Starting phenix.real_space_refine on Thu Mar 14 22:52:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olt_16962/03_2024/8olt_16962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olt_16962/03_2024/8olt_16962.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olt_16962/03_2024/8olt_16962_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/8olt_16962/03_2024/8olt_16962_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olt_16962/03_2024/8olt_16962_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olt_16962/03_2024/8olt_16962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olt_16962/03_2024/8olt_16962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olt_16962/03_2024/8olt_16962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olt_16962/03_2024/8olt_16962_updated.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 36 5.49 5 Mg 1 5.21 5 S 494 5.16 5 Na 1 4.78 5 C 43793 2.51 5 N 11169 2.21 5 O 12552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E ASP 114": "OD1" <-> "OD2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F GLU 388": "OE1" <-> "OE2" Residue "F ARG 423": "NH1" <-> "NH2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F ARG 432": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G ARG 394": "NH1" <-> "NH2" Residue "G ARG 396": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G GLU 441": "OE1" <-> "OE2" Residue "G ARG 460": "NH1" <-> "NH2" Residue "G GLU 512": "OE1" <-> "OE2" Residue "G ARG 515": "NH1" <-> "NH2" Residue "G ARG 534": "NH1" <-> "NH2" Residue "G ARG 579": "NH1" <-> "NH2" Residue "G ARG 594": "NH1" <-> "NH2" Residue "G TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 614": "OD1" <-> "OD2" Residue "G GLU 624": "OE1" <-> "OE2" Residue "G ASP 634": "OD1" <-> "OD2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H ARG 279": "NH1" <-> "NH2" Residue "H PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 21": "OD1" <-> "OD2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I GLU 166": "OE1" <-> "OE2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J GLU 168": "OE1" <-> "OE2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "K PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 197": "OE1" <-> "OE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 436": "NH1" <-> "NH2" Residue "L GLU 445": "OE1" <-> "OE2" Residue "L PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 535": "NH1" <-> "NH2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "M ASP 46": "OD1" <-> "OD2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 187": "OD1" <-> "OD2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 433": "OE1" <-> "OE2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 269": "OE1" <-> "OE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 67": "NH1" <-> "NH2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O ARG 145": "NH1" <-> "NH2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "O GLU 191": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 216": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "O ASP 265": "OD1" <-> "OD2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P ARG 186": "NH1" <-> "NH2" Residue "P PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P ARG 322": "NH1" <-> "NH2" Residue "P TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 14": "OD1" <-> "OD2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q ASP 91": "OD1" <-> "OD2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "S ARG 16": "NH1" <-> "NH2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "S ARG 39": "NH1" <-> "NH2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T GLU 49": "OE1" <-> "OE2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T ASP 82": "OD1" <-> "OD2" Residue "U ASP 9": "OD1" <-> "OD2" Residue "U GLU 28": "OE1" <-> "OE2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 77": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "W ARG 25": "NH1" <-> "NH2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 63": "OD1" <-> "OD2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W ARG 107": "NH1" <-> "NH2" Residue "W ARG 116": "NH1" <-> "NH2" Residue "W ASP 119": "OD1" <-> "OD2" Residue "X GLU 15": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 79": "OE1" <-> "OE2" Residue "X GLU 83": "OE1" <-> "OE2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 148": "OE1" <-> "OE2" Residue "Y TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 12": "OE1" <-> "OE2" Residue "Y ASP 87": "OD1" <-> "OD2" Residue "Y ARG 105": "NH1" <-> "NH2" Residue "Y GLU 132": "OE1" <-> "OE2" Residue "Z TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 57": "NH1" <-> "NH2" Residue "Z ASP 63": "OD1" <-> "OD2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z GLU 77": "OE1" <-> "OE2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z GLU 107": "OE1" <-> "OE2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "Z GLU 122": "OE1" <-> "OE2" Residue "a PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 37": "NH1" <-> "NH2" Residue "a ARG 40": "NH1" <-> "NH2" Residue "a TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "c PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 5": "NH1" <-> "NH2" Residue "c TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "d GLU 9": "OE1" <-> "OE2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 55": "NH1" <-> "NH2" Residue "d PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 120": "NH1" <-> "NH2" Residue "e PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e GLU 41": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 100": "NH1" <-> "NH2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "f TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 30": "OD1" <-> "OD2" Residue "f GLU 46": "OE1" <-> "OE2" Residue "f GLU 51": "OE1" <-> "OE2" Residue "g GLU 29": "OE1" <-> "OE2" Residue "g ARG 57": "NH1" <-> "NH2" Residue "g GLU 85": "OE1" <-> "OE2" Residue "g ARG 88": "NH1" <-> "NH2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "g ARG 93": "NH1" <-> "NH2" Residue "g GLU 