Starting phenix.real_space_refine (version: dev) on Wed Dec 14 09:32:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsk_14132/12_2022/7qsk_14132_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsk_14132/12_2022/7qsk_14132.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsk_14132/12_2022/7qsk_14132_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsk_14132/12_2022/7qsk_14132_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsk_14132/12_2022/7qsk_14132_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsk_14132/12_2022/7qsk_14132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsk_14132/12_2022/7qsk_14132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsk_14132/12_2022/7qsk_14132_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsk_14132/12_2022/7qsk_14132_updated.pdb" } resolution = 2.84 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= -0.001 sd= 0.943 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 "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ASP 114": "OD1" <-> "OD2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ASP 114": "OD1" <-> "OD2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 248": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 170": "OD1" <-> "OD2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 314": "OD1" <-> "OD2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G GLU 512": "OE1" <-> "OE2" Residue "G TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "J TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "L PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 416": "NH1" <-> "NH2" Residue "M TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O ASP 110": "OD1" <-> "OD2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 219": "OE1" <-> "OE2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "O ARG 254": "NH1" <-> "NH2" Residue "O PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 298": "OE1" <-> "OE2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P GLU 100": "OE1" <-> "OE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "P TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 224": "NH1" <-> "NH2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P GLU 285": "OE1" <-> "OE2" Residue "P GLU 306": "OE1" <-> "OE2" Residue "P ARG 325": "NH1" <-> "NH2" Residue "Q ARG 36": "NH1" <-> "NH2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 104": "OD1" <-> "OD2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S ARG 25": "NH1" <-> "NH2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 59": "OD1" <-> "OD2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "T ASP 39": "OD1" <-> "OD2" Residue "T GLU 49": "OE1" <-> "OE2" Residue "T GLU 55": "OE1" <-> "OE2" Residue "T TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 21": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ASP 32": "OD1" <-> "OD2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W GLU 42": "OE1" <-> "OE2" Residue "W ASP 53": "OD1" <-> "OD2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "W ARG 114": "NH1" <-> "NH2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X ARG 54": "NH1" <-> "NH2" Residue "X PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 154": "OE1" <-> "OE2" Residue "Y ARG 6": "NH1" <-> "NH2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 50": "OE1" <-> "OE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 80": "NH1" <-> "NH2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Y TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 130": "OE1" <-> "OE2" Residue "Z TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 28": "NH1" <-> "NH2" Residue "Z GLU 63": "OE1" <-> "OE2" Residue "Z ARG 68": "NH1" <-> "NH2" Residue "Z GLU 78": "OE1" <-> "OE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 123": "OE1" <-> "OE2" Residue "Z ARG 128": "NH1" <-> "NH2" Residue "a PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b ARG 46": "NH1" <-> "NH2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 59": "OD1" <-> "OD2" Residue "b ARG 82": "NH1" <-> "NH2" Residue "c PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 5": "NH1" <-> "NH2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d ARG 60": "NH1" <-> "NH2" Residue "d PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "e ARG 63": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 82": "NH1" <-> "NH2" Residue "e TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 9": "OD1" <-> "OD2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ASP 31": "OD1" <-> "OD2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "g GLU 28": "OE1" <-> "OE2" Residue "g GLU 31": "OE1" <-> "OE2" Residue "g ASP 43": "OD1" <-> "OD2" Residue "g PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "h PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h ARG 26": "NH1" <-> "NH2" Residue "h GLU 54": "OE1" <-> "OE2" Residue "h TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h GLU 131": "OE1" <-> "OE2" Residue "i ARG 15": "NH1" <-> "NH2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i ARG 44": "NH1" <-> "NH2" Residue "i PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "i ASP 124": "OD1" <-> "OD2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 19": "NH1" <-> "NH2" Residue "j GLU 26": "OE1" <-> "OE2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "k ASP 17": "OD1" <-> "OD2" Residue "k TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k GLU 84": "OE1" <-> "OE2" Residue "k TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 88": "OE1" <-> "OE2" Residue "l GLU 19": "OE1" <-> "OE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "m PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 21": "OE1" <-> "OE2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m GLU 45": "OE1" <-> "OE2" Residue "m ARG 56": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 107": "OD1" <-> "OD2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n GLU 68": "OE1" <-> "OE2" Residue "n GLU 69": "OE1" <-> "OE2" Residue "n PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 91": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 134": "NH1" <-> "NH2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n GLU 151": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ARG 20": "NH1" <-> "NH2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 32": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 37": "OE1" <-> "OE2" Residue "o ARG 64": "NH1" <-> "NH2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o ARG 114": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 53": "NH1" <-> "NH2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 86": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q ASP 76": "OD1" <-> "OD2" Residue "q ASP 78": "OD1" <-> "OD2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 5": "NH1" <-> "NH2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 90": "OE1" <-> "OE2" Residue "r GLU 109": "OE1" <-> "OE2" Residue "r TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 69986 Number of models: 1 Model: "" Number of chains: 116 Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 921 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1738 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 16, 'TRANS': 192} Chain: "D" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 192} Chain: "F" Number of atoms: 3347 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3326 Classifications: {'peptide': 432} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 410} Conformer: "B" Number of residues, atoms: 432, 3326 Classifications: {'peptide': 432} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 410} bond proxies already assigned to first conformer: 3376 Chain: "G" Number of atoms: 5366 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 699, 5355 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 33, 'TRANS': 665} Conformer: "B" Number of residues, atoms: 699, 5355 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 33, 'TRANS': 665} bond proxies already assigned to first conformer: 5432 Chain: "H" Number of atoms: 