'OB' and resid 75 through 92 removed outlier: 4.321A pdb=" N GLUOB 79 " --> pdb=" O GLUOB 75 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARGOB 80 " --> pdb=" O GLUOB 76 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYSOB 81 " --> pdb=" O GLUOB 77 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASPOB 82 " --> pdb=" O ARGOB 78 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLNOB 83 " --> pdb=" O GLUOB 79 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VALOB 85 " --> pdb=" O LYSOB 81 " (cutoff:3.500A) Proline residue: OB 86 - end of helix removed outlier: 4.274A pdb=" N LEUOB 91 " --> pdb=" O GLUOB 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASPOB 92 " --> pdb=" O VALOB 88 " (cutoff:3.500A) Processing helix chain 'OB' and resid 103 through 114 removed outlier: 3.834A pdb=" N SEROB 107 " --> pdb=" O ASPOB 103 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VALOB 110 " --> pdb=" O THROB 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SEROB 112 " --> pdb=" O ASPOB 108 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEUOB 113 " --> pdb=" O LEUOB 109 " (cutoff:3.500A) Processing helix chain 'PB' and resid 27 through 32 removed outlier: 3.533A pdb=" N LEUPB 32 " --> pdb=" O ILEPB 28 " (cutoff:3.500A) Processing helix chain 'PB' and resid 39 through 51 removed outlier: 3.509A pdb=" N ASNPB 44 " --> pdb=" O ARGPB 40 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEUPB 45 " --> pdb=" O ARGPB 41 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VALPB 46 " --> pdb=" O TYRPB 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYSPB 48 " --> pdb=" O ASNPB 44 " (cutoff:3.500A) Processing helix chain 'PB' and resid 62 through 73 removed outlier: 3.554A pdb=" N ILEPB 69 " --> pdb=" O GLUPB 65 " (cutoff:3.500A) Processing helix chain 'PB' and resid 82 through 87 removed outlier: 7.328A pdb=" N LEUPB 86 " --> pdb=" O PROPB 82 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASNPB 87 " --> pdb=" O ALAPB 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'PB' and resid 82 through 87' Processing helix chain 'PB' and resid 103 through 120 removed outlier: 5.401A pdb=" N SERPB 107 " --> pdb=" O ASNPB 103 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARGPB 110 " --> pdb=" O GLUPB 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASPPB 112 " --> pdb=" O LYSPB 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUPB 113 " --> pdb=" O LEUPB 109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLUPB 114 " --> pdb=" O ARGPB 110 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARGPB 115 " --> pdb=" O ASPPB 111 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEUPB 116 " --> pdb=" O ASPPB 112 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYSPB 117 " --> pdb=" O LEUPB 113 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILEPB 119 " --> pdb=" O ARGPB 115 " (cutoff:3.500A) Processing helix chain 'PB' and resid 121 through 130 removed outlier: 3.633A pdb=" N HISPB 127 " --> pdb=" O ARGPB 123 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRPPB 129 " --> pdb=" O ILEPB 125 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYPB 130 " --> pdb=" O ARGPB 126 " (cutoff:3.500A) Processing helix chain 'QB' and resid 5 through 10 removed outlier: 3.810A pdb=" N VALQB 9 " --> pdb=" O SERQB 5 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALAQB 10 " --> pdb=" O VALQB 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'QB' and resid 5 through 10' Processing helix chain 'QB' and resid 11 through 25 removed outlier: 3.714A pdb=" N ASNQB 16 " --> pdb=" O GLNQB 12 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEUQB 22 " --> pdb=" O TYRQB 18 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLNQB 23 " --> pdb=" O ALAQB 19 " (cutoff:3.500A) Processing helix chain 'QB' and resid 52 through 69 removed outlier: 5.428A pdb=" N LYSQB 56 " --> pdb=" O GLYQB 52 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARGQB 57 " --> pdb=" O TRPQB 53 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARGQB 63 " --> pdb=" O ALAQB 59 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N METQB 67 " --> pdb=" O ARGQB 63 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARGQB 68 " --> pdb=" O HISQB 64 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYSQB 69 " --> pdb=" O ILEQB 65 " (cutoff:3.500A) Processing helix chain 'QB' and resid 72 through 81 removed outlier: 4.116A pdb=" N LEUQB 76 " --> pdb=" O GLYQB 72 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYSQB 78 " --> pdb=" O GLYQB 74 " (cutoff:3.500A) Processing helix chain 'QB' and resid 98 through 112 removed outlier: 3.567A pdb=" N VALQB 104 " --> pdb=" O ILEQB 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILEQB 111 " --> pdb=" O ALAQB 107 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLYQB 112 " --> pdb=" O LEUQB 108 " (cutoff:3.500A) Processing helix chain 'QB' and resid 125 through 144 removed outlier: 3.541A pdb=" N GLNQB 129 " --> pdb=" O SERQB 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARGQB 130 " --> pdb=" O GLUQB 126 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARGQB 134 " --> pdb=" O ARGQB 130 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEUQB 140 " --> pdb=" O ALAQB 136 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLUQB 141 " --> pdb=" O ALAQB 137 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLUQB 142 " --> pdb=" O GLNQB 138 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASPQB 143 " --> pdb=" O THRQB 139 " (cutoff:3.500A) Processing helix chain 'RB' and resid 30 through 49 removed outlier: 3.537A pdb=" N SERRB 39 " --> pdb=" O GLURB 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASNRB 40 " --> pdb=" O ASNRB 36 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILERB 41 " --> pdb=" O VALRB 37 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALARB 45 " --> pdb=" O ILERB 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLNRB 47 " --> pdb=" O LYSRB 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HISRB 48 " --> pdb=" O ASNRB 44 " (cutoff:3.500A) Processing helix chain 'RB' and resid 96 through 107 removed outlier: 3.750A pdb=" N VALRB 100 " --> pdb=" O PRORB 96 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYSRB 101 " --> pdb=" O VALRB 97 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLNRB 105 " --> pdb=" O LYSRB 101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILERB 106 " --> pdb=" O ARGRB 102 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THRRB 107 " --> pdb=" O ILERB 103 " (cutoff:3.500A) Processing helix chain 'SB' and resid 56 through 63 removed outlier: 3.566A pdb=" N ARGSB 62 " --> pdb=" O TYRSB 58 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLYSB 63 " --> pdb=" O VALSB 59 " (cutoff:3.500A) Processing helix chain 'SB' and resid 64 through 77 removed outlier: 3.566A pdb=" N LEUSB 69 " --> pdb=" O SERSB 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASNSB 75 " --> pdb=" O ARGSB 71 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASPSB 76 " --> pdb=" O LEUSB 72 " (cutoff:3.500A) Processing helix chain 'TB' and resid 5 through 21 removed outlier: 3.503A pdb=" N ASPTB 9 " --> pdb=" O SERTB 5 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILETB 14 " --> pdb=" O ALATB 10 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALATB 17 " --> pdb=" O ALATB 13 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYSTB 19 " --> pdb=" O ASNTB 15 " (cutoff:3.500A) Processing helix chain 'TB' and resid 31 through 45 removed outlier: 3.539A pdb=" N GLNTB 39 " --> pdb=" O ILETB 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VALTB 40 " --> pdb=" O LYSTB 36 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N METTB 41 " --> pdb=" O PHETB 37 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HISTB 44 " --> pdb=" O VALTB 40 " (cutoff:3.500A) Processing helix chain 'TB' and resid 82 through 94 removed outlier: 5.506A pdb=" N ILETB 86 " --> pdb=" O LYSTB 82 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLUTB 87 " --> pdb=" O ILETB 83 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYSTB 88 " --> pdb=" O GLYTB 84 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALATB 91 " --> pdb=" O GLUTB 87 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASNTB 92 " --> pdb=" O LYSTB 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEUTB 94 " --> pdb=" O THRTB 90 " (cutoff:3.500A) Processing helix chain 'TB' and resid 112 through 120 removed outlier: 3.615A pdb=" N LYSTB 119 " --> pdb=" O GLUTB 115 " (cutoff:3.500A) Processing helix chain 'UB' and resid 11 through 26 removed outlier: 3.749A pdb=" N TRPUB 24 " --> pdb=" O ARGUB 20 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALAUB 25 " --> pdb=" O ASNUB 21 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLUUB 26 " --> pdb=" O ASNUB 22 " (cutoff:3.500A) Processing helix chain 'UB' and resid 27 through 35 removed outlier: 3.531A pdb=" N ARGUB 32 " --> pdb=" O ASNUB 28 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYUB 35 " --> pdb=" O LYSUB 31 " (cutoff:3.500A) Processing helix chain 'UB' and resid 92 through 97 removed outlier: 3.863A pdb=" N VALUB 96 " --> pdb=" O CYSUB 92 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASPUB 97 " --> pdb=" O LEUUB 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'UB' and resid 92 through 97' Processing helix chain 'UB' and resid 131 through 138 removed outlier: 3.548A pdb=" N GLUUB 138 " --> pdb=" O ALAUB 134 " (cutoff:3.500A) Processing helix chain 'VB' and resid 36 through 49 removed outlier: 5.416A pdb=" N LEUVB 40 " --> pdb=" O SERVB 36 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLUVB 46 " --> pdb=" O GLUVB 42 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VALVB 47 " --> pdb=" O LYSVB 43 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYRVB 48 " --> pdb=" O LEUVB 44 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYSVB 49 " --> pdb=" O ALAVB 45 " (cutoff:3.500A) Processing helix chain 'VB' and resid 51 through 56 removed outlier: 3.942A pdb=" N VALVB 55 " --> pdb=" O GLUVB 51 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SERVB 56 " --> pdb=" O LYSVB 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'VB' and resid 51 through 56' Processing helix chain 'VB' and resid 78 through 85 removed outlier: 3.517A pdb=" N LYSVB 84 " --> pdb=" O ALAVB 80 " (cutoff:3.500A) Processing helix chain 'VB' and resid 87 through 95 removed outlier: 3.505A pdb=" N LEUVB 91 " --> pdb=" O PROVB 87 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARGVB 93 " --> pdb=" O TYRVB 89 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYRVB 94 " --> pdb=" O ARGVB 90 " (cutoff:3.500A) Processing helix chain 'VB' and resid 104 through 119 removed outlier: 3.550A pdb=" N LYSVB 109 " --> pdb=" O ARGVB 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYSVB 116 " --> pdb=" O LYSVB 112 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYSVB 117 " --> pdb=" O ASNVB 113 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N PHEVB 119 " --> pdb=" O ASPVB 115 " (cutoff:3.500A) Processing helix chain 'VB' and resid 122 through 135 removed outlier: 3.633A pdb=" N LYSVB 127 " --> pdb=" O LYSVB 123 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALAVB 130 " --> pdb=" O ALAVB 126 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARGVB 131 " --> pdb=" O LYSVB 127 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARGVB 132 " --> pdb=" O LYSVB 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASNVB 133 " --> pdb=" O VALVB 129 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALAVB 134 " --> pdb=" O ALAVB 130 " (cutoff:3.500A) Processing helix chain 'WB' and resid 43 through 55 removed outlier: 3.600A pdb=" N ILEWB 50 " --> pdb=" O LYSWB 46 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEUWB 51 " --> pdb=" O TYRWB 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYSWB 52 " --> pdb=" O ASPWB 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VALWB 54 " --> pdb=" O ILEWB 50 " (cutoff:3.500A) Proline residue: WB 55 - end of helix Processing helix chain 'WB' and resid 61 through 69 removed outlier: 3.557A pdb=" N VALWB 66 " --> pdb=" O VALWB 62 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARGWB 68 " --> pdb=" O VALWB 64 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEUWB 69 " --> pdb=" O LEUWB 65 " (cutoff:3.500A) Processing helix chain 'WB' and resid 72 through 86 removed outlier: 4.393A pdb=" N ARGWB 77 " --> pdb=" O GLYWB 73 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILEWB 78 " --> pdb=" O SERWB 74 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARGWB 81 " --> pdb=" O ARGWB 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HISWB 82 " --> pdb=" O ILEWB 78 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLUWB 84 " --> pdb=" O LEUWB 80 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYSWB 85 " --> pdb=" O ARGWB 81 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLUWB 86 " --> pdb=" O HISWB 82 " (cutoff:3.500A) Processing helix chain 'XB' and resid 31 through 36 removed outlier: 5.931A pdb=" N ILEXB 36 " --> pdb=" O LYSXB 32 " (cutoff:3.500A) Processing helix chain 'XB' and resid 48 through 57 removed outlier: 4.511A pdb=" N ASPXB 52 " --> pdb=" O ALAXB 48 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SERXB 54 " --> pdb=" O VALXB 50 " (cutoff:3.500A) Processing helix chain 'XB' and resid 74 through 82 removed outlier: 5.722A pdb=" N ALAXB 78 " --> pdb=" O CYSXB 74 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALAXB 81 " --> pdb=" O CYSXB 77 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARGXB 82 " --> pdb=" O ALAXB 78 " (cutoff:3.500A) Processing helix chain 'XB' and resid 89 through 95 removed outlier: 4.606A pdb=" N LYSXB 93 " --> pdb=" O ARGXB 89 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASNXB 94 " --> pdb=" O GLUXB 90 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARGXB 95 " --> pdb=" O ASPXB 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'XB' and resid 89 through 95' Processing helix chain 'YB' and resid 11 through 18 removed outlier: 3.546A pdb=" N ALAYB 16 " --> pdb=" O ALAYB 12 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARGYB 17 " --> pdb=" O ALAYB 13 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYSYB 18 " --> pdb=" O SERYB 14 " (cutoff:3.500A) Processing helix chain 'YB' and resid 19 through 24 removed outlier: 5.724A pdb=" N LEUYB 24 " --> pdb=" O LYSYB 20 " (cutoff:3.500A) Processing helix chain 'AC' and resid 15 through 20 removed outlier: 4.801A pdb=" N ARGAC 19 " --> pdb=" O GLYAC 15 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLNAC 20 " --> pdb=" O LYSAC 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 15 through 20' Processing helix chain 'AC' and resid 39 through 47 removed outlier: 4.338A pdb=" N GLUAC 45 " --> pdb=" O GLNAC 41 " (cutoff:3.500A) Processing helix chain 'AC' and resid 5 through 10 removed outlier: 3.832A pdb=" N SERAC 9 " --> pdb=" O VALAC 6 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N HISAC 10 " --> pdb=" O TRPAC 7 " (cutoff:3.500A) Processing helix chain 'BC' and resid 12 through 19 removed outlier: 3.503A pdb=" N SERBC 16 " --> pdb=" O GLYBC 12 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THRBC 18 " --> pdb=" O VALBC 14 " (cutoff:3.500A) Proline residue: BC 19 - end of helix Processing helix chain 'BC' and resid 32 through 44 removed outlier: 3.594A pdb=" N LEUBC 38 " --> pdb=" O ALABC 34 " (cutoff:3.500A) Processing helix chain 'DC' and resid 5 through 16 removed outlier: 3.966A pdb=" N LYSDC 15 " --> pdb=" O SERDC 11 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N VALDC 16 " --> pdb=" O LEUDC 12 " (cutoff:3.500A) Processing helix chain 'DC' and resid 31 through 43 removed outlier: 3.601A pdb=" N LEUDC 35 " --> pdb=" O GLYDC 31 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SERDC 38 " --> pdb=" O THRDC 34 " (cutoff:3.500A) Processing helix chain 'DC' and resid 82 through 90 removed outlier: 3.582A pdb=" N LYSDC 87 " --> pdb=" O ASPDC 83 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLUDC 88 " --> pdb=" O GLUDC 84 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILEDC 89 " --> pdb=" O ASPDC 85 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYSDC 90 " --> pdb=" O VALDC 86 " (cutoff:3.500A) Processing helix chain 'DC' and resid 112 through 122 removed outlier: 3.582A pdb=" N THRDC 116 " --> pdb=" O SERDC 112 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALADC 117 " --> pdb=" O SERDC 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARGDC 120 " --> pdb=" O THRDC 116 " (cutoff:3.500A) Processing helix chain 'DC' and resid 136 through 150 removed outlier: 3.502A pdb=" N ALADC 146 " --> pdb=" O VALDC 142 " (cutoff:3.500A) Processing helix chain 'DC' and resid 159 through 165 removed outlier: 3.763A pdb=" N ALADC 163 " --> pdb=" O LYSDC 159 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEUDC 164 " --> pdb=" O VALDC 160 " (cutoff:3.500A) Processing helix chain 'DC' and resid 173 through 192 removed outlier: 3.756A pdb=" N ILEDC 188 " --> pdb=" O SERDC 184 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VALDC 189 " --> pdb=" O VALDC 185 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THRDC 191 " --> pdb=" O VALDC 187 " (cutoff:3.500A) Processing helix chain 'DC' and resid 221 through 234 removed outlier: 3.851A pdb=" N PHEDC 225 " --> pdb=" O THRDC 221 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALADC 226 " --> pdb=" O ILEDC 222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARGDC 228 " --> pdb=" O GLNDC 224 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYSDC 231 " --> pdb=" O THRDC 227 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYSDC 232 " --> pdb=" O ARGDC 228 " (cutoff:3.500A) Processing helix chain 'DC' and resid 236 through 246 removed outlier: 4.107A pdb=" N TRPDC 245 " --> pdb=" O METDC 241 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLYDC 246 " --> pdb=" O ASPDC 242 " (cutoff:3.500A) Processing helix chain 'DC' and resid 271 through 291 removed outlier: 4.006A pdb=" N LEUDC 278 " --> pdb=" O ASNDC 274 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASPDC 279 " --> pdb=" O METDC 275 " (cutoff:3.500A) Proline residue: DC 280 - end of helix Processing helix chain 'DC' and resid 292 through 304 Proline residue: DC 297 - end of helix Processing helix chain 'DC' and resid 308 through 314 removed outlier: 4.922A pdb=" N LYSDC 312 " --> pdb=" O LYSDC 308 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASPDC 313 " --> pdb=" O GLYDC 309 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEUDC 314 " --> pdb=" O ASPDC 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'DC' and resid 308 through 314' Processing helix chain 'DC' and resid 316 through 328 removed outlier: 3.545A pdb=" N ARGDC 325 " --> pdb=" O LYSDC 321 " (cutoff:3.500A) Processing helix chain 'DC' and resid 330 through 341 removed outlier: 3.722A pdb=" N LEUDC 334 " --> pdb=" O ALADC 330 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N METDC 337 " --> pdb=" O ALADC 333 " (cutoff:3.500A) Processing helix chain 'DC' and resid 346 through 358 removed outlier: 3.967A pdb=" N ALADC 350 " --> pdb=" O VALDC 346 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYRDC 351 " --> pdb=" O THRDC 347 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLUDC 354 " --> pdb=" O ALADC 350 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLNDC 355 " --> pdb=" O TYRDC 351 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLUDC 358 " --> pdb=" O GLUDC 354 " (cutoff:3.500A) Processing helix chain 'DC' and resid 363 through 372 removed outlier: 3.531A pdb=" N ILEDC 369 " --> pdb=" O ASNDC 365 " (cutoff:3.500A) Processing helix chain 'DC' and resid 500 through 515 removed outlier: 3.611A pdb=" N LEUDC 504 " --> pdb=" O ASPDC 500 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VALDC 505 " --> pdb=" O LEUDC 501 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEUDC 508 " --> pdb=" O LEUDC 504 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYSDC 509 " --> pdb=" O VALDC 505 " (cutoff:3.500A) Processing helix chain 'DC' and resid 534 through 548 removed outlier: 3.544A pdb=" N HISDC 547 " --> pdb=" O GLNDC 543 " (cutoff:3.500A) Processing helix chain 'DC' and resid 594 through 604 removed outlier: 3.515A pdb=" N ALADC 600 " --> pdb=" O GLUDC 596 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILEDC 601 " --> pdb=" O VALDC 597 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLUDC 602 " --> pdb=" O SERDC 598 " (cutoff:3.500A) Processing helix chain 'DC' and resid 611 through 621 Processing helix chain 'DC' and resid 626 through 633 Processing helix chain 'DC' and resid 655 through 674 removed outlier: 3.889A pdb=" N ILEDC 659 " --> pdb=" O TYRDC 655 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYSDC 660 " --> pdb=" O LEUDC 656 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASPDC 661 " --> pdb=" O HISDC 657 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SERDC 662 " --> pdb=" O GLUDC 658 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLYDC 674 " --> pdb=" O ALADC 670 " (cutoff:3.500A) Processing helix chain 'DC' and resid 696 through 701 removed outlier: 3.735A pdb=" N ARGDC 700 " --> pdb=" O ASPDC 696 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLYDC 701 " --> pdb=" O ALADC 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'DC' and resid 696 through 701' Processing helix chain 'DC' and resid 702 through 721 Proline residue: DC 707 - end of helix removed outlier: 3.543A pdb=" N ARGDC 711 " --> pdb=" O PRODC 707 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASPDC 721 " --> pdb=" O PHEDC 717 " (cutoff:3.500A) Processing helix chain 'DC' and resid 738 through 751 removed outlier: 4.837A pdb=" N GLYDC 742 " --> pdb=" O GLNDC 738 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SERDC 745 " --> pdb=" O GLYDC 741 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARGDC 751 " --> pdb=" O LEUDC 747 " (cutoff:3.500A) Processing helix chain 'DC' and resid 773 through 778 removed outlier: 3.632A pdb=" N SERDC 777 " --> pdb=" O PRODC 773 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHEDC 778 " --> pdb=" O VALDC 774 " (cutoff:3.500A) No H-bonds generated for 'chain 'DC' and resid 773 through 778' Processing helix chain 'DC' and resid 779 through 789 removed outlier: 3.690A pdb=" N GLUDC 783 " --> pdb=" O GLYDC 779 " (cutoff:3.500A) Processing helix chain 'DC' and resid 813 through 827 removed outlier: 3.728A pdb=" N ILEDC 818 " --> pdb=" O LYSDC 814 " (cutoff:3.500A) Processing helix chain 'DC' and resid 834 through 839 removed outlier: 3.844A pdb=" N TYRDC 838 " --> pdb=" O GLYDC 834 " (cutoff:3.500A) Processing helix chain 'DC' and resid 457 through 462 removed outlier: 6.070A pdb=" N ASPDC 460 " --> pdb=" O VALDC 457 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLNDC 461 " --> pdb=" O GLYDC 458 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'E' and resid 203 through 207 removed outlier: 3.780A pdb=" N LEU E 204 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 216 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE E 214 " --> pdb=" O VAL E 206 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.558A pdb=" N ILE F 44 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS F 46 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS F 60 " --> pdb=" O LYS F 46 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 49 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLN F 47 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'F' and resid 134 through 137 removed outlier: 5.616A pdb=" N ARG F 147 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 156 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'F' and resid 58 through 64 removed outlier: 3.534A pdb=" N VAL F 61 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'G' and resid 44 through 49 removed outlier: 7.953A pdb=" N THR G 44 " --> pdb=" O LYS G 340 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'G' and resid 52 through 60 removed outlier: 5.346A pdb=" N ASN G 319 " --> pdb=" O GLY G 288 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'G' and resid 98 through 101 removed outlier: 7.750A pdb=" N VAL G 87 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'G' and resid 178 through 182 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'G' and resid 84 through 88 removed outlier: 6.133A pdb=" N LEU G 161 " --> pdb=" O VAL G 87 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.584A pdb=" N VAL H 8 " --> pdb=" O ASN H 18 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASN H 18 " --> pdb=" O VAL H 8 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 224 through 229 removed outlier: 3.556A pdb=" N GLU H 226 " --> pdb=" O PRO H 205 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR H 209 " --> pdb=" O ALA H 228 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE H 247 " --> pdb=" O GLY H 204 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'I' and