120": "OE1" <-> "OE2" Residue "h ASP 18": "OD1" <-> "OD2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h GLU 97": "OE1" <-> "OE2" Residue "h GLU 99": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "h ASP 134": "OD1" <-> "OD2" Residue "h ASP 142": "OD1" <-> "OD2" Residue "i GLU 7": "OE1" <-> "OE2" Residue "i ARG 10": "NH1" <-> "NH2" Residue "i TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 102": "NH1" <-> "NH2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "j GLU 62": "OE1" <-> "OE2" Residue "k TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 25": "NH1" <-> "NH2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "k GLU 54": "OE1" <-> "OE2" Residue "k PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 14": "NH1" <-> "NH2" Residue "l ARG 29": "NH1" <-> "NH2" Residue "l ASP 58": "OD1" <-> "OD2" Residue "l GLU 67": "OE1" <-> "OE2" Residue "l ARG 85": "NH1" <-> "NH2" Residue "l ARG 87": "NH1" <-> "NH2" Residue "l GLU 140": "OE1" <-> "OE2" Residue "l ASP 144": "OD1" <-> "OD2" Residue "l GLU 148": "OE1" <-> "OE2" Residue "m ASP 18": "OD1" <-> "OD2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m ARG 41": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 66": "NH1" <-> "NH2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "m ARG 113": "NH1" <-> "NH2" Residue "m ASP 121": "OD1" <-> "OD2" Residue "m ARG 122": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "n GLU 49": "OE1" <-> "OE2" Residue "n GLU 65": "OE1" <-> "OE2" Residue "n GLU 94": "OE1" <-> "OE2" Residue "n ARG 121": "NH1" <-> "NH2" Residue "n GLU 122": "OE1" <-> "OE2" Residue "n GLU 151": "OE1" <-> "OE2" Residue "n ARG 157": "NH1" <-> "NH2" Residue "n ARG 158": "NH1" <-> "NH2" Residue "n ARG 174": "NH1" <-> "NH2" Residue "o ARG 7": "NH1" <-> "NH2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "o ARG 33": "NH1" <-> "NH2" Residue "o PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o ARG 110": "NH1" <-> "NH2" Residue "p ARG 15": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p ARG 53": "NH1" <-> "NH2" Residue "p ARG 65": "NH1" <-> "NH2" Residue "p ASP 72": "OD1" <-> "OD2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 32": "OD1" <-> "OD2" Residue "q ARG 34": "NH1" <-> "NH2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "q ASP 78": "OD1" <-> "OD2" Residue "q ASP 95": "OD1" <-> "OD2" Residue "q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 122": "OE1" <-> "OE2" Residue "q ARG 131": "NH1" <-> "NH2" Residue "r ARG 11": "NH1" <-> "NH2" Residue "r ASP 18": "OD1" <-> "OD2" Residue "r ARG 26": "NH1" <-> "NH2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r ARG 33": "NH1" <-> "NH2" Residue "r TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 56": "NH1" <-> "NH2" Residue "s ARG 64": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68075 Number of models: 1 Model: "" Number of chains: 106 Chain: "A" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 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: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1730 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "D" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3464 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 403} 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: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1660 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 192} Chain: "F" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3321 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "G" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5296 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 31, 'TRANS': 656} Chain: "H" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2540 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 Chain: "I" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 168} Chain: "J" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1308 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 3, 'TRANS': 168} 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: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} 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: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} 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: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3632 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: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2703 Classifications: {'peptide': 345} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 324} 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: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2607 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "P" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2748 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain: "Q" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1015 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 748 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 628 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "U" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1396 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain: "Y" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1050 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "Z" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1161 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "a" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 564 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "b" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 648 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "c" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 398 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 996 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain: "e" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 877 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "f" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 439 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "g" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 