2517 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2572 Chain: "I" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1345 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 745 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4802 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 27, 'TRANS': 578} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3654 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2733 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2589 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "P" Number of atoms: 2768 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 342, 2754 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Conformer: "B" Number of residues, atoms: 342, 2754 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} bond proxies already assigned to first conformer: 2814 Chain: "Q" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1049 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "R" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 740 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "S" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 700 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "T" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 688 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "U" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "V" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 928 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 106} Chain: "W" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 976 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "X" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1402 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Y" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1030 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1152 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "a" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 569 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 414 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "d" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 999 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 9, 'TRANS': 110} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "f" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 492 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 839 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 8, 'TRANS': 91} Chain: "h" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1154 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "i" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1097 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 113} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 597 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 7, 'TRANS': 63} Chain: "k" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 653 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "l" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1314 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "m" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1067 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain: "n" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1492 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 15, 'TRANS': 156} Chain: "o" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1048 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "p" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1453 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 10, 'TRANS': 162} Chain: "q" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "r" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 776 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 391 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 45, 380 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Conformer: "B" Number of residues, atoms: 45, 380 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} bond proxies already assigned to first conformer: 380 Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 150 Unusual residues: {'3PE': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {'U10': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Chain: "I" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "L" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 211 Unusual residues: {'3PE': 3, 'CDL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "M" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'3PE': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "N" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'3PE': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 86 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "Y" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 207 Unusual residues: {'3PE': 5, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 102 Chain: "Z" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "d" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Chain: "g" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "h" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "i" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CHD': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "o" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "r" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "G" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 128 Classifications: {'water': 128} Link IDs: {None: 127} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "V" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "W" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "X" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Z" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "e" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "f" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "h" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "i" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "m" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "n" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "o" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "p" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "r" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "s" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1668 SG CYS B 119 98.938 95.239 204.447 1.00 34.02 S ATOM 1898 SG CYS B 149 96.515 92.727 208.699 1.00 34.07 S ATOM 1164 SG CYS B 54 93.286 91.542 204.175 1.00 37.83 S ATOM 1170 SG CYS B 55 92.755 97.129 206.537 1.00 36.50 S ATOM 8167 SG CYS E 103 120.503 47.030 258.551 1.00 49.02 S ATOM 8201 SG CYS E 108 119.230 44.165 260.590 1.00 50.20 S ATOM 8481 SG CYS E 144 123.198 43.869 255.281 1.00 49.06 S ATOM 8504 SG CYS E 148 122.155 41.106 256.265 1.00 51.32 S ATOM 11750 SG CYS F 362 124.703 54.477 235.072 1.00 37.14 S ATOM 11770 SG CYS F 365 121.889 53.625 240.131 1.00 38.94 S ATOM 12094 SG CYS F 405 126.289 49.507 238.887 1.00 40.76 S ATOM 11731 SG CYS F 359 128.363 55.394 240.346 1.00 39.30 S ATOM 13191 SG CYS G 114 120.042 72.722 226.326 1.00 33.04 S ATOM 13130 SG CYS G 105 114.046 74.849 228.353 1.00 31.92 S ATOM 13151 SG CYS G 108 119.515 77.695 230.272 1.00 33.40 S ATOM 13523 SG CYS G 156 128.900 67.209 230.786 1.00 35.19 S ATOM 13500 SG CYS G 153 125.928 69.031 236.406 1.00 34.28 S ATOM 13547 SG CYS G 159 132.058 70.435 235.093 1.00 36.46 S ATOM 13877 SG CYS G 203 127.277 73.071 231.309 1.00 33.83 S ATOM 12636 SG CYS G 41 129.531 60.593 228.182 1.00 35.71 S ATOM 12722 SG CYS G 52 125.546 60.531 227.374 1.00 35.05 S ATOM 12747 SG CYS G 55 127.327 56.269 224.277 1.00 36.24 S ATOM 12848 SG CYS G 69 130.560 57.055 225.361 1.00 37.59 S ATOM 21202 SG CYS I 119 100.332 86.837 214.925 1.00 31.54 S ATOM 21176 SG CYS I 116 100.065 93.365 215.742 1.00 31.49 S ATOM 21223 SG CYS I 122 102.049 89.231 220.485 1.00 31.33 S ATOM 20950 SG CYS I 87 105.715 90.232 215.152 1.00 30.86 S ATOM 21252 SG CYS I 126 104.765 86.078 227.760 1.00 31.22 S ATOM 20881 SG CYS I 77 109.580 90.484 228.804 1.00 32.99 S ATOM 20923 SG CYS I 83 108.060 88.845 222.753 1.00 31.41 S ATOM 20900 SG CYS