resid 60 through 66 removed outlier: 3.577A pdb=" N GLN I 63 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL I 52 " --> pdb=" O GLN I 63 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE I 145 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL I 53 " --> pdb=" O ASP I 147 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'J' and resid 49 through 52 removed outlier: 3.698A pdb=" N LYS J 50 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL J 39 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE J 41 " --> pdb=" O ILE J 85 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE J 85 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU J 43 " --> pdb=" O TYR J 83 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR J 83 " --> pdb=" O LEU J 43 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'J' and resid 62 through 66 Processing sheet with id= 15, first strand: chain 'K' and resid 112 through 118 removed outlier: 4.267A pdb=" N SER K 113 " --> pdb=" O ARG K 88 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL K 84 " --> pdb=" O VAL K 117 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TYR K 133 " --> pdb=" O ILE K 89 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'K' and resid 152 through 156 removed outlier: 7.171A pdb=" N GLY K 152 " --> pdb=" O LEU K 163 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 175 through 179 removed outlier: 3.546A pdb=" N VAL L 151 " --> pdb=" O PRO L 176 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE L 153 " --> pdb=" O ALA L 178 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU L 150 " --> pdb=" O LEU L 200 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA L 196 " --> pdb=" O ALA L 154 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'M' and resid 17 through 20 removed outlier: 3.576A pdb=" N LYS M 36 " --> pdb=" O VAL M 25 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'M' and resid 43 through 48 removed outlier: 6.661A pdb=" N LEU M 52 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'M' and resid 100 through 103 removed outlier: 3.576A pdb=" N ASN M 102 " --> pdb=" O GLU M 113 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU M 113 " --> pdb=" O ASN M 102 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS M 110 " --> pdb=" O VAL M 128 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 132 through 136 removed outlier: 3.544A pdb=" N THR M 133 " --> pdb=" O SER M 147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER M 147 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU M 135 " --> pdb=" O VAL M 145 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR M 86 " --> pdb=" O GLY M 148 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 86 through 90 removed outlier: 3.541A pdb=" N HIS M 183 " --> pdb=" O LYS M 89 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.933A pdb=" N TYR N 34 " --> pdb=" O VAL N 89 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ALA N 84 " --> pdb=" O LYS N 141 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS N 141 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE N 135 " --> pdb=" O ARG N 90 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE N 136 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N CYS N 49 " --> pdb=" O SER N 168 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER N 168 " --> pdb=" O CYS N 49 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLN N 162 " --> pdb=" O ASN N 55 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 189 through 192 removed outlier: 6.581A pdb=" N GLU N 189 " --> pdb=" O LEU N 200 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS N 191 " --> pdb=" O LYS N 198 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS N 198 " --> pdb=" O LYS N 191 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'O' and resid 45 through 49 removed outlier: 3.576A pdb=" N HIS O 68 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA O 66 " --> pdb=" O SER O 48 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE O 65 " --> pdb=" O VAL O 23 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL O 23 " --> pdb=" O ILE O 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL O 67 " --> pdb=" O ILE O 21 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS O 16 " --> pdb=" O VAL O 130 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR O 128 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER O 22 " --> pdb=" O GLY O 124 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY O 124 " --> pdb=" O SER O 22 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 52 through 55 removed outlier: 4.562A pdb=" N THR O 53 " --> pdb=" O ARG O 60 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG O 60 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ARG O 55 " --> pdb=" O GLY O 58 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 101 through 104 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'Q' and resid 55 through 59 Processing sheet with id= 29, first strand: chain 'R' and resid 20 through 23 removed outlier: 3.550A pdb=" N ILE R 23 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS R 31 " --> pdb=" O ILE R 23 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S' and resid 35 through 39 removed outlier: 6.961A pdb=" N VAL S 35 " --> pdb=" O ARG S 65 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG S 65 " --> pdb=" O VAL S 35 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS S 37 " --> pdb=" O ARG S 63 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE S 61 " --> pdb=" O ALA S 39 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TYR S 129 " --> pdb=" O VAL S 121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL S 121 " --> pdb=" O TYR S 129 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'T' and resid 6 through 10 Processing sheet with id= 32, first strand: chain 'U' and resid 16 through 20 removed outlier: 6.616A pdb=" N LYS U 111 " --> pdb=" O LYS U 153 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'U' and resid 116 through 122 removed outlier: 3.657A pdb=" N HIS U 116 " --> pdb=" O VAL U 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA U 122 " --> pdb=" O PRO U 143 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'V' and resid 119 through 122 removed outlier: 3.503A pdb=" N GLU V 120 " --> pdb=" O THR V 99 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA V 103 " --> pdb=" O ILE V 122 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR V 100 " --> pdb=" O LYS V 79 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'X' and resid 28 through 31 removed outlier: 4.529A pdb=" N GLU X 6 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN X 62 " --> pdb=" O GLN X 8 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE X 10 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER X 60 " --> pdb=" O ILE X 10 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'X' and resid 88 through 96 removed outlier: 3.586A pdb=" N ILE X 94 " --> pdb=" O PHE X 75 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE X 75 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS X 73 " --> pdb=" O ASP X 96 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY X 76 " --> pdb=" O ALA X 127 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA X 127 " --> pdb=" O GLY X 76 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS X 125 " --> pdb=" O TRP X 78 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Y' and resid 73 through 79 Processing sheet with id= 38, first strand: chain 'Z' and resid 54 through 58 removed outlier: 3.520A pdb=" N VAL Z 63 " --> pdb=" O VAL Z 17 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN Z 101 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR Z 16 " --> pdb=" O ASN Z 101 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP Z 18 " --> pdb=" O TYR Z 103 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA Z 106 " --> pdb=" O ARG Z 94 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'AA' and resid 32 through 35 removed outlier: 6.447A pdb=" N ASNAA 98 " --> pdb=" O ILEAA 22 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASNAA 24 " --> pdb=" O ASNAA 98 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILEAA 102 " --> pdb=" O ALAAA 26 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALAAA 99 " --> pdb=" O VALAA 79 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VALAA 78 " --> pdb=" O ASPAA 56 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASPAA 56 " --> pdb=" O VALAA 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'AA' and resid 84 through 87 removed outlier: 4.337A pdb=" N VALAA 91 " --> pdb=" O ARGAA 87 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BA' and resid 3 through 6 removed outlier: 4.350A pdb=" N ALABA 11 " --> pdb=" O ASPBA 6 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BA' and resid 18 through 22 removed outlier: 3.543A pdb=" N PHEBA 31 " --> pdb=" O THRBA 19 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHEBA 29 " --> pdb=" O PHEBA 21 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'CA' and resid 64 through 67 removed outlier: 3.637A pdb=" N GLNCA 65 " --> pdb=" O GLNCA 85 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILECA 67 " --> pdb=" O VALCA 83 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VALCA 83 " --> pdb=" O ILECA 67 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHECA 84 " --> pdb=" O ALACA 122 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALACA 122 " --> pdb=" O PHECA 84 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYSCA 120 " --> pdb=" O VALCA 86 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'DA' and resid 54 through 57 removed outlier: 4.357A pdb=" N ASPDA 54 " --> pdb=" O ILEDA 70 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'DA' and resid 72 through 75 removed outlier: 3.538A pdb=" N SERDA 72 " --> pdb=" O GLNDA 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYRDA 74 " --> pdb=" O ALADA 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALADA 79 " --> pdb=" O TYRDA 74 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'DA' and resid 86 through 89 removed outlier: 3.886A pdb=" N ALADA 93 " --> pdb=" O LYSDA 89 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'EA' and resid 10 through 14 removed outlier: 6.661A pdb=" N ALAEA 11 " --> pdb=" O LYSEA 22 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYSEA 22 " --> pdb=" O ALAEA 11 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VALEA 13 " --> pdb=" O GLYEA 20 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'FA' and resid 71 through 74 removed outlier: 3.600A pdb=" N LYSFA 111 " --> pdb=" O PROFA 71 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'HA' and resid 22 through 25 removed outlier: 6.755A pdb=" N LYSHA 22 " --> pdb=" O LEUHA 93 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYSHA 66 " --> pdb=" O LYSHA 40 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILEHA 42 " --> pdb=" O LYSHA 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYRHA 68 " --> pdb=" O ILEHA 42 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'IA' and resid 48 through 51 removed outlier: 5.711A pdb=" N ASPIA 48 " --> pdb=" O LEUIA 89 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERIA 91 " --> pdb=" O ASPIA 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYSIA 78 " --> pdb=" O PHEIA 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SERIA 76 " --> pdb=" O TYRIA 92 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALIA 8 " --> pdb=" O ARGIA 77 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N THRIA 9 " --> pdb=" O VALIA 109 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'JA' and resid 70 through 74 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'KA' and resid 11 through 14 removed outlier: 5.600A pdb=" N LEUKA 29 " --> pdb=" O LEUKA 14 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARGKA 82 " --> pdb=" O THRKA 72 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N METKA 67 " --> pdb=" O TYRKA 51 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LYSKA 47 " --> pdb=" O VALKA 71 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARGKA 48 " --> pdb=" O PHEKA 101 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'KA' and resid 8 through 14 removed outlier: 3.531A pdb=" N ILEKA 100 " --> pdb=" O VALKA 9 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALAKA 96 " --> pdb=" O HISKA 13 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'LA' and resid 17 through 24 removed