842 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 8, 'TRANS': 91} Chain: "h" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1162 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain: "i" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 869 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1, 'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "j" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 562 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 6, 'TRANS': 58} Chain: "k" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 630 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "l" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1302 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 18, 'TRANS': 136} Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 11, 'TRANS': 114} Chain: "n" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1534 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "o" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1005 Classifications: {'peptide': 117} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 109} Chain: "p" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1439 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain: "q" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1203 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} 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: "r" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 767 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: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 361 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'LMT': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'HQH': 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: {' NA': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'CDL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 219 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 53 Chain: "M" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'3PE': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "N" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "O" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 98 Unusual residues: {' MG': 1, '3PE': 1, 'GTP': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'LMT': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "Y" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "d" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "h" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'CDL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'CDL:plan-2': 1, 'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "j" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "r" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "R" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Z" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "r" 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 1688 SG CYS B 129 96.180 93.500 201.039 1.00 29.19 S ATOM 1191 SG CYS B 65 90.330 95.550 203.274 1.00 31.82 S ATOM 1185 SG CYS B 64 90.788 90.120 200.043 1.00 31.55 S ATOM 1918 SG CYS B 159 93.730 90.586 205.851 1.00 29.53 S ATOM 8180 SG CYS E 103 114.743 44.163 255.669 1.00 46.31 S ATOM 8214 SG CYS E 108 113.040 41.435 257.486 1.00 46.47 S ATOM 8498 SG CYS E 144 117.045 40.922 252.279 1.00 45.92 S ATOM 8521 SG CYS E 148 115.810 38.254 253.163 1.00 47.44 S ATOM 11739 SG CYS F 362 119.712 51.418 232.250 1.00 33.60 S ATOM 11759 SG CYS F 365 116.875 50.633 237.111 1.00 34.39 S ATOM 12081 SG CYS F 405 121.516 46.329 236.106 1.00 36.57 S ATOM 11720 SG CYS F 359 123.248 52.269 237.671 1.00 37.13 S ATOM 13180 SG CYS G 114 115.814 70.119 223.481 1.00 30.83 S ATOM 13119 SG CYS G 105 110.009 72.323 225.257 1.00 29.08 S ATOM 13140 SG CYS G 108 115.552 74.936 227.370 1.00 29.76 S ATOM 13512 SG CYS G 156 124.312 64.042 228.233 1.00 31.70 S ATOM 13489 SG CYS G 153 121.502 66.171 233.759 1.00 30.85 S ATOM 13536 SG CYS G 159 127.534 67.154 232.579 1.00 34.28 S ATOM 13865 SG CYS G 203 123.223 70.125 228.709 1.00 32.12 S ATOM 12626 SG CYS G 41 125.004 57.392 225.591 1.00 32.19 S ATOM 12712 SG CYS G 52 121.211 57.807 224.714 1.00 31.73 S ATOM 12737 SG CYS G 55 122.826 53.361 221.324 1.00 32.52 S ATOM 12838 SG CYS G 69 126.062 54.189 222.526 1.00 32.68 S ATOM 21162 SG CYS I 121 97.312 85.074 211.594 1.00 27.21 S ATOM 21136 SG CYS I 118 97.322 91.541 212.639 1.00 27.25 S ATOM 21183 SG CYS I 124 98.730 87.121 217.281 1.00 27.17 S ATOM 20910 SG CYS I 89 102.749 88.132 212.192 1.00 27.65 S ATOM 21212 SG CYS I 128 101.277 83.902 224.584 1.00 27.78 S ATOM 20882 SG CYS I 85 104.728 86.521 219.791 1.00 27.24 S ATOM 20840 SG CYS I 79 106.079 88.185 225.748 1.00 29.35 S ATOM 20859 SG CYS I 82 106.837 81.948 223.138 1.00 29.19 S ATOM 41652 SG CYS R 59 103.058 79.034 239.772 1.00 35.08 S ATOM 41828 SG CYS R 84 106.043 79.705 237.765 1.00 34.62 S ATOM 41850 SG CYS R 87 103.773 82.283 238.584 1.00 33.39 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C10 HQH D 601 " occ=0.50 ... (28 atoms not shown) pdb=" O4 HQH D 601 " occ=0.50 Time building chain proxies: 28.37, per 1000 atoms: 0.42 Number of scatterers: 68075 At special positions: 0 Unit cell: (187, 191.25, 289, 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 S 494 16.00 P 36 15.00 Mg 1 11.99 Na 1 11.00 O 12552 8.00 N 11169 7.00 C 43793 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=2.04 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 19 " - pdb=" SG CYS Y 76 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 96 " - pdb=" SG CYS Y 116 " 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=2.04 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.34 Conformation dependent library (CDL) restraints added in 10.