I 80 110.259 84.279 226.360 1.00 32.81 S ATOM 41806 SG CYS R 59 107.031 81.387 242.838 1.00 37.91 S ATOM 41984 SG CYS R 84 110.078 82.074 240.697 1.00 38.36 S ATOM 42006 SG CYS R 87 107.874 84.563 241.774 1.00 36.83 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE F 73 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE F 73 " occ=0.50 residue: pdb=" N AHIS F 356 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 356 " occ=0.50 residue: pdb=" N APHE G 642 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE G 642 " occ=0.50 residue: pdb=" N ALEU H 61 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU H 61 " occ=0.50 residue: pdb=" N ATRP P 265 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP P 265 " occ=0.50 residue: pdb=" N AARG s 74 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG s 74 " occ=0.50 Time building chain proxies: 34.40, per 1000 atoms: 0.49 Number of scatterers: 69986 At special positions: 0 Unit cell: (188.899, 201.642, 290.845, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 473 16.00 P 56 15.00 Mg 1 11.99 O 13434 8.00 N 11328 7.00 C 44664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.03 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.04 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb=" FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb=" FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb=" FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb=" FES G 803 " pdb=" FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb=" FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb=" FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb=" FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb=" FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb=" FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb=" FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb=" FE2 SF4 B 201 " - pdb=" SG CYS B 149 " pdb=" SF4 F 502 " pdb=" FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb=" FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb=" FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb=" FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb=" FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb=" FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb=" FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb=" SF4 G 802 " pdb=" FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb=" FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb=" FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb=" SF4 I 202 " pdb=" FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb=" FE4 SF4 I 202 " - pdb=" SG CYS I 87 " pdb=" FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb=" FE1 SF4 I 202 " - pdb=" SG CYS I 119 " pdb=" SF4 I 203 " pdb=" FE4 SF4 I 203 " - pdb=" SG CYS I 80 " pdb=" FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb=" FE3 SF4 I 203 " - pdb=" SG CYS I 83 " pdb=" FE1 SF4 I 203 " - pdb=" SG CYS I 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 357 helices and 30 sheets defined 53.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 3 through 24 Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.519A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.425A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'B' and resid 26 through 42 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 94 through 106 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.036A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.571A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.647A pdb=" N ASN C 128 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.906A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.741A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 Proline residue: D 101 - end of helix removed outlier: 3.693A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.609A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 218 through 227 Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 4.005A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.502A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 394 through 400 Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 411 through 421 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.716A pdb=" N LYS E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.410A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.632A pdb=" N ASN E 58 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 106 through 109 No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 166 through 178 removed outlier: 3.595A pdb=" N GLU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 62 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 106 through 113 removed outlier: 3.593A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 129 Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 189 through 197 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 237 removed outlier: 3.724A pdb=" N SER F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 276 through 283 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 309 through 314 removed outlier: 5.021A pdb=" N THR F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.508A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.695A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 421 Proline residue: F 414 - end of helix Processing helix chain 'F' and resid 423 through 436 Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.623A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.620A pdb=" N ILE G 202 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 265 through 269 Processing helix chain 'G' and resid 271 through 275 Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.608A pdb=" N MET G 306 " --> pdb=" O ARG G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.614A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 362 Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 removed outlier: 3.726A pdb=" N ILE G 432 " --> pdb=" O LEU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 445 Processing helix chain 'G' and resid 455 through 459 removed outlier: 3.599A pdb=" N GLN G 459 " --> pdb=" O SER G 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 455 through 459' Processing helix chain 'G' and resid 463 through 479 Processing helix chain 'G' and resid 499 through 505 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 596 through 607 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.699A pdb=" N VAL G 631 " --> pdb=" O PRO G 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 628 through 631' Processing helix chain 'G' and resid 642 through 652 removed outlier: 3.526A pdb=" N LEU G 648 " --> pdb=" O GLN G 644 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL G 652 " --> pdb=" O LEU G 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 683 through 693 Processing helix chain 'G' and resid 695 through 698 No H-bonds generated for 'chain 'G' and resid 695 through 698' Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix removed outlier: 3.754A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.269A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.576A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 5.031A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.984A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 removed outlier: 3.576A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 207 No H-bonds generated for 'chain 'H' and resid 204 through 207' Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 217 through 242 removed outlier: 3.651A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 291 removed outlier: 3.724A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 42 removed outlier: 3.522A pdb=" N MET I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 151 through 172 removed outlier: 5.879A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 47 Processing helix chain 'J' and resid 50 through 74 removed outlier: 3.501A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.626A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 