outlier: 7.869A pdb=" N SERLA 17 " --> pdb=" O LYSLA 37 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LYSLA 37 " --> pdb=" O SERLA 17 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYSLA 19 " --> pdb=" O VALLA 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VALLA 35 " --> pdb=" O LYSLA 19 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLNLA 33 " --> pdb=" O LYSLA 21 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VALLA 23 " --> pdb=" O ARGLA 31 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'PA' and resid 51 through 57 removed outlier: 3.555A pdb=" N TYRPA 52 " --> pdb=" O VALPA 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEUPA 54 " --> pdb=" O PHEPA 43 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'TA' and resid 6 through 12 removed outlier: 5.820A pdb=" N LYSTA 6 " --> pdb=" O VALTA 25 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VALTA 25 " --> pdb=" O LYSTA 6 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARGTA 8 " --> pdb=" O HISTA 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYSTA 19 " --> pdb=" O CYSTA 12 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VALTA 68 " --> pdb=" O LEUTA 85 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'UA' and resid 53 through 58 removed outlier: 5.285A pdb=" N GLYUA 53 " --> pdb=" O GLYUA 66 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLYUA 66 " --> pdb=" O GLYUA 53 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'VA' and resid 49 through 53 removed outlier: 3.576A pdb=" N VALVA 50 " --> pdb=" O PHEVA 88 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUVA 52 " --> pdb=" O PHEVA 86 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASNVA 83 " --> pdb=" O VALVA 30 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SERVA 24 " --> pdb=" O THRVA 89 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYSVA 23 " --> pdb=" O ASNVA 193 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASNVA 193 " --> pdb=" O LYSVA 23 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEUVA 25 " --> pdb=" O TYRVA 191 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYRVA 191 " --> pdb=" O LEUVA 25 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VALVA 27 " --> pdb=" O GLNVA 189 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'WA' and resid 5 through 9 removed outlier: 3.556A pdb=" N VALWA 8 " --> pdb=" O GLNWA 314 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLNWA 314 " --> pdb=" O VALWA 8 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VALWA 309 " --> pdb=" O TYRWA 305 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYRWA 305 " --> pdb=" O VALWA 309 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARGWA 311 " --> pdb=" O ALAWA 303 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLNWA 299 " --> pdb=" O VALWA 315 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N THRWA 300 " --> pdb=" O SERWA 295 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHEWA 302 " --> pdb=" O ALAWA 293 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALAWA 293 " --> pdb=" O PHEWA 302 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SERWA 291 " --> pdb=" O GLYWA 304 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'WA' and resid 22 through 25 removed outlier: 3.542A pdb=" N ALAWA 24 " --> pdb=" O LEUWA 34 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEUWA 34 " --> pdb=" O ALAWA 24 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'WA' and resid 54 through 57 removed outlier: 7.006A pdb=" N PHEWA 54 " --> pdb=" O THRWA 48 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEUWA 42 " --> pdb=" O PHEWA 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHEWA 61 " --> pdb=" O LEUWA 42 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'WA' and resid 80 through 83 removed outlier: 3.514A pdb=" N ALAWA 80 " --> pdb=" O TRPWA 92 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRPWA 92 " --> pdb=" O ALAWA 80 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEUWA 89 " --> pdb=" O PHEWA 103 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLNWA 101 " --> pdb=" O LEUWA 91 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'WA' and resid 122 through 125 removed outlier: 3.648A pdb=" N ILEWA 122 " --> pdb=" O TRPWA 134 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SERWA 124 " --> pdb=" O LYSWA 132 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYSWA 132 " --> pdb=" O SERWA 124 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILEWA 131 " --> pdb=" O LEUWA 144 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALAWA 142 " --> pdb=" O VALWA 133 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'WA' and resid 153 through 156 removed outlier: 3.570A pdb=" N ILEWA 169 " --> pdb=" O TRPWA 181 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VALWA 178 " --> pdb=" O PHEWA 192 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALAWA 190 " --> pdb=" O ALAWA 180 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'WA' and resid 200 through 205 removed outlier: 3.529A pdb=" N ALAWA 214 " --> pdb=" O THRWA 201 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALAWA 212 " --> pdb=" O THRWA 203 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SERWA 205 " --> pdb=" O LEUWA 210 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEUWA 210 " --> pdb=" O SERWA 205 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THRWA 209 " --> pdb=" O LEUWA 225 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEWA 211 " --> pdb=" O TRPWA 223 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N METWA 221 " --> pdb=" O SERWA 213 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLYWA 215 " --> pdb=" O GLUWA 219 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLUWA 219 " --> pdb=" O GLYWA 215 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILEWA 220 " --> pdb=" O THRWA 233 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THRWA 233 " --> pdb=" O ILEWA 220 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEUWA 222 " --> pdb=" O METWA 231 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'WA' and resid 243 through 246 removed outlier: 5.803A pdb=" N TRPWA 251 " --> pdb=" O SERWA 246 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'XA' and resid 73 through 77 removed outlier: 3.532A pdb=" N ILEXA 122 " --> pdb=" O VALXA 74 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THRXA 124 " --> pdb=" O ILEXA 76 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEUXA 146 " --> pdb=" O VALXA 123 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'YA' and resid 43 through 47 Processing sheet with id= 69, first strand: chain 'YA' and resid 64 through 67 removed outlier: 5.234A pdb=" N ARGYA 64 " --> pdb=" O VALYA 88 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEUYA 86 " --> pdb=" O VALYA 66 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'YA' and resid 119 through 126 removed outlier: 4.845A pdb=" N THRYA 119 " --> pdb=" O THRYA 143 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALAYA 123 " --> pdb=" O ALAYA 139 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALAYA 139 " --> pdb=" O ALAYA 123 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYSYA 216 " --> pdb=" O ARGYA 136 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LYSYA 214 " --> pdb=" O PHEYA 138 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'ZA' and resid 76 through 81 removed outlier: 3.559A pdb=" N GLYZA 105 " --> pdb=" O GLNZA 77 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLUZA 79 " --> pdb=" O VALZA 103 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALZA 103 " --> pdb=" O GLUZA 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N METZA 81 " --> pdb=" O VALZA 101 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VALZA 101 " --> pdb=" O METZA 81 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'ZA' and resid 157 through 161 removed outlier: 3.535A pdb=" N ASNZA 201 " --> pdb=" O THRZA 166 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARGZA 168 " --> pdb=" O GLNZA 199 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALAZA 172 " --> pdb=" O ASPZA 195 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASPZA 195 " --> pdb=" O ALAZA 172 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'ZA' and resid 97 through 105 removed outlier: 3.562A pdb=" N PHEZA 98 " --> pdb=" O ALAZA 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VALZA 104 " --> pdb=" O GLYZA 112 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'AB' and resid 36 through 40 removed outlier: 3.620A pdb=" N GLYAB 36 " --> pdb=" O ARGAB 51 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAB 47 " --> pdb=" O ARGAB 40 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'AB' and resid 148 through 155 removed outlier: 3.570A pdb=" N GLYAB 140 " --> pdb=" O LYSAB 148 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N METAB 150 " --> pdb=" O VALAB 138 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHEAB 152 " --> pdb=" O VALAB 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VALAB 136 " --> pdb=" O PHEAB 152 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASPAB 154 " --> pdb=" O CYSAB 134 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYSAB 134 " --> pdb=" O ASPAB 154 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLYAB 133 " --> pdb=" O METAB 189 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYSAB 185 " --> pdb=" O VALAB 137 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SERAB 139 " --> pdb=" O GLYAB 183 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLYAB 183 " --> pdb=" O SERAB 139 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLYAB 180 " --> pdb=" O METAB 177 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N METAB 177 " --> pdb=" O GLYAB 180 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VALAB 175 " --> pdb=" O LEUAB 182 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALAAB 171 " --> pdb=" O VALAB 186 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'BB' and resid 88 through 93 removed outlier: 3.972A pdb=" N ASPBB 88 " --> pdb=" O LEUBB 101 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLUBB 97 " --> pdb=" O LEUBB 92 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASNBB 98 " --> pdb=" O ILEBB 114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILEBB 114 " --> pdb=" O ASNBB 98 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HISBB 112 " --> pdb=" O ARGBB 100 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VALBB 102 " --> pdb=" O ALABB 110 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'BB' and resid 138 through 141 No H-bonds generated for sheet with id= 77 Processing sheet with id= 78, first strand: chain 'BB' and resid 158 through 161 removed outlier: 3.737A pdb=" N THRBB 159 " --> pdb=" O ILEBB 173 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASPBB 171 " --> pdb=" O LYSBB 161 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'BB' and resid 180 through 183 No H-bonds generated for sheet with id= 79 Processing sheet with id= 80, first strand: chain 'BB' and resid 196 through 200 removed outlier: 3.560A pdb=" N HISBB 197 " --> pdb=" O HISBB 209 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUBB 207 " --> pdb=" O GLUBB 199 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASPBB 212 " --> pdb=" O ASNBB 216 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASNBB 216 " --> pdb=" O ASPBB 212 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'DB' and resid 12 through 17 removed outlier: 3.518A pdb=" N LYSDB 14 " --> pdb=" O ILEDB 5 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEDB 5 " --> pdb=" O LYSDB 14 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUDB 3 " --> pdb=" O PHEDB 16 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEUDB 109 " --> pdb=" O LYSDB 2 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILEDB 113 " --> pdb=" O SERDB 6 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLYDB 54 " --> pdb=" O ALADB 110 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'DB' and resid 28 through 31 No H-bonds generated for sheet with id= 82 Processing sheet with id= 83, first strand: chain 'DB' and resid 33 through 37 removed outlier: 3.854A pdb=" N GLNDB 34 " --> pdb=" O ILEDB 52 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'DB' and resid 73 through 78 removed outlier: 3.553A pdb=" N LYSDB 93 " --> pdb=" O LEUDB 77 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'DB' and resid 159 through 164 removed outlier: 3.590A