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb=" FES G 803 " 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="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 159 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 65 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 365 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 405 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 359 " pdb="FE1 SF4 F 501 " - 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="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 118 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 89 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 124 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 121 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 85 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 128 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 82 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 79 " 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 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 360 helices and 29 sheets defined 52.7% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.53 Creating SS restraints... Processing helix chain 'A' and resid 3 through 24 removed outlier: 3.705A pdb=" N ILE A 7 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 34 No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.598A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.511A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.732A 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 35 through 53 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 104 through 115 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 163 through 178 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'C' and resid 17 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.817A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.691A pdb=" N PHE C 63 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 64 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.058A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 134 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 137 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 3.815A 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: 3.937A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 removed outlier: 4.311A pdb=" N HIS D 27 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.788A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 removed outlier: 3.833A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 105' 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: 3.589A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.926A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) 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: 4.444A 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 293 through 317 removed outlier: 3.646A 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 removed outlier: 3.576A pdb=" N HIS D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 420 removed outlier: 3.798A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 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 29 through 37 removed outlier: 3.534A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 56 removed outlier: 4.460A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.768A pdb=" N ALA E 54 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.664A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 4.145A pdb=" N ARG E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 166 through 177 removed outlier: 3.625A 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 38 removed outlier: 4.069A pdb=" N ARG F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) 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 80 Processing helix chain 'F' and resid 106 through 113 removed outlier: 3.672A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 128 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 196 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: 3.691A pdb=" N VAL F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.725A 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 removed outlier: 3.613A pdb=" N HIS F 283 " --> pdb=" O LEU F 279 " (cutoff:3.500A) 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 310 through 312 No H-bonds generated for 'chain 'F' and resid 310 through 312' Processing helix chain 'F' and resid 321 through 324 No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.668A pdb=" N ARG F 349 " --> pdb=" O LYS F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.007A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG F 378 " --> pdb=" O LYS F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 4.463A pdb=" N ASP F 390 " --> pdb=" O PRO F 386 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 421 Proline residue: F 414 - end of helix Processing helix chain 'F' and resid 423 through 437 removed outlier: 3.690A pdb=" N GLN F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 32 removed outlier: 3.718A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 97 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 122 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 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 275 removed outlier: 4.950A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.919A pdb=" N ASN G 309 " --> pdb=" O GLY G 305 " (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: 3.783A pdb=" N ALA G 330 " --> pdb=" O GLU G 326 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' 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 400 Processing helix chain 'G' and resid 428 through 434 Processing helix chain 'G' and resid 438 through 445 removed outlier: 3.939A pdb=" N LYS G 444 " --> pdb=" O GLU G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 480 removed outlier: 3.708A pdb=" N GLN G 475 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL G 479 " --> pdb=" O GLN G 475 " (cutoff:3.500A) 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 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 606 removed outlier: 3.815A pdb=" N ILE G 600 " --> pdb=" O ASP G 596 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 630 No H-bonds generated for 'chain 'G' and resid 628 through 630' Processing helix chain 'G' and