146 removed outlier: 3.730A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 173 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.717A pdb=" N ASN K 7 " --> pdb=" O MET K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 59 through 85 removed outlier: 3.542A pdb=" N CYS K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 3 through 24 removed outlier: 3.637A pdb=" N LEU L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU L 15 " --> pdb=" O THR L 11 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.703A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.553A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 157 removed outlier: 3.834A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.615A pdb=" N ILE L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 230 through 238 Proline residue: L 234 - end of helix Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.127A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE L 257 " --> pdb=" O VAL L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.130A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.570A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.948A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 389 through 400 removed outlier: 5.078A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.748A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE L 426 " --> pdb=" O TYR L 422 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE L 427 " --> pdb=" O SER L 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 6.110A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 506 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 Proline residue: L 530 - end of helix removed outlier: 3.936A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.641A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 560 No H-bonds generated for 'chain 'L' and resid 557 through 560' Processing helix chain 'L' and resid 563 through 578 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.140A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 4.163A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL M 25 " --> pdb=" O MET M 22 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 83 Proline residue: M 64 - end of helix removed outlier: 3.696A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 4.772A pdb=" N HIS M 82 " --> pdb=" O MET M 78 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HIS M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 136 removed outlier: 3.639A pdb=" N THR M 125 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.516A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.510A pdb=" N ILE M 165 " --> pdb=" O VAL M 162 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.962A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 3.539A pdb=" N PHE M 194 " --> pdb=" O TRP M 190 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 221 removed outlier: 3.846A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 249 removed outlier: 4.535A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 278 removed outlier: 3.737A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA M 258 " --> pdb=" O ASP M 255 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR M 259 " --> pdb=" O PHE M 256 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 3.622A pdb=" N MET M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU M 264 " --> pdb=" O PHE M 261 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP M 267 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY M 268 " --> pdb=" O SER M 265 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET M 269 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR M 272 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER M 273 " --> pdb=" O ILE M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.733A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.667A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 367 Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.680A pdb=" N PHE M 380 " --> pdb=" O ILE M 376 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.609A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU M 411 " --> pdb=" O LEU M 408 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE M 412 " --> pdb=" O TYR M 409 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 removed outlier: 3.593A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 4.066A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 453 No H-bonds generated for 'chain 'M' and resid 451 through 453' Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 45 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 120 removed outlier: 4.097A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 131 removed outlier: 3.662A pdb=" N ILE N 129 " --> pdb=" O SER N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 148 removed outlier: 4.781A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 4.649A pdb=" N PHE N 146 " --> pdb=" O TYR N 143 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.518A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 194 removed outlier: 3.638A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.785A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.627A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS N 236 " --> pdb=" O HIS N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 252 removed outlier: 3.620A pdb=" N VAL N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix removed outlier: 3.507A pdb=" N MET N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN N 268 " --> pdb=" O MET N 265 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET N 270 " --> pdb=" O ILE N 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 298 removed outlier: 3.724A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.719A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 removed outlier: 3.514A pdb=" N VAL N 331 " --> pdb=" O PRO N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 346 Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 14 through 17 No H-bonds generated for 'chain 'O' and resid 14 through 17' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 through 141 removed outlier: 3.522A pdb=" N PHE O 134 " --> pdb=" O ASP O 131 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA O 137 " --> pdb=" O PHE O 134 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG O 140 " --> pdb=" O ALA O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 4.500A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 208 Processing helix chain 'O' and resid 210 through 217 removed outlier: 4.059A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS O 217 " --> pdb=" O GLU O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 228 No H-bonds generated for 'chain 'O' and resid 225 through 228' Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.615A pdb=" N TYR O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 250 No H-bonds generated for 'chain 'O' and resid 248 through 250' Processing helix chain 'O' and resid 253 through 264 Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 271 through 274 removed outlier: 3.838A pdb=" N SER O 274 " --> pdb=" O ASN O 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 271 through 274' Processing helix chain 'O' and resid 286 through 297 Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' Processing helix chain 'P' and resid 3 through 5 No H-bonds generated for 'chain 'P' and resid 3 through 5' Processing helix chain 'P' and resid 29 through 40 removed outlier: 4.079A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 5.085A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Proline residue: P 61 - end of helix Processing helix chain 'P' and resid 78 through 85 removed outlier: 3.863A pdb=" N ALA P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 123 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 188 removed outlier: 4.292A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE P 188 " --> pdb=" O ASN P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 218 