pdb=" N LYSDB 164 " --> pdb=" O LYSDB 167 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'EB' and resid 44 through 50 removed outlier: 3.512A pdb=" N ILEEB 49 " --> pdb=" O ALAEB 57 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILEEB 91 " --> pdb=" O LEUEB 58 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILEEB 60 " --> pdb=" O ILEEB 91 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'EB' and resid 137 through 143 removed outlier: 3.535A pdb=" N LYSEB 151 " --> pdb=" O ARGEB 139 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILEEB 149 " --> pdb=" O ARGEB 141 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEUEB 143 " --> pdb=" O ASNEB 147 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASNEB 147 " --> pdb=" O LEUEB 143 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLNEB 180 " --> pdb=" O LYSEB 148 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLNEB 150 " --> pdb=" O GLNEB 180 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLUEB 184 " --> pdb=" O VALEB 152 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'FB' and resid 71 through 75 removed outlier: 3.854A pdb=" N ILEFB 72 " --> pdb=" O TRPFB 67 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEFB 65 " --> pdb=" O LYSFB 74 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASNFB 64 " --> pdb=" O CYSFB 179 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALAFB 68 " --> pdb=" O ILEFB 183 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'FB' and resid 101 through 105 removed outlier: 3.509A pdb=" N ALAFB 167 " --> pdb=" O VALFB 102 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEFB 104 " --> pdb=" O LEUFB 165 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEUFB 165 " --> pdb=" O ILEFB 104 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'HB' and resid 19 through 24 removed outlier: 7.797A pdb=" N GLYHB 19 " --> pdb=" O LEUHB 68 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEUHB 68 " --> pdb=" O GLYHB 19 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VALHB 21 " --> pdb=" O TYRHB 66 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALAHB 23 " --> pdb=" O TYRHB 64 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYRHB 64 " --> pdb=" O ALAHB 23 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'JB' and resid 40 through 43 removed outlier: 5.901A pdb=" N GLYJB 40 " --> pdb=" O LYSJB 124 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYSJB 124 " --> pdb=" O GLYJB 40 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SERJB 119 " --> pdb=" O VALJB 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VALJB 63 " --> pdb=" O SERJB 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VALJB 121 " --> pdb=" O VALJB 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VALJB 61 " --> pdb=" O VALJB 121 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEUJB 59 " --> pdb=" O VALJB 123 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VALJB 60 " --> pdb=" O PROJB 87 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEUJB 62 " --> pdb=" O ILEJB 89 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'LB' and resid 13 through 21 removed outlier: 3.515A pdb=" N ALALB 78 " --> pdb=" O VALLB 13 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLYLB 15 " --> pdb=" O ALALB 78 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYSLB 82 " --> pdb=" O ALALB 17 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'MB' and resid 93 through 97 removed outlier: 3.549A pdb=" N VALMB 94 " --> pdb=" O VALMB 105 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'NB' and resid 6 through 12 removed outlier: 3.547A pdb=" N THRNB 9 " --> pdb=" O ALANB 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THRNB 17 " --> pdb=" O THRNB 70 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THRNB 70 " --> pdb=" O THRNB 17 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARGNB 68 " --> pdb=" O VALNB 19 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'QB' and resid 114 through 117 removed outlier: 4.105A pdb=" N GLYQB 121 " --> pdb=" O SERQB 117 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'RB' and resid 58 through 68 removed outlier: 5.340A pdb=" N LYSRB 88 " --> pdb=" O PRORB 59 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYSRB 61 " --> pdb=" O ILERB 86 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILERB 65 " --> pdb=" O TYRRB 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SERRB 28 " --> pdb=" O HISRB 87 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARGRB 89 " --> pdb=" O LEURB 26 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THRRB 25 " --> pdb=" O GLURB 115 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'SB' and resid 32 through 37 removed outlier: 3.524A pdb=" N LEUSB 55 " --> pdb=" O VALSB 32 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VALSB 36 " --> pdb=" O VALSB 51 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'TB' and resid 23 through 28 removed outlier: 5.932A pdb=" N ARGTB 23 " --> pdb=" O LEUTB 65 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILETB 61 " --> pdb=" O ILETB 27 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYSTB 60 " --> pdb=" O ILETB 53 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLUTB 49 " --> pdb=" O GLNTB 64 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'TB' and resid 71 through 75 removed outlier: 3.991A pdb=" N LYSTB 71 " --> pdb=" O TYRTB 130 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEUTB 126 " --> pdb=" O ILETB 75 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLYTB 123 " --> pdb=" O VALTB 81 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHETB 79 " --> pdb=" O ILETB 125 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'UB' and resid 48 through 52 removed outlier: 3.566A pdb=" N ALAUB 49 " --> pdb=" O LEUUB 104 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEUUB 103 " --> pdb=" O VALUB 125 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYSUB 123 " --> pdb=" O ALAUB 105 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'UB' and resid 71 through 75 No H-bonds generated for sheet with id=101 Processing sheet with id=102, first strand: chain 'VB' and resid 22 through 29 removed outlier: 3.512A pdb=" N HISVB 29 " --> pdb=" O GLYVB 67 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLYVB 67 " --> pdb=" O HISVB 29 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYSVB 68 " --> pdb=" O GLNVB 63 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALVB 70 " --> pdb=" O ARGVB 61 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHEVB 72 " --> pdb=" O GLYVB 59 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLYVB 59 " --> pdb=" O PHEVB 72 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEUVB 74 " --> pdb=" O VALVB 57 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VALVB 57 " --> pdb=" O LEUVB 74 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'XB' and resid 20 through 23 removed outlier: 6.485A pdb=" N VALXB 21 " --> pdb=" O SERXB 29 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SERXB 29 " --> pdb=" O VALXB 21 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYSXB 23 " --> pdb=" O SERXB 27 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'XB' and resid 37 through 41 removed outlier: 3.503A pdb=" N ARGXB 38 " --> pdb=" O LEUXB 71 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASNXB 69 " --> pdb=" O ALAXB 40 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'YB' and resid 43 through 48 removed outlier: 3.527A pdb=" N VALYB 35 " --> pdb=" O THRYB 44 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYRYB 31 " --> pdb=" O SERYB 48 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHEYB 32 " --> pdb=" O LYSYB 82 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARGYB 80 " --> pdb=" O ASPYB 34 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SERYB 78 " --> pdb=" O LYSYB 36 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'ZB' and resid 9 through 13 removed outlier: 3.906A pdb=" N ASPZB 52 " --> pdb=" O VALZB 12 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'ZB' and resid 14 through 17 removed outlier: 6.568A pdb=" N GLNZB 27 " --> pdb=" O LEUZB 16 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THRZB 26 " --> pdb=" O VALZB 44 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VALZB 28 " --> pdb=" O ARGZB 42 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILEZB 40 " --> pdb=" O VALZB 30 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'DC' and resid 74 through 81 removed outlier: 3.605A pdb=" N LEUDC 77 " --> pdb=" O ILEDC 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N METDC 81 " --> pdb=" O ASNDC 96 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASNDC 96 " --> pdb=" O METDC 81 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASNDC 18 " --> pdb=" O SERDC 97 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VALDC 24 " --> pdb=" O ILEDC 103 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SERDC 105 " --> pdb=" O VALDC 24 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALADC 26 " --> pdb=" O SERDC 105 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SERDC 23 " --> pdb=" O GLYDC 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLYDC 212 " --> pdb=" O ILEDC 157 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'DC' and resid 248 through 252 removed outlier: 3.671A pdb=" N LYSDC 256 " --> pdb=" O ASNDC 251 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'DC' and resid 384 through 387 removed outlier: 6.906A pdb=" N PHEDC 397 " --> pdb=" O SERDC 383 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N METDC 379 " --> pdb=" O PHEDC 401 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEUDC 378 " --> pdb=" O THRDC 471 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHEDC 427 " --> pdb=" O ILEDC 413 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASPDC 425 " --> pdb=" O GLYDC 415 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'DC' and resid 403 through 406 removed outlier: 5.947A pdb=" N GLYDC 403 " --> pdb=" O ALADC 450 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYSDC 448 " --> pdb=" O VALDC 405 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'DC' and resid 434 through 438 removed outlier: 3.734A pdb=" N VALDC 434 " --> pdb=" O ILEDC 445 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEUDC 436 " --> pdb=" O GLUDC 443 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLUDC 443 " --> pdb=" O LEUDC 436 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'DC' and resid 528 through 532 removed outlier: 4.510A pdb=" N HISDC 528 " --> pdb=" O VALDC 493 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VALDC 489 " --> pdb=" O GLYDC 532 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SERDC 557 " --> pdb=" O ALADC 492 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'DC' and resid 563 through 567 removed outlier: 3.528A pdb=" N ARGDC 564 " --> pdb=" O GLNDC 725 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THRDC 566 " --> pdb=" O LYSDC 723 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VALDC 731 " --> pdb=" O ALADC 770 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYSDC 735 " --> pdb=" O PHEDC 766 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYSDC 769 " --> pdb=" O VALDC 755 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'DC' and resid 574 through 579 removed outlier: 3.641A pdb=" N LEUDC 588 " --> pdb=" O ALADC 575 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SERDC 577 " --> pdb=" O ILEDC 586 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASNDC 584 " --> pdb=" O SERDC 579 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N SERDC 683 " --> pdb=" O ILEDC 593 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VALDC 684 " --> pdb=" O PRODC 643 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEUDC 645 " --> pdb=" O VALDC 684 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'DC' and resid 397 through 401 removed outlier: 3.521A pdb=" N ASNDC 452 " --> pdb=" O VALDC 400 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'DC' and resid 583 through 588 removed outlier: 9.721A pdb=" N HISDC 583 " --> pdb=" O HISDC 694 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N HISDC 694 " --> pdb=" O HISDC 583 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASPDC 690 " --> pdb=" O TYRDC 587 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'DC' and resid 727 through 735 removed outlier: 6.160A pdb=" N VALDC 728 " --> pdb=" O ASPDC 799 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VALDC 797 " --> pdb=" O LEUDC 730 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHEDC 793 " --> pdb=" O GLNDC 734 " (cutoff:3.500A) 2692 hydrogen bonds defined for protein. 