resid 642 through 649 Processing helix chain 'G' and resid 668 through 671 Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 682 through 692 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix 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 57 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.300A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.743A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 155 removed outlier: 4.974A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 170 removed outlier: 4.143A pdb=" N THR H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU H 170 " --> pdb=" O ILE H 166 " (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 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: 3.626A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 291 removed outlier: 3.594A 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 16 through 27 Processing helix chain 'I' and resid 30 through 44 removed outlier: 3.719A pdb=" N PHE I 44 " --> pdb=" O LEU I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'I' and resid 153 through 172 removed outlier: 5.358A pdb=" N ALA I 165 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLU I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA I 169 " --> pdb=" O ALA I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 177 No H-bonds generated for 'chain 'I' and resid 175 through 177' Processing helix chain 'J' and resid 4 through 21 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 50 through 73 removed outlier: 3.617A pdb=" N ALA J 72 " --> pdb=" O GLY J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 106 removed outlier: 3.511A pdb=" N CYS J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 119 No H-bonds generated for 'chain 'J' and resid 117 through 119' Processing helix chain 'J' and resid 137 through 145 removed outlier: 4.806A pdb=" N MET J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 170 removed outlier: 3.775A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 26 through 51 removed outlier: 3.522A pdb=" N VAL K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 85 Proline residue: K 58 - end of helix removed outlier: 3.557A pdb=" N ALA K 68 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N CYS K 69 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY K 74 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL K 81 " --> pdb=" O LEU K 78 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN K 83 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR K 84 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' 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 23 removed outlier: 4.171A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE L 13 " --> pdb=" O LEU L 9 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.535A pdb=" N MET L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 28 Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.983A pdb=" N LEU 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 removed outlier: 3.638A pdb=" N SER L 91 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN L 102 " --> pdb=" O TRP L 98 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TRP L 106 " --> pdb=" O GLN L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 removed outlier: 3.527A pdb=" N LYS L 119 " --> pdb=" O ASN L 115 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 removed outlier: 3.557A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 192 removed outlier: 4.103A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.220A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 3.907A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.508A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 269 removed outlier: 4.215A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE L 263 " --> pdb=" O LEU L 260 " (cutoff:3.500A) Proline residue: L 265 - end of helix removed outlier: 4.414A pdb=" N THR L 268 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 4.466A pdb=" N THR L 294 " --> pdb=" O ILE L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 319 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.305A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.102A 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 380 Processing helix chain 'L' and resid 389 through 400 removed outlier: 5.568A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN L 400 " --> pdb=" O ILE L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 4.004A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 Proline residue: L 453 - end of helix removed outlier: 6.269A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE L 466 " --> pdb=" O ILE 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: 3.687A pdb=" N ILE L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE L 536 " --> pdb=" O ILE L 533 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.703A pdb=" N SER L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER L 545 " --> pdb=" O LEU L 542 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS L 547 " --> pdb=" O LEU L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 576 Processing helix chain 'L' and resid 584 through 605 removed outlier: 3.673A pdb=" N ASN L 605 " --> pdb=" O LEU L 601 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 17 removed outlier: 3.571A pdb=" N LEU M 11 " --> pdb=" O PRO M 7 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU M 12 " --> pdb=" O SER M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 3.681A pdb=" N PHE M 32 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 136 removed outlier: 3.537A pdb=" N THR M 125 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE 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: 3.591A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY M 146 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE M 147 " --> pdb=" O ASN M 144 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE M 158 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.505A pdb=" N LEU M 164 