Processing helix chain 'P' and resid 238 through 249 Processing helix chain 'P' and resid 260 through 270 removed outlier: 3.622A pdb=" N GLY P 267 " --> pdb=" O TYR P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 287 Processing helix chain 'P' and resid 300 through 303 No H-bonds generated for 'chain 'P' and resid 300 through 303' Processing helix chain 'P' and resid 310 through 321 removed outlier: 5.602A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL P 317 " --> pdb=" O LYS P 313 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 22 No H-bonds generated for 'chain 'Q' and resid 20 through 22' Processing helix chain 'Q' and resid 27 through 31 removed outlier: 4.086A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 52 No H-bonds generated for 'chain 'Q' and resid 50 through 52' Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 119 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.700A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU R 46 " --> pdb=" O ASP R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.959A pdb=" N TYR S 40 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU S 42 " --> pdb=" O LYS S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 8 through 21 Processing helix chain 'T' and resid 44 through 58 removed outlier: 3.673A pdb=" N ASP T 56 " --> pdb=" O MET T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 67 No H-bonds generated for 'chain 'T' and resid 64 through 67' Processing helix chain 'T' and resid 73 through 84 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44 through 58 removed outlier: 3.672A pdb=" N ASP U 56 " --> pdb=" O MET U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 67 No H-bonds generated for 'chain 'U' and resid 64 through 67' Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 19 through 36 removed outlier: 3.946A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 removed outlier: 3.521A pdb=" N GLN V 49 " --> pdb=" O LYS V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 4.058A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 removed outlier: 3.682A pdb=" N ARG W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 69 Processing helix chain 'W' and resid 76 through 94 Processing helix chain 'W' and resid 100 through 106 removed outlier: 4.446A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 34 Processing helix chain 'X' and resid 36 through 49 removed outlier: 3.513A pdb=" N MET X 43 " --> pdb=" O ASN X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 56 through 75 removed outlier: 3.567A pdb=" N LEU X 61 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE X 73 " --> pdb=" O PHE X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 100 through 113 Processing helix chain 'Y' and resid 3 through 9 Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 80 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 32 through 97 Proline residue: Z 73 - end of helix removed outlier: 3.717A pdb=" N GLN Z 85 " --> pdb=" O ARG Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 124 No H-bonds generated for 'chain 'Z' and resid 121 through 124' Processing helix chain 'Z' and resid 130 through 142 removed outlier: 5.795A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 4 No H-bonds generated for 'chain 'a' and resid 2 through 4' Processing helix chain 'a' and resid 6 through 30 Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'b' and resid 2 through 14 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.805A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 removed outlier: 3.699A pdb=" N ARG b 82 " --> pdb=" O GLU b 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 78 through 82' Processing helix chain 'c' and resid 14 through 46 removed outlier: 3.511A pdb=" N ASN c 46 " --> pdb=" O TYR c 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 20 removed outlier: 3.570A pdb=" N SER d 20 " --> pdb=" O GLU d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.576A pdb=" N LEU d 63 " --> pdb=" O HIS d 59 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 42 Processing helix chain 'e' and resid 47 through 54 removed outlier: 4.181A pdb=" N LYS e 53 " --> pdb=" O ILE e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 88 Processing helix chain 'e' and resid 95 through 98 No H-bonds generated for 'chain 'e' and resid 95 through 98' Processing helix chain 'f' and resid 3 through 6 No H-bonds generated for 'chain 'f' and resid 3 through 6' Processing helix chain 'f' and resid 12 through 33 removed outlier: 4.728A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.952A pdb=" N TYR f 25 " --> pdb=" O PHE f 22 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG f 28 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS f 33 " --> pdb=" O ASN f 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 65 Processing helix chain 'g' and resid 72 through 78 Processing helix chain 'g' and resid 83 through 102 removed outlier: 3.867A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRP g 88 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA g 89 " --> pdb=" O GLN g 86 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG g 100 " --> pdb=" O VAL g 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU g 101 " --> pdb=" O LYS g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 117 No H-bonds generated for 'chain 'g' and resid 115 through 117' Processing helix chain 'h' and resid 16 through 45 removed outlier: 4.101A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE h 34 " --> pdb=" O LEU h 30 " (cutoff:3.500A) Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 63 through 66 removed outlier: 3.680A pdb=" N TYR h 66 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 66' Processing helix chain 'h' and resid 70 through 78 Processing helix chain 'h' and resid 83 through 117 Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 25 Processing helix chain 'i' and resid 41 through 52 removed outlier: 3.564A pdb=" N TRP i 46 " --> pdb=" O VAL i 42 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU i 50 " --> pdb=" O TRP i 46 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN i 51 " --> pdb=" O ASN i 47 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP i 52 " --> pdb=" O LYS i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 73 removed outlier: 3.882A pdb=" N ILE i 60 " --> pdb=" O TRP i 56 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 48 removed outlier: 7.271A pdb=" N ASP j 45 " --> pdb=" O TRP j 41 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA j 46 " --> pdb=" O HIS j 42 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL j 47 " --> pdb=" O ASP j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'k' and resid 18 through 20 No H-bonds generated for 'chain 'k' and resid 18 through 20' Processing helix chain 'k' and resid 27 through 38 removed outlier: 3.544A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 52 removed outlier: 4.831A pdb=" N TRP k 50 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ARG k 51 " --> pdb=" O ASN k 47 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR k 52 " --> pdb=" O GLU k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 62 through 66 Processing helix chain 'k' and resid 70 through 89 Processing helix chain 'l' and resid 17 through 26 Processing helix chain 'l' and resid 81 through 84 No H-bonds generated for 'chain 'l' and resid 81 through 84' Processing helix chain 'l' and resid 98 through 121 Processing helix chain 'l' and resid 134 through 138 Processing helix chain 'm' and resid 19 through 22 No H-bonds generated for 'chain 'm' and resid 19 through 22' Processing helix chain 'm' and resid 26 through 50 removed outlier: 3.537A pdb=" N ALA m 33 " --> pdb=" O ARG m 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU m 34 " --> pdb=" O LYS m 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU m 36 " --> pdb=" O GLN m 32 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 70 Processing helix chain 'm' and resid 83 through 92 Processing helix chain 'm' and resid 95 through 117 Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 46 removed outlier: 3.526A pdb=" N LEU n 42 " --> pdb=" O TYR n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 removed outlier: 3.593A pdb=" N HIS n 72 " --> pdb=" O GLU n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 96 removed outlier: 4.213A pdb=" N CYS n 95 " --> pdb=" O ARG n 92 " (cutoff:3.500A) Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 142 removed outlier: 3.646A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.835A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 3 through 9 removed outlier: 3.511A pdb=" N ARG o 7 " --> pdb=" O HIS o 3 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 47 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 121 removed outlier: 3.545A pdb=" N MET o 121 " --> pdb=" O ARG o 117 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 57 Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 6.259A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 173 Processing helix chain 'q' and resid 2 through 16 removed outlier: 4.065A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 30 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.207A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 'r' and resid 59 through 61 No H-bonds generated for 'chain 'r' and resid 59 through 61' Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 50 through 57 Processing sheet with id= A, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.680A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 144 " --> pdb=" O SER B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.954A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE C 52 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.570A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 removed outlier: 3.600A pdb=" N ARG D 388 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.843A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 219 through 224 removed outlier: 6.499A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 266 through 271 Processing sheet with id= I, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= J, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= K, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= L, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.681A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= N, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.498A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.313A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= R, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.993A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.822A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.341A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.522A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= Y, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= Z, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= AA, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= AB, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AC, first strand: chain 'S' and resid 51 through 56 removed outlier: 3.552A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 60 through 63 removed outlier: 3.521A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2858 hydrogen bonds defined for protein. 7946 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.47 Time building geometry restraints manager: 25.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 28360 1.40 - 1.63: 41314 1.63 - 1.85: 880 1.85 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 70634 Sorted by residual: bond pdb=" C15 CHD i 201 " pdb=" C16 CHD i 201 " ideal model delta sigma weight residual 1.541 1.728 -0.187 2.00e-02 2.50e+03 8.72e+01 bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.521 -0.171 2.00e-02 2.50e+03 7.28e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.397 -0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" C HIS D 84 " pdb=" N 2MR D 85 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.16e+01 bond pdb=" C11 CHD i 201 " pdb=" C12 CHD i 201 " ideal model delta sigma weight residual 1.533 1.670 -0.137 2.00e-02 2.50e+03 4.72e+01 ... (remaining 70629 not shown) Histogram of bond angle deviations from ideal: 72.68 - 86.95: 76 86.95 - 101.21: 305 101.21 - 115.47: 45894 115.47 - 129.73: 48623 129.73 - 144.00: 565 Bond angle restraints: 95463 Sorted by residual: angle pdb=" O HIS D 84 " pdb=" C HIS D 84 " pdb=" N 2MR D 85 " ideal model delta sigma weight residual 123.00 144.00 -21.00 1.60e+00 3.91e-01 1.72e+02 angle pdb=" CA HIS D 84 " pdb=" C HIS D 84 " pdb=" N 2MR D 85 " ideal model delta sigma weight residual 116.20 94.90 21.30 2.00e+00 2.50e-01 1.13e+02 angle pdb=" C HIS D 84 " pdb=" N 2MR D 85 " pdb=" CA 2MR D 85 " ideal model delta sigma weight residual 121.70 104.10 17.60 1.80e+00 3.09e-01 9.56e+01 angle pdb=" O 2MR D 85 " pdb=" C 2MR D 85 " pdb=" N GLY D 86 " ideal model delta sigma weight residual 123.00 110.49 12.51 1.60e+00 3.91e-01 6.11e+01 angle pdb=" C14 EHZ T 101 " pdb=" N2 EHZ T 101 " pdb=" C15 EHZ T 101 " ideal model delta sigma weight residual 120.00 140.61 -20.61 3.00e+00 1.11e-01 4.72e+01 ... (remaining 95458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 41448 35.91 - 71.83: 848 71.83 - 107.74: 95 107.74 - 143.65: 6 143.65 - 179.56: 9 Dihedral angle restraints: 42406 sinusoidal: 18222 harmonic: 24184 Sorted by residual: dihedral pdb=" C31 U10 D 701 " pdb=" C32 U10 D 701 " pdb=" C33 U10 D 701 " pdb=" C34 U10 D 701 " ideal model delta sinusoidal sigma weight residual 262.12 82.55 179.56 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C37 U10 D 701 " pdb=" C38 U10 D 701 " pdb=" C39 U10 D 701 " pdb=" C41 U10 D 701 " ideal model delta sinusoidal sigma weight residual 354.37 175.17 179.20 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 89.19 168.40 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 42403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.260: 10247 4.260 - 8.519: 0 8.519 - 12.779: 0 12.779 - 17.039: 0 17.039 - 21.299: 16 Chirality restraints: 10263 Sorted by residual: chirality pdb=" FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.74 -21.30 2.00e-01 2.50e+01 1.13e+04 chirality pdb=" FE3 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.74 -21.29 2.00e-01 2.50e+01 1.13e+04 chirality pdb=" FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.71 21.26 2.00e-01 2.50e+01 1.13e+04 ... (remaining 10260 not shown) Planarity restraints: 11899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA 2MR D 85 " 0.087 2.00e-02 2.50e+03 1.62e-01 2.62e+02 pdb=" C 2MR D 85 " -0.280 2.00e-02 2.50e+03 pdb=" O 2MR D 85 " 0.094 2.00e-02 2.50e+03 pdb=" N GLY D 86 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " -0.035 2.00e-02 2.50e+03 2.94e-02 1.73e+01 pdb=" CG TYR B 125 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 73 " 0.025 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP P 73 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP P 73 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP P 73 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP P 73 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 73 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP P 73 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 73 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 73 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP P 73 " 0.002 2.00e-02 2.50e+03 ... (remaining 11896 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.54: 511 2.54 - 3.19: 64998 3.19 - 3.84: 141415 3.84 - 4.49: 212758 4.49 - 5.14: 326051 Nonbonded interactions: 745733 Sorted by model distance: nonbonded pdb=" OG1 THR L 439 " pdb=" OE1 GLU U 57 " model vdw 1.896 2.440 nonbonded pdb=" OG SER H 209 " pdb=" OD1 ASN H 212 " model vdw 1.911 2.440 nonbonded pdb=" OG SER N 182 " pdb=" OH TYR N 293 " model vdw 1.918 2.440 nonbonded pdb=" O LEU M 14 " pdb=" OG SER M 18 " model vdw 1.944 2.440 nonbonded pdb=" O HOH N 527 " pdb=" O HOH N 528 " model vdw 1.970 2.440 ... (remaining 745728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 4 through 88 or resid 101)) } 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: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 56 5.49 5 Mg 1 5.21 5 S 473 5.16 5 C 44664 2.51 5 N 11328 2.21 5 O 13434 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 54.470 Check model and map are aligned: 0.760 Convert atoms to be neutral: 0.510 Process input model: 168.810 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 252.