7986 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3345 hydrogen bonds 5490 hydrogen bond angles 0 basepair planarities 1378 basepair parallelities 2568 stacking parallelities Total time for adding SS restraints: 296.86 Time building geometry restraints manager: 76.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 57996 1.36 - 1.52: 99585 1.52 - 1.67: 72922 1.67 - 1.83: 76 1.83 - 1.98: 280 Bond restraints: 230859 Sorted by residual: bond pdb=" C1 SO1DC 903 " pdb=" C2 SO1DC 903 " ideal model delta sigma weight residual 0.000 1.651 -1.651 2.00e-02 2.50e+03 6.81e+03 bond pdb=" C12 SO1DC 903 " pdb=" C4 SO1DC 903 " ideal model delta sigma weight residual 1.038 1.606 -0.568 2.00e-02 2.50e+03 8.08e+02 bond pdb=" C2 SO1DC 903 " pdb=" C7 SO1DC 903 " ideal model delta sigma weight residual 2.108 1.593 0.515 2.00e-02 2.50e+03 6.62e+02 bond pdb=" C12 SO1DC 903 " pdb=" C6 SO1DC 903 " ideal model delta sigma weight residual 1.115 1.629 -0.514 2.00e-02 2.50e+03 6.59e+02 bond pdb=" C16 SO1DC 903 " pdb=" C7 SO1DC 903 " ideal model delta sigma weight residual 1.126 1.558 -0.432 2.00e-02 2.50e+03 4.67e+02 ... (remaining 230854 not shown) Histogram of bond angle deviations from ideal: 85.94 - 97.68: 4 97.68 - 109.43: 81486 109.43 - 121.18: 188385 121.18 - 132.92: 68531 132.92 - 144.67: 112 Bond angle restraints: 338518 Sorted by residual: angle pdb=" N GLU F 118 " pdb=" CA GLU F 118 " pdb=" C GLU F 118 " ideal model delta sigma weight residual 114.62 100.31 14.31 1.14e+00 7.69e-01 1.58e+02 angle pdb=" O THRXA 192 " pdb=" C THRXA 192 " pdb=" N GLNXA 193 " ideal model delta sigma weight residual 122.59 105.98 16.61 1.33e+00 5.65e-01 1.56e+02 angle pdb=" N SEROB 96 " pdb=" CA SEROB 96 " pdb=" C SEROB 96 " ideal model delta sigma weight residual 108.90 129.21 -20.31 1.63e+00 3.76e-01 1.55e+02 angle pdb=" O3' A A 103 " pdb=" C3' A A 103 " pdb=" C2' A A 103 " ideal model delta sigma weight residual 109.50 127.36 -17.86 1.50e+00 4.44e-01 1.42e+02 angle pdb=" CA ALADC 3 " pdb=" C ALADC 3 " pdb=" O ALADC 3 " ideal model delta sigma weight residual 121.87 108.09 13.78 1.16e+00 7.43e-01 1.41e+02 ... (remaining 338513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 120888 35.92 - 71.84: 5553 71.84 - 107.76: 413 107.76 - 143.68: 42 143.68 - 179.60: 105 Dihedral angle restraints: 127001 sinusoidal: 91688 harmonic: 35313 Sorted by residual: dihedral pdb=" C5' C B3228 " pdb=" C4' C B3228 " pdb=" C3' C B3228 " pdb=" O3' C B3228 " ideal model delta sinusoidal sigma weight residual 147.00 68.20 78.80 1 8.00e+00 1.56e-02 1.21e+02 dihedral pdb=" C5' G B 547 " pdb=" C4' G B 547 " pdb=" C3' G B 547 " pdb=" O3' G B 547 " ideal model delta sinusoidal sigma weight residual 147.00 73.23 73.77 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C5' C B 637 " pdb=" C4' C B 637 " pdb=" C3' C B 637 " pdb=" O3' C B 637 " ideal model delta sinusoidal sigma weight residual 147.00 73.70 73.30 1 8.00e+00 1.56e-02 1.07e+02 ... (remaining 126998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.361: 41877 0.361 - 0.721: 407 0.721 - 1.082: 5 1.082 - 1.443: 1 1.443 - 1.804: 1 Chirality restraints: 42291 Sorted by residual: chirality pdb=" C3' A A 103 " pdb=" C4' A A 103 " pdb=" O3' A A 103 " pdb=" C2' A A 103 " both_signs ideal model delta sigma weight residual False -2.74 -0.94 -1.80 2.00e-01 2.50e+01 8.13e+01 chirality pdb=" C9 SO1DC 903 " pdb=" C16 SO1DC 903 " pdb=" C18 SO1DC 903 " pdb=" C3 SO1DC 903 " both_signs ideal model delta sigma weight residual False -1.65 -3.07 1.43 2.00e-01 2.50e+01 5.09e+01 chirality pdb=" C16 SO1DC 903 " pdb=" C22 SO1DC 903 " pdb=" C7 SO1DC 903 " pdb=" C9 SO1DC 903 " both_signs ideal model delta sigma weight residual False -1.56 -2.50 0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 42288 not shown) Planarity restraints: 22554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B2110 " -0.229 2.00e-02 2.50e+03 9.50e-02 2.71e+02 pdb=" N9 G B2110 " 0.012 2.00e-02 2.50e+03 pdb=" C8 G B2110 " 0.094 2.00e-02 2.50e+03 pdb=" N7 G B2110 " 0.087 2.00e-02 2.50e+03 pdb=" C5 G B2110 " 0.048 2.00e-02 2.50e+03 pdb=" C6 G B2110 " -0.041 2.00e-02 2.50e+03 pdb=" O6 G B2110 " -0.147 2.00e-02 2.50e+03 pdb=" N1 G B2110 " -0.030 2.00e-02 2.50e+03 pdb=" C2 G B2110 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G B2110 " 0.031 2.00e-02 2.50e+03 pdb=" N3 G B2110 " 0.074 2.00e-02 2.50e+03 pdb=" C4 G B2110 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B1218 " -0.185 2.00e-02 2.50e+03 1.03e-01 2.38e+02 pdb=" N1 U B1218 " 0.002 2.00e-02 2.50e+03 pdb=" C2 U B1218 " 0.034 2.00e-02 2.50e+03 pdb=" O2 U B1218 " 0.073 2.00e-02 2.50e+03 pdb=" N3 U B1218 " 0.033 2.00e-02 2.50e+03 pdb=" C4 U B1218 " 0.035 2.00e-02 2.50e+03 pdb=" O4 U B1218 " -0.184 2.00e-02 2.50e+03 pdb=" C5 U B1218 " 0.104 2.00e-02 2.50e+03 pdb=" C6 U B1218 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B2141 " 0.190 2.00e-02 2.50e+03 1.02e-01 2.36e+02 pdb=" N1 U B2141 " -0.007 2.00e-02 2.50e+03 pdb=" C2 U B2141 " -0.037 2.00e-02 2.50e+03 pdb=" O2 U B2141 " -0.077 2.00e-02 2.50e+03 pdb=" N3 U B2141 " -0.027 2.00e-02 2.50e+03 pdb=" C4 U B2141 " -0.021 2.00e-02 2.50e+03 pdb=" O4 U B2141 " 0.175 2.00e-02 2.50e+03 pdb=" C5 U B2141 " -0.100 2.00e-02 2.50e+03 pdb=" C6 U B2141 " -0.096 2.00e-02 2.50e+03 ... (remaining 22551 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 17188 2.73 - 3.27: 209464 3.27 - 3.82: 413118 3.82 - 4.36: 541272 4.36 - 4.90: 719370 Nonbonded interactions: 1900412 Sorted by model distance: nonbonded pdb=" OD1 ASPOB 103 " pdb=" N ASNOB 104 " model vdw 2.191 2.520 nonbonded pdb=" N ASNOB 97 " pdb=" N GLYOB 98 " model vdw 2.196 2.560 nonbonded pdb=" O PRO P 75 " pdb=" O MET P 116 " model vdw 2.203 3.040 nonbonded pdb=" O ALADC 3 " pdb=" O ILEDC 46 " model vdw 2.216 3.040 nonbonded pdb=" O GLUDC 270 " pdb=" O ARGDC 271 " model vdw 2.257 3.040 ... (remaining 1900407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5569 5.49 5 Mg 1 5.21 5 S 219 5.16 5 C 114010 2.51 5 N 39311 2.21 5 O 56112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 36.880 Check model and map are aligned: 2.140 Convert atoms to be neutral: 1.190 Process input model: 660.470 Find NCS groups from input model: 6.200 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 716.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 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 : 0.019 1.651 230859 Z= 1.211 Angle : 1.258 30.826 338518 Z= 0.816 Chirality : 0.139 1.804 42291 Planarity : 0.012 0.117 22554 Dihedral : 17.338 179.598 104350 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 40.18 Ramachandran Plot: Outliers : 7.80 % Allowed : 20.70 % Favored : 71.50 % Rotamer Outliers : 10.31 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -6.42 (0.05), residues: 12205 helix: -4.47 (0.04), residues: 3416 sheet: -3.88 (0.12), residues: 1304 loop : -4.49 (0.05), residues: 7485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2935 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1055 poor density : 1880 time to evaluate : 10.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1055 outliers final: 419 residues processed: 2743 average time/residue: 1.8093 time to fit residues: 8477.6675 Evaluate side-chains 1611 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 1192 time to evaluate : 10.294 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 419 outliers final: 7 residues processed: 419 average time/residue: 1.7060 time to fit residues: 1253.0787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1756 random chunks: chunk 1482 optimal weight: 0.0980 chunk 1330 optimal weight: 0.4980 chunk 738 optimal weight: 8.9990 chunk 454 optimal weight: 5.9990 chunk 897 optimal weight: 10.0000 chunk 711 optimal weight: 0.0040 chunk 1376 optimal weight: 2.9990 chunk 532 optimal weight: 5.9990 chunk 836 optimal weight: 10.0000 chunk 1024 optimal weight: 30.0000 chunk 1594 optimal weight: 5.9990 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 38 HIS ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 HIS F 215 ASN G 11 HIS G 177 HIS G 211 GLN G 293 ASN G 313 HIS G 331 ASN H 110 ASN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 HIS H 260 GLN H 291 ASN H 296 GLN ** H 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 322 GLN ** H 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN I 151 GLN ** I 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 ASN K 37 ASN K 93 ASN K 157 ASN K 209 ASN ** K 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 HIS L 252 ASN M 49 ASN M 50 ASN M 77 ASN M 100 ASN M 125 ASN M 157 ASN M 183 HIS ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 ASN N 133 GLN N 144 ASN N 209 ASN O 43 GLN O 90 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 GLN P 100 HIS Q 28 GLN Q 112 ASN Q 162 ASN R 119 GLN ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 ASN ** S 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 50 ASN T 122 GLN U 28 ASN ** U 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 GLN V 135 GLN V 145 ASN W 39 ASN W 92 GLN W 118 HIS ** W 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 8 GLN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 108 GLN ** X 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 122 GLN Z 9 GLN Z 87 ASN ** CA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 137 ASN ** DA 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 78 ASN EA 122 HIS EA 123 GLN EA 127 ASN FA 44 ASN ** FA 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 12 GLN ** IA 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IA 57 GLN ** IA 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JA 31 ASN ** JA 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JA 49 ASN ** JA 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JA 104 ASN KA 87 ASN LA 11 ASN LA 18 ASN LA 33 GLN LA 69 HIS MA 59 ASN ** MA 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 68 GLN MA 104 GLN OA 13 ASN ** OA 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PA 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 4 GLN ** QA 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 32 ASN QA 38 ASN QA 50 ASN RA 90 ASN RA 120 GLN TA 3 ASN TA 47 GLN TA 99 GLN UA 32 GLN ** VA 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VA 83 ASN VA 103 ASN VA 137 GLN WA 224 ASN WA 248 ASN WA 314 GLN ** XA 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** XA 49 ASN ** XA 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 109 ASN YA 118 GLN YA 146 GLN YA 177 GLN YA 199 ASN ZA 87 GLN ZA 89 GLN ** ZA 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 209 ASN ** ZA 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 62 ASN AB 159 HIS ** AB 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 259 GLN CB 34 GLN CB 79 ASN CB 103 ASN CB 224 ASN DB 34 GLN DB 80 ASN DB 139 ASN EB 22 GLN EB 74 GLN ** EB 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 174 ASN EB 180 GLN ** FB 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 64 ASN ** FB 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 138 ASN FB 175 GLN GB 38 ASN ** GB 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 112 GLN GB 123 HIS GB 131 GLN HB 9 ASN HB 29 GLN HB 62 GLN HB 96 ASN IB 14 GLN IB 21 ASN ** IB 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IB 152 GLN KB 21 ASN ** KB 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KB 123 HIS LB 80 HIS MB 98 ASN MB 104 GLN OB 29 GLN PB 6 GLN PB 19 ASN PB 25 ASN PB 44 ASN PB 74 GLN PB 75 ASN PB 89 GLN PB 103 ASN ** QB 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RB 44 ASN RB 48 HIS RB 98 GLN SB 21 ASN ** SB 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SB 33 GLN ** SB 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TB 12 ASN TB 16 ASN TB 64 GLN TB 80 ASN ** UB 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** VB 31 ASN ** XB 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 20 GLN BC 17 GLN ** DC 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 21 ASN ** DC 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DC 96 ASN DC 101 ASN ** DC 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 224 GLN DC 259 ASN ** DC 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 365 ASN DC 371 ASN DC 409 GLN DC 414 GLN DC 537 HIS ** DC 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DC 644 ASN DC 687 ASN DC 725 GLN DC 734 GLN DC 753 GLN DC 759 GLN Total number of N/Q/H flips: 177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.462 230859 Z= 0.253 Angle : 0.854 17.501 338518 Z= 0.435 Chirality : 0.045 0.323 42291 Planarity : 0.007 0.169 22554 Dihedral : 16.356 179.686 80095 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 1.52 % Allowed : 14.32 % Favored : 84.16 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -5.09 (0.06), residues: 12205 helix: -3.16 (0.06), residues: 3696 sheet: -3.11 (0.11), residues: 1529 loop : -3.72 (0.06), residues: 6980 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1969 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 446 poor density : 1523 time to evaluate : 10.