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 181 Processing helix chain 'M' and resid 190 through 206 removed outlier: 3.701A pdb=" N LEU M 194 " --> pdb=" O TRP M 190 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.587A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU M 222 " --> pdb=" O LYS M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 250 removed outlier: 4.120A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 4.324A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 277 removed outlier: 3.930A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.058A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE M 303 " --> pdb=" O ALA M 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.599A pdb=" N SER M 324 " --> pdb=" O GLY M 320 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.604A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE M 402 " --> pdb=" O ASN M 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE M 412 " --> pdb=" O TYR M 409 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR M 414 " --> pdb=" O ILE M 411 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 44 removed outlier: 3.726A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) 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: 4.337A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 131 Processing helix chain 'N' and resid 133 through 145 removed outlier: 4.507A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.660A pdb=" N ILE N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.942A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Proline residue: N 214 - end of helix removed outlier: 4.283A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.741A pdb=" N LEU N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 4.302A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE N 244 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER N 245 " --> pdb=" O THR N 242 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU N 246 " --> pdb=" O MET N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 276 through 300 removed outlier: 3.654A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN N 289 " --> pdb=" O MET N 285 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 324 through 332 Processing helix chain 'N' and resid 337 through 344 Proline residue: N 341 - end of helix removed outlier: 4.318A pdb=" N ILE N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 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 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 through 140 Processing helix chain 'O' and resid 146 through 162 Proline residue: O 161 - end of helix 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 214 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 238 Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 263 removed outlier: 3.758A pdb=" N TYR O 258 " --> pdb=" O TRP O 254 " (cutoff:3.500A) 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 Processing helix chain 'O' and resid 286 through 298 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 29 through 40 removed outlier: 4.183A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 3.534A pdb=" N MET P 57 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU P 61 " --> pdb=" O HIS P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 87 removed outlier: 5.586A pdb=" N HIS P 87 " --> pdb=" O LYS P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 Processing helix chain 'P' and resid 144 through 159 removed outlier: 3.501A pdb=" N ALA P 150 " --> pdb=" O LEU P 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 188 removed outlier: 3.601A pdb=" N TYR P 185 " --> pdb=" O HIS P 181 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 4.736A 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 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 249 Processing helix chain 'P' and resid 260 through 272 removed outlier: 3.547A pdb=" N LEU P 269 " --> pdb=" O TRP P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 288 removed outlier: 3.607A pdb=" N HIS P 288 " --> pdb=" O VAL P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 303 No H-bonds generated for 'chain 'P' and resid 301 through 303' Processing helix chain 'P' and resid 310 through 321 removed outlier: 5.204A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL P 317 " --> pdb=" O LYS P 313 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 324 through 326 No H-bonds generated for 'chain 'P' and resid 324 through 326' Processing helix chain 'P' and resid 331 through 333 No H-bonds generated for 'chain 'P' and resid 331 through 333' 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: 4.065A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 removed outlier: 3.653A pdb=" N PHE Q 122 " --> pdb=" O GLY Q 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 28 removed outlier: 3.613A pdb=" N ARG R 27 " --> pdb=" O ARG R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.670A pdb=" N GLN 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 27 through 46 removed outlier: 4.943A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN S 38 " --> pdb=" O PHE S 35 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR S 40 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL S 41 " --> pdb=" O GLN S 38 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS S 44 " --> pdb=" O VAL S 41 " (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 removed outlier: 3.517A pdb=" N ALA S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 21 removed outlier: 3.524A pdb=" N LEU T 16 " --> pdb=" O LYS T 12 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU T 19 " --> pdb=" O VAL T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 58 removed outlier: 3.577A pdb=" N GLU T 49 " --> pdb=" O LEU T 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.866A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 removed outlier: 3.547A pdb=" N LEU U 21 " --> pdb=" O TYR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 27 through 