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 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 : 0.008 0.187 70634 Z= 0.529 Angle : 0.911 21.296 95463 Z= 0.414 Chirality : 0.841 21.299 10263 Planarity : 0.004 0.162 11899 Dihedral : 15.030 179.564 26801 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 0.26 (0.09), residues: 8202 helix: 0.51 (0.08), residues: 4319 sheet: 0.37 (0.26), residues: 397 loop : -0.12 (0.10), residues: 3486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1142 time to evaluate : 6.263 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 1148 average time/residue: 1.5742 time to fit residues: 2337.3608 Evaluate side-chains 783 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 781 time to evaluate : 6.161 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.3461 time to fit residues: 10.0753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 682 optimal weight: 0.9990 chunk 612 optimal weight: 0.9990 chunk 339 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 413 optimal weight: 1.9990 chunk 327 optimal weight: 0.9990 chunk 633 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 385 optimal weight: 0.8980 chunk 471 optimal weight: 0.5980 chunk 733 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN C 200 ASN F 431 GLN G 654 GLN L 510 ASN O 184 GLN O 291 GLN P 335 GLN R 16 GLN R 32 GLN V 49 GLN c 13 ASN e 96 HIS g 119 GLN ** i 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 58 ASN n 52 ASN q 69 ASN q 116 ASN q 135 GLN r 24 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.265 70634 Z= 0.407 Angle : 1.300 50.694 95463 Z= 0.832 Chirality : 0.258 6.556 10263 Planarity : 0.004 0.045 11899 Dihedral : 12.296 179.405 10420 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.82 % Favored : 98.17 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.07 (0.09), residues: 8202 helix: 1.34 (0.08), residues: 4353 sheet: 0.41 (0.26), residues: 378 loop : 0.06 (0.11), residues: 3471 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 851 time to evaluate : 6.345 Fit side-chains outliers start: 84 outliers final: 30 residues processed: 888 average time/residue: 1.5468 time to fit residues: 1808.0300 Evaluate side-chains 791 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 761 time to evaluate : 6.222 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 16 residues processed: 14 average time/residue: 0.8882 time to fit residues: 27.2323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 407 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 610 optimal weight: 6.9990 chunk 499 optimal weight: 0.0470 chunk 202 optimal weight: 8.9990 chunk 735 optimal weight: 6.9990 chunk 794 optimal weight: 7.9990 chunk 654 optimal weight: 0.9990 chunk 728 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 589 optimal weight: 0.6980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 ASN C 200 ASN G 654 GLN M 83 HIS O 204 ASN R 32 GLN R 74 ASN V 95 GLN X 102 GLN X 105 GLN Y 128 GLN a 40 HIS c 13 ASN e 26 HIS e 96 HIS ** i 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN n 52 ASN o 43 GLN s 35 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.249 70634 Z= 0.407 Angle : 1.276 50.623 95463 Z= 0.823 Chirality : 0.253 6.422 10263 Planarity : 0.004 0.047 11899 Dihedral : 11.632 177.105 10420 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.09 % Favored : 97.90 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.40 (0.09), residues: 8202 helix: 1.64 (0.08), residues: 4329 sheet: 0.39 (0.26), residues: 397 loop : 0.20 (0.11), residues: 3476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 819 time to evaluate : 9.508 Fit side-chains revert: symmetry clash outliers start: 108 outliers final: 38 residues processed: 869 average time/residue: 1.5572 time to fit residues: 1789.3525 Evaluate side-chains 791 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 753 time to evaluate : 6.328 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 24 residues processed: 14 average time/residue: 0.7711 time to fit residues: 26.0499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 726 optimal weight: 6.9990 chunk 552 optimal weight: 4.9990 chunk 381 optimal weight: 7.9990 chunk 81 optimal weight: 0.1980 chunk 350 optimal weight: 6.9990 chunk 493 optimal weight: 1.9990 chunk 737 optimal weight: 8.9990 chunk 781 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 699 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN J 78 GLN K 97 GLN O 204 ASN R 32 GLN ** S 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 45 ASN X 102 GLN X 105 GLN e 96 HIS g 119 GLN ** i 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 127 HIS n 52 ASN n 77 GLN q 112 ASN r 51 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.241 70634 Z= 0.457 Angle : 1.301 50.734 95463 Z= 0.832 Chirality : 0.255 6.475 10263 Planarity : 0.004 0.053 11899 Dihedral : 11.445 177.136 10420 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.24 (0.09), residues: 8202 helix: 1.47 (0.08), residues: 4355 sheet: 0.33 (0.26), residues: 387 loop : 0.17 (0.11), residues: 3460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 780 time to evaluate : 6.305 Fit side-chains outliers start: 134 outliers final: 53 residues processed: 846 average time/residue: 1.5915 time to fit residues: 1765.3630 Evaluate side-chains 789 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 736 time to evaluate : 6.226 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 31 residues processed: 22 average time/residue: 1.0851 time to fit residues: 42.3154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 650 optimal weight: 2.9990 chunk 443 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 581 optimal weight: 7.9990 chunk 322 optimal weight: 0.0470 chunk 666 optimal weight: 3.9990 chunk 539 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 398 optimal weight: 0.6980 chunk 701 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN K 97 GLN O 204 ASN R 32 GLN ** S 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 HIS g 119 GLN ** i 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 127 HIS n 52 ASN o 46 ASN o 53 GLN p 123 ASN s 35 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.244 70634 Z= 0.416 Angle : 1.277 50.567 95463 Z= 0.823 Chirality : 0.253 6.424 10263 Planarity : 0.004 0.051 11899 Dihedral : 11.148 174.933 10420 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.03 % Favored : 97.96 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.41 (0.09), residues: 8202 helix: 1.62 (0.08), residues: 4336 sheet: 0.32 (0.26), residues: 385 loop : 0.25 (0.11), residues: 3481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 764 time to evaluate : 6.350 Fit side-chains outliers start: 99 outliers final: 48 residues processed: 827 average time/residue: 1.5626 time to fit residues: 1703.5734 Evaluate side-chains 789 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 741 time to evaluate : 6.352 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 37 residues processed: 11 average time/residue: 0.9823 time to fit residues: 24.3482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 262 optimal weight: 10.0000 chunk 703 optimal weight: 0.6980 chunk 154 optimal weight: 0.4980 chunk 458 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 781 optimal weight: 3.9990 chunk 648 optimal weight: 3.9990 chunk 361 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 258 optimal weight: 0.7980 chunk 410 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN F 29 HIS K 97 GLN R 32 GLN ** S 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 