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 446 outliers final: 172 residues processed: 1865 average time/residue: 1.8258 time to fit residues: 5901.1684 Evaluate side-chains 1263 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1091 time to evaluate : 10.420 Switching outliers to nearest non-outliers outliers start: 172 outliers final: 0 residues processed: 172 average time/residue: 1.5655 time to fit residues: 502.5915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1756 random chunks: chunk 886 optimal weight: 9.9990 chunk 494 optimal weight: 40.0000 chunk 1327 optimal weight: 8.9990 chunk 1085 optimal weight: 30.0000 chunk 439 optimal weight: 30.0000 chunk 1597 optimal weight: 30.0000 chunk 1725 optimal weight: 30.0000 chunk 1422 optimal weight: 10.0000 chunk 1584 optimal weight: 0.6980 chunk 544 optimal weight: 40.0000 chunk 1281 optimal weight: 50.0000 overall best weight: 11.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN G 3 HIS H 114 ASN ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN K 93 ASN K 146 GLN ** K 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 ASN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 ASN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 GLN R 56 GLN ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN S 95 GLN ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 ASN ** U 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 GLN W 130 ASN X 89 ASN Y 5 HIS Y 58 GLN Z 9 GLN Z 40 HIS AA 4 ASN ** CA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 66 GLN ** DA 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 122 HIS ** FA 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 6 ASN ** IA 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KA 26 ASN KA 87 ASN KA 88 ASN ** LA 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 98 GLN ** NA 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 28 ASN QA 19 GLN ** VA 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VA 137 GLN WA 200 ASN ** XA 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 92 HIS XA 109 ASN ** ZA 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 197 HIS ** BB 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 37 GLN ** DB 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 5 GLN ** FB 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** GB 176 ASN ** IB 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 81 HIS KB 62 GLN MB 82 ASN ** MB 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MB 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PB 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QB 12 GLN ** QB 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RB 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TB 15 ASN ** TB 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TB 70 ASN ** TB 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TB 120 HIS UB 65 ASN ** UB 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UB 99 ASN ** VB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** WB 95 HIS ** XB 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** YB 51 GLN ** ZB 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZB 43 ASN DC 108 HIS ** DC 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 414 GLN ** DC 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.266 230859 Z= 0.328 Angle : 0.858 43.313 338518 Z= 0.435 Chirality : 0.046 0.478 42291 Planarity : 0.007 0.142 22554 Dihedral : 16.630 179.197 80095 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 31.44 Ramachandran Plot: Outliers : 1.30 % Allowed : 15.40 % Favored : 83.29 % Rotamer Outliers : 4.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -4.45 (0.06), residues: 12205 helix: -2.58 (0.07), residues: 3696 sheet: -2.76 (0.12), residues: 1556 loop : -3.34 (0.06), residues: 6953 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1718 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 490 poor density : 1228 time to evaluate : 10.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 490 outliers final: 245 residues processed: 1612 average time/residue: 1.7827 time to fit residues: 4999.4895 Evaluate side-chains 1282 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1037 time to evaluate : 10.722 Switching outliers to nearest non-outliers outliers start: 245 outliers final: 0 residues processed: 245 average time/residue: 1.4609 time to fit residues: 680.9539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1756 random chunks: chunk 1578 optimal weight: 30.0000 chunk 1201 optimal weight: 30.0000 chunk 829 optimal weight: 20.0000 chunk 176 optimal weight: 30.0000 chunk 762 optimal weight: 30.0000 chunk 1072 optimal weight: 30.0000 chunk 1603 optimal weight: 40.0000 chunk 1697 optimal weight: 10.0000 chunk 837 optimal weight: 6.9990 chunk 1519 optimal weight: 0.9990 chunk 457 optimal weight: 20.0000 overall best weight: 11.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS H 45 ASN ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 ASN K 199 ASN K 200 ASN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 ASN ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 ASN ** Q 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 GLN ** X 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN ** CA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 26 GLN FA 44 ASN ** FA 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 92 ASN ** OA 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QA 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** WA 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 33 GLN ** XA 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 122 ASN ** DB 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HB 58 GLN IB 21 ASN ** MB 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MB 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NB 103 ASN OB 42 GLN ** PB 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RB 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UB 79 ASN ** UB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UB 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** VB 113 ASN ** XB 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** YB 9 HIS ** ZB 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.285 230859 Z= 0.310 Angle : 0.806 22.612 338518 Z= 0.410 Chirality : 0.044 0.335 42291 Planarity : 0.007 0.134 22554 Dihedral : 16.827 179.926 80095 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 30.84 Ramachandran Plot: Outliers : 1.19 % Allowed : 13.98 % Favored : 84.83 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.02 % 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: -4.11 (0.07), residues: 12205 helix: -2.26 (0.07), residues: 3677 sheet: -2.58 (0.12), residues: 1542 loop : -3.15 (0.07), residues: 6986 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1490 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 1115 time to evaluate : 11.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 375 outliers final: 180 residues processed: 1410 average time/residue: 1.7252 time to fit residues: 4221.9427 Evaluate side-chains 1168 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 988 time to evaluate : 11.213 Switching outliers to nearest non-outliers outliers start: 180 outliers final: 0 residues processed: 180 average time/residue: 1.4868 time to fit residues: 511.6195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1756 random chunks: chunk 1413 optimal weight: 20.0000 chunk 963 optimal weight: 30.0000 chunk 24 optimal weight: 50.0000 chunk 1263 optimal weight: 7.9990 chunk 700 optimal weight: 4.9990 chunk 1448 optimal weight: 50.0000 chunk 1173 optimal weight: 0.7980 chunk 2 optimal weight: 30.0000 chunk 866 optimal weight: 5.9990 chunk 1523 optimal weight: 50.0000 chunk 428 optimal weight: 30.0000 overall best weight: 7.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 GLN ** J 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** K 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN R 56 GLN ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 142 GLN ** Y 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN ** BA 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JA 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** OA 76 ASN OA 79 GLN ** QA 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** WA 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 69 GLN ** WA 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 170 GLN ** FB 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IB 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MB 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 44 ASN PB 89 GLN ** SB 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XB 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZB 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.130 230859 Z= 0.244 Angle : 0.747 16.100 338518 Z= 0.380 Chirality : 0.041 0.326 42291 Planarity : 0.006 0.143 22554 Dihedral : 16.825 179.937 80095 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.69 % Favored : 85.24 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.02 % 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: -3.82 (0.07), residues: 12205 helix: -1.95 (0.07), residues: 3714 sheet: -2.48 (0.12), residues: 1562 loop : -2.98 (0.07), residues: 6929 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1105 time to evaluate : 10.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 288 outliers final: 128 residues processed: 1326 average time/residue: 1.7210 time to fit residues: 3976.9443 Evaluate side-chains 1107 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 979 time to evaluate : 10.445 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 128 outliers final: 1 residues processed: 128 average time/residue: 1.4738 time to fit residues: 362.6295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1756 random chunks: chunk 571 optimal weight: 9.9990 chunk 1528 optimal weight: 5.9990 chunk 335 optimal weight: 30.0000 chunk 996 optimal weight: 50.0000 chunk 419 optimal weight: 50.0000 chunk 1699 optimal weight: 0.4980 chunk 1410 optimal weight: 10.0000 chunk 786 optimal weight: 5.9990 chunk 141 optimal weight: 50.0000 chunk 562 optimal weight: 0.0270 chunk 891 optimal weight: 20.0000 overall best weight: 4.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 95 GLN ** S 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 HIS ** U 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 42 GLN ** CA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 11 ASN ** IA 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JA 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 10 GLN PA 57 ASN ** RA 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 17 ASN ** WA 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 37 GLN ** CB 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 116 HIS ** FB 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** IB 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MB 103 ASN ** NB 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PB 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QB 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** QB 138 GLN SB 29 HIS ** SB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UB 10 ASN ** VB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XB 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZB 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZB 51 ASN ** DC 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.134 230859 Z= 0.227 Angle : 0.746 19.175 338518 Z= 0.379 Chirality : 0.041 0.402 42291 Planarity : 0.006 0.191 22554 Dihedral : 16.822 179.930 80095 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 28.70 Ramachandran Plot: Outliers : 1.06 % Allowed : 13.55 % Favored : 85.39 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.02 % 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: -3.73 (0.07), residues: 12205 helix: -1.90 (0.07), residues: 3710 sheet: -2.40 (0.12), residues: 1545 loop : -2.92 (0.07), residues: 6950 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1041 time to evaluate : 11.