29 No H-bonds generated for 'chain 'U' and resid 27 through 29' Processing helix chain 'U' and resid 44 through 58 removed outlier: 3.996A pdb=" N GLU U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 69 removed outlier: 5.106A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 83 Processing helix chain 'V' and resid 19 through 36 removed outlier: 3.701A pdb=" N LYS V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 removed outlier: 3.569A pdb=" N MET V 57 " --> pdb=" O GLU V 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL V 58 " --> pdb=" O LYS V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 71 removed outlier: 3.642A pdb=" N ALA V 69 " --> pdb=" O LYS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.683A pdb=" N LYS V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 51 removed outlier: 4.120A pdb=" N ARG W 33 " --> pdb=" O GLU W 29 " (cutoff:3.500A) Proline residue: W 46 - end of helix Processing helix chain 'W' and resid 58 through 70 Processing helix chain 'W' and resid 78 through 96 Processing helix chain 'W' and resid 102 through 109 removed outlier: 4.241A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE W 109 " --> pdb=" O VAL W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 33 Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 55 removed outlier: 3.530A pdb=" N CYS X 55 " --> pdb=" O PRO X 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 52 through 55' Processing helix chain 'X' and resid 58 through 73 removed outlier: 3.619A pdb=" N ASN X 63 " --> pdb=" O GLY X 59 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE X 73 " --> pdb=" O PHE X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 88 removed outlier: 3.507A pdb=" N TYR X 84 " --> pdb=" O PRO X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 100 through 114 removed outlier: 3.561A pdb=" N LYS X 105 " --> pdb=" O GLN X 101 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP X 112 " --> pdb=" O GLN X 108 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 11 removed outlier: 3.780A pdb=" N PHE Y 7 " --> pdb=" O VAL Y 3 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR Y 10 " --> pdb=" O PHE Y 6 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS Y 11 " --> pdb=" O PHE Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 44 Processing helix chain 'Y' and resid 51 through 81 removed outlier: 3.698A pdb=" N CYS Y 76 " --> pdb=" O GLY Y 72 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN Y 80 " --> pdb=" O CYS Y 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 106 Processing helix chain 'Y' and resid 109 through 132 Processing helix chain 'Z' and resid 31 through 96 Proline residue: Z 72 - end of helix removed outlier: 3.518A pdb=" N GLU Z 92 " --> pdb=" O GLU Z 88 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE Z 95 " --> pdb=" O GLU Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 123 No H-bonds generated for 'chain 'Z' and resid 120 through 123' Processing helix chain 'Z' and resid 129 through 141 removed outlier: 5.759A pdb=" N PHE Z 139 " --> pdb=" O ALA Z 135 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N THR Z 140 " --> pdb=" O ASN Z 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 29 Proline residue: a 7 - end of helix removed outlier: 3.853A pdb=" N ALA a 10 " --> pdb=" O PRO a 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET a 12 " --> pdb=" O LEU a 9 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.566A pdb=" N SER a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS a 27 " --> pdb=" O ALA a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 3 through 14 Processing helix chain 'b' and resid 16 through 34 removed outlier: 3.609A pdb=" N ILE b 29 " --> pdb=" O TRP b 25 " (cutoff:3.500A) Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 46 removed outlier: 4.538A pdb=" N SER b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 81 No H-bonds generated for 'chain 'b' and resid 78 through 81' Processing helix chain 'c' and resid 14 through 46 removed outlier: 3.528A pdb=" N ASN c 46 " --> pdb=" O TYR c 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 Processing helix chain 'd' and resid 98 through 100 No H-bonds generated for 'chain 'd' and resid 98 through 100' 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 48 through 54 removed outlier: 4.043A pdb=" N LYS e 53 " --> pdb=" O THR 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 97 No H-bonds generated for 'chain 'e' and resid 95 through 97' Processing helix chain 'f' and resid 10 through 31 removed outlier: 4.645A pdb=" N VAL f 15 " --> pdb=" O HIS f 12 " (cutoff:3.500A) Proline residue: f 16 - end of helix removed outlier: 3.694A pdb=" N ASP f 30 " --> pdb=" O ARG f 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 38 No H-bonds generated for 'chain 'g' and resid 35 through 38' Processing helix chain 'g' and resid 49 through 63 Processing helix chain 'g' and resid 67 through 76 Processing helix chain 'g' and resid 81 through 83 No H-bonds generated for 'chain 'g' and resid 81 through 83' Processing helix chain 'g' and resid 86 through 100 Processing helix chain 'g' and resid 113 through 115 No H-bonds generated for 'chain 'g' and resid 113 through 115' Processing helix chain 'h' and resid 16 through 45 removed outlier: 3.835A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 63 through 66 Processing helix chain 'h' and resid 70 through 79 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 removed outlier: 3.657A pdb=" N ASP i 24 " --> pdb=" O ARG i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 64 through 70 removed outlier: 3.588A pdb=" N LEU i 68 " --> pdb=" O TYR i 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE i 69 " --> pdb=" O ARG i 65 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA i 70 " --> pdb=" O SER i 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 64 through 70' Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 44 through 48 removed outlier: 3.518A pdb=" N LEU j 48 " --> pdb=" O ASP j 