102 GLN e 96 HIS ** i 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 127 HIS n 52 ASN r 28 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.243 70634 Z= 0.418 Angle : 1.278 50.557 95463 Z= 0.823 Chirality : 0.253 6.421 10263 Planarity : 0.004 0.052 11899 Dihedral : 10.861 174.421 10420 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.14 % Favored : 97.85 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.46 (0.09), residues: 8202 helix: 1.64 (0.08), residues: 4354 sheet: 0.32 (0.26), residues: 385 loop : 0.29 (0.11), residues: 3463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 771 time to evaluate : 6.941 Fit side-chains revert: symmetry clash outliers start: 105 outliers final: 57 residues processed: 826 average time/residue: 1.5563 time to fit residues: 1697.0740 Evaluate side-chains 796 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 739 time to evaluate : 6.227 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 40 residues processed: 17 average time/residue: 1.2441 time to fit residues: 37.5293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 753 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 445 optimal weight: 0.9990 chunk 570 optimal weight: 5.9990 chunk 442 optimal weight: 0.6980 chunk 658 optimal weight: 0.0770 chunk 436 optimal weight: 6.9990 chunk 778 optimal weight: 6.9990 chunk 487 optimal weight: 3.9990 chunk 474 optimal weight: 4.9990 chunk 359 optimal weight: 0.9980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN R 32 GLN S 79 ASN e 96 HIS g 119 GLN i 13 GLN n 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.245 70634 Z= 0.401 Angle : 1.269 50.550 95463 Z= 0.820 Chirality : 0.252 6.388 10263 Planarity : 0.004 0.051 11899 Dihedral : 10.445 173.904 10420 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.98 % Favored : 98.01 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.63 (0.09), residues: 8202 helix: 1.79 (0.08), residues: 4343 sheet: 0.19 (0.25), residues: 414 loop : 0.39 (0.11), residues: 3445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 784 time to evaluate : 6.327 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 55 residues processed: 847 average time/residue: 1.5717 time to fit residues: 1763.7816 Evaluate side-chains 802 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 747 time to evaluate : 6.295 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 42 residues processed: 14 average time/residue: 1.2306 time to fit residues: 32.2846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 481 optimal weight: 0.6980 chunk 311 optimal weight: 7.9990 chunk 465 optimal weight: 0.7980 chunk 234 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 495 optimal weight: 3.9990 chunk 530 optimal weight: 5.9990 chunk 385 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 612 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN F 257 ASN K 97 GLN M 175 ASN R 32 GLN e 96 HIS g 119 GLN n 52 ASN o 43 GLN s 35 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.244 70634 Z= 0.413 Angle : 1.277 50.552 95463 Z= 0.822 Chirality : 0.253 6.409 10263 Planarity : 0.004 0.053 11899 Dihedral : 10.324 173.846 10420 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.08 % Favored : 97.91 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.62 (0.09), residues: 8202 helix: 1.78 (0.08), residues: 4344 sheet: 0.20 (0.25), residues: 412 loop : 0.41 (0.11), residues: 3446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 755 time to evaluate : 6.499 Fit side-chains revert: symmetry clash outliers start: 93 outliers final: 53 residues processed: 813 average time/residue: 1.5453 time to fit residues: 1657.8946 Evaluate side-chains 793 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 740 time to evaluate : 6.322 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 45 residues processed: 8 average time/residue: 1.4990 time to fit residues: 24.5563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 708 optimal weight: 5.9990 chunk 746 optimal weight: 4.9990 chunk 680 optimal weight: 1.9990 chunk 725 optimal weight: 10.0000 chunk 745 optimal weight: 0.9980 chunk 436 optimal weight: 9.9990 chunk 316 optimal weight: 0.3980 chunk 569 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 chunk 655 optimal weight: 0.8980 chunk 686 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN R 32 GLN X 76 HIS e 96 HIS g 119 GLN n 52 ASN o 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.245 70634 Z= 0.401 Angle : 1.273 50.542 95463 Z= 0.821 Chirality : 0.252 6.386 10263 Planarity : 0.004 0.052 11899 Dihedral : 10.048 173.525 10420 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.96 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.72 (0.09), residues: 8202 helix: 1.86 (0.08), residues: 4334 sheet: 0.22 (0.25), residues: 412 loop : 0.45 (0.11), residues: 3456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 775 time to evaluate : 6.572 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 49 residues processed: 821 average time/residue: 1.5805 time to fit residues: 1715.1396 Evaluate side-chains 791 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 742 time to evaluate : 6.233 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 45 residues processed: 4 average time/residue: 1.1136 time to fit residues: 14.6244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 723 optimal weight: 8.9990 chunk 476 optimal weight: 4.9990 chunk 767 optimal weight: 4.9990 chunk 468 optimal weight: 1.9990 chunk 364 optimal weight: 6.9990 chunk 533 optimal weight: 2.9990 chunk 804 optimal weight: 10.0000 chunk 740 optimal weight: 0.9990 chunk 641 optimal weight: 1.9990 chunk 66 optimal weight: 0.0070 chunk 495 optimal weight: 5.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN D 50 ASN R 32 GLN e 96 HIS g 119 GLN n 52 ASN s 35 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.243 70634 Z= 0.426 Angle : 1.287 50.553 95463 Z= 0.825 Chirality : 0.254 6.424 10263 Planarity : 0.004 0.053 11899 Dihedral : 10.088 173.449 10420 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.86 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.61 (0.09), residues: 8202 helix: 1.75 (0.08), residues: 4354 sheet: 0.22 (0.25), residues: 412 loop : 0.42 (0.11), residues: 3436 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16404 Ramachandran restraints generated. 8202 Oldfield, 0 Emsley, 8202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 750 time to evaluate : 6.276 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 46 residues processed: 798 average time/residue: 1.5887 time to fit residues: 1678.8726 Evaluate side-chains 785 residues out of total 7218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 739 time to evaluate : 6.284 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 42 residues processed: 4 average time/residue: 1.5031 time to fit residues: 16.4986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 393 optimal weight: 0.9990 chunk 509 optimal weight: 0.4980 chunk 682 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 591 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 642 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 659 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN R 32 GLN n 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.071357 restraints weight = 228816.405| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.07 r_work: 0.2917 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.245 70634 Z= 0.400 Angle : 1.275 50.545 95463 Z= 0.821 Chirality : 0.252 6.384 10263 Planarity : 0.004 0.053 11899 Dihedral : 9.837 172.749 10420 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.01 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.75 (0.09), residues: 8202 helix: 1.88 (0.08), residues: 4333 sheet: 0.20 (0.25), residues: 424 loop : 0.48 (0.11), residues: 3445 =============================================================================== Job complete usr+sys time: 26194.76 seconds wall clock time: 455 minutes 11.82 seconds (27311.82 seconds total)