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 190 outliers final: 90 residues processed: 1181 average time/residue: 1.7948 time to fit residues: 3694.1862 Evaluate side-chains 1071 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 981 time to evaluate : 10.486 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 90 outliers final: 1 residues processed: 90 average time/residue: 1.4279 time to fit residues: 250.4298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1756 random chunks: chunk 1638 optimal weight: 8.9990 chunk 191 optimal weight: 30.0000 chunk 968 optimal weight: 30.0000 chunk 1240 optimal weight: 40.0000 chunk 961 optimal weight: 20.0000 chunk 1430 optimal weight: 9.9990 chunk 948 optimal weight: 30.0000 chunk 1692 optimal weight: 10.0000 chunk 1059 optimal weight: 20.0000 chunk 1031 optimal weight: 40.0000 chunk 781 optimal weight: 9.9990 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 50 ASN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JA 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** KA 39 GLN ** LA 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 17 ASN ** WA 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 37 GLN ** CB 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 22 HIS ** FB 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** IB 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PB 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QB 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XB 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZB 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZB 51 ASN ** DC 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.602 230859 Z= 0.336 Angle : 0.781 56.677 338518 Z= 0.409 Chirality : 0.041 0.402 42291 Planarity : 0.008 0.252 22554 Dihedral : 16.822 179.930 80095 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 32.19 Ramachandran Plot: Outliers : 1.06 % Allowed : 13.55 % Favored : 85.39 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.02 % 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: -3.73 (0.07), residues: 12205 helix: -1.90 (0.07), residues: 3710 sheet: -2.40 (0.12), residues: 1545 loop : -2.92 (0.07), residues: 6950 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 991 time to evaluate : 13.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 8 outliers final: 3 residues processed: 994 average time/residue: 1.7201 time to fit residues: 2964.0847 Evaluate side-chains 986 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 983 time to evaluate : 10.389 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 1.5133 time to fit residues: 20.1627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1756 random chunks: chunk 1047 optimal weight: 40.0000 chunk 675 optimal weight: 9.9990 chunk 1010 optimal weight: 10.0000 chunk 509 optimal weight: 30.0000 chunk 332 optimal weight: 30.0000 chunk 327 optimal weight: 30.0000 chunk 1076 optimal weight: 4.9990 chunk 1153 optimal weight: 0.8980 chunk 836 optimal weight: 7.9990 chunk 157 optimal weight: 40.0000 chunk 1330 optimal weight: 0.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JA 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 17 ASN ** WA 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 37 GLN ** CB 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 22 HIS ** DB 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** IB 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PB 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QB 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XB 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XB 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZB 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZB 51 ASN ** DC 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.596 230859 Z= 0.334 Angle : 0.781 56.571 338518 Z= 0.409 Chirality : 0.041 0.402 42291 Planarity : 0.008 0.252 22554 Dihedral : 16.822 179.930 80095 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 32.34 Ramachandran Plot: Outliers : 1.06 % Allowed : 13.55 % Favored : 85.39 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.02 % 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: -3.73 (0.07), residues: 12205 helix: -1.90 (0.07), residues: 3710 sheet: -2.40 (0.12), residues: 1545 loop : -2.92 (0.07), residues: 6950 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 982 time to evaluate : 10.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 985 average time/residue: 1.7289 time to fit residues: 2944.1189 Evaluate side-chains 983 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 982 time to evaluate : 10.414 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.5199 time to fit residues: 14.6257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1756 random chunks: chunk 1539 optimal weight: 0.6980 chunk 1621 optimal weight: 7.9990 chunk 1479 optimal weight: 30.0000 chunk 1577 optimal weight: 30.0000 chunk 1620 optimal weight: 5.9990 chunk 949 optimal weight: 20.0000 chunk 687 optimal weight: 7.9990 chunk 1238 optimal weight: 30.0000 chunk 484 optimal weight: 40.0000 chunk 1425 optimal weight: 8.9990 chunk 1491 optimal weight: 10.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JA 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 17 ASN ** WA 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 37 GLN ** CB 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 22 HIS ** DB 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** IB 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PB 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QB 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XB 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XB 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZB 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZB 51 ASN ** DC 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.555 230859 Z= 0.329 Angle : 0.783 55.784 338518 Z= 0.409 Chirality : 0.041 0.402 42291 Planarity : 0.008 0.250 22554 Dihedral : 16.822 179.930 80095 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 32.46 Ramachandran Plot: Outliers : 1.06 % Allowed : 13.54 % Favored : 85.40 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.02 % 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: -3.73 (0.07), residues: 12205 helix: -1.90 (0.07), residues: 3710 sheet: -2.40 (0.12), residues: 1545 loop : -2.92 (0.07), residues: 6950 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 981 time to evaluate : 11.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 10 outliers final: 5 residues processed: 984 average time/residue: 1.7564 time to fit residues: 3003.9517 Evaluate side-chains 986 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 981 time to evaluate : 13.346 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 1.4851 time to fit residues: 25.5290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1756 random chunks: chunk 1571 optimal weight: 1.9990 chunk 1035 optimal weight: 8.9990 chunk 1667 optimal weight: 5.9990 chunk 1017 optimal weight: 5.9990 chunk 791 optimal weight: 5.9990 chunk 1159 optimal weight: 40.0000 chunk 1749 optimal weight: 50.0000 chunk 1610 optimal weight: 30.0000 chunk 1393 optimal weight: 30.0000 chunk 144 optimal weight: 50.0000 chunk 1076 optimal weight: 0.0670 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 GLN ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN ** S 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 58 ASN ** X 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 56 ASN ** IA 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JA 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LA 18 ASN ** MA 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** WA 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 37 GLN ** CB 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 22 HIS ** DB 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EB 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 116 HIS ** FB 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** IB 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 136 GLN ** QB 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RB 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XB 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XB 94 ASN ** ZB 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZB 51 ASN ** DC 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 176 GLN ** DC 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.662 230859 Z= 0.226 Angle : 0.741 28.628 338518 Z= 0.377 Chirality : 0.040 0.382 42291 Planarity : 0.006 0.186 22554 Dihedral : 16.734 179.887 80095 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 1.03 % Allowed : 12.63 % Favored : 86.34 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -3.56 (0.07), residues: 12205 helix: -1.75 (0.08), residues: 3706 sheet: -2.26 (0.12), residues: 1557 loop : -2.83 (0.07), residues: 6942 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24410 Ramachandran restraints generated. 12205 Oldfield, 0 Emsley, 12205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1067 time to evaluate : 11.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 58 outliers final: 33 residues processed: 1091 average time/residue: 1.8274 time to fit residues: 3474.1444 Evaluate side-chains 1022 residues out of total 10421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 989 time to evaluate : 10.494 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 1.6356 time to fit residues: 108.5729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1756 random chunks: chunk 854 optimal weight: 5.9990 chunk 1106 optimal weight: 5.9990 chunk 1483 optimal weight: 30.0000 chunk 426 optimal weight: 30.0000 chunk 1284 optimal weight: 20.0000 chunk 205 optimal weight: 30.0000 chunk 387 optimal weight: 30.0000 chunk 1395 optimal weight: 40.0000 chunk 583 optimal weight: 2.9990 chunk 1432 optimal weight: 8.9990 chunk 176 optimal weight: 30.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 ASN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 58 ASN ** X 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN ** AA 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JA 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QA 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** WA 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 153 ASN ** BB 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 37 GLN ** CB 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 122 HIS ** EB 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PB 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QB 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RB 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SB 33 GLN ** TB 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UB 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XB 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZB 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZB 51 ASN ** DC 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 826 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.068701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.054684 restraints weight = 1802294.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.056019 restraints weight = 985675.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.056838 restraints weight = 658153.405| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.214 230859 Z= 0.269 Angle : 0.757 19.410 338518 Z= 0.385 Chirality : 0.041 0.410 42291 Planarity : 0.006 0.168 22554 Dihedral : 16.803 179.991 80095 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 29.80 Ramachandran Plot: Outliers : 1.03 % Allowed : 13.56 % Favored : 85.41 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.54 (0.07), residues: 12205 helix: -1.73 (0.08), residues: 3714 sheet: -2.30 (0.12), residues: 1584 loop : -2.80 (0.07), residues: 6907 =============================================================================== Job complete usr+sys time: 60651.74 seconds wall clock time: 1056 minutes 18.64 seconds (63378.64 seconds total)