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 33 through 44 removed outlier: 4.088A pdb=" N ARG k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 53 No H-bonds generated for 'chain 'k' and resid 51 through 53' Processing helix chain 'k' and resid 55 through 58 Processing helix chain 'k' and resid 60 through 62 No H-bonds generated for 'chain 'k' and resid 60 through 62' Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 76 through 93 Processing helix chain 'l' and resid 5 through 7 No H-bonds generated for 'chain 'l' and resid 5 through 7' Processing helix chain 'l' and resid 16 through 26 Processing helix chain 'l' and resid 54 through 56 No H-bonds generated for 'chain 'l' and resid 54 through 56' Processing helix chain 'l' and resid 80 through 83 No H-bonds generated for 'chain 'l' and resid 80 through 83' Processing helix chain 'l' and resid 97 through 120 Processing helix chain 'l' and resid 133 through 137 Processing helix chain 'm' and resid 15 through 17 No H-bonds generated for 'chain 'm' and resid 15 through 17' Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 50 removed outlier: 3.677A pdb=" N LEU m 36 " --> pdb=" O GLN m 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 70 Processing helix chain 'm' and resid 76 through 78 No H-bonds generated for 'chain 'm' and resid 76 through 78' Processing helix chain 'm' and resid 83 through 116 Proline residue: m 96 - end of helix removed outlier: 3.559A pdb=" N GLN m 116 " --> pdb=" O GLU m 112 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 51 removed outlier: 4.409A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS n 51 " --> pdb=" O PHE n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 70 removed outlier: 3.612A pdb=" N GLU n 65 " --> pdb=" O GLN n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 96 No H-bonds generated for 'chain 'n' and resid 94 through 96' Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 113 removed outlier: 4.147A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 119 through 141 removed outlier: 3.714A pdb=" N GLN n 123 " --> pdb=" O SER n 119 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP n 124 " --> pdb=" O LYS n 120 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.767A 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 2 through 7 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 116 removed outlier: 3.556A pdb=" N GLU o 100 " --> pdb=" O LYS o 96 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE o 101 " --> pdb=" O ARG o 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS o 112 " --> pdb=" O LEU o 108 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 removed outlier: 3.537A pdb=" N LEU p 32 " --> pdb=" O PRO p 28 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS p 34 " --> pdb=" O THR p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 57 removed outlier: 3.504A pdb=" N LYS p 57 " --> pdb=" O ARG p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 81 through 123 removed outlier: 3.777A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 removed outlier: 3.589A pdb=" N LYS p 136 " --> pdb=" O THR p 132 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 169 removed outlier: 3.797A pdb=" N ALA p 168 " --> pdb=" O GLU p 164 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 14 Processing helix chain 'q' and resid 19 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: 3.703A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 3.972A 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 's' and resid 36 through 39 Processing helix chain 's' and resid 44 through 54 removed outlier: 3.595A pdb=" N LEU s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER s 53 " --> pdb=" O ASN s 49 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.394A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE B 154 " --> pdb=" O SER B 125 " (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: 6.702A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR C 110 " --> pdb=" O ILE C 52 " (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: 3.538A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.270A 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 368 Processing sheet with id= F, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.624A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS E 103 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N MET E 153 " --> pdb=" O CYS E 103 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 220 through 224 removed outlier: 6.813A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 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 56 through 58 Processing sheet with id= K, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= L, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= M, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.702A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= O, first strand: chain 'G' and resid 342 through 345 removed outlier: 4.768A pdb=" N ASN G 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.278A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU G 378 " --> pdb=" O VAL G 452 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= R, first strand: chain 'I' and resid 67 through 69 Processing sheet with id= S, first strand: chain 'I' and resid 94 through 100 removed outlier: 6.213A pdb=" N GLU I 99 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR I 108 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.683A pdb=" N MET L 78 " --> pdb=" O THR L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.224A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.786A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL P 90 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= X, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= Y, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= Z, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= AA, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AB, first strand: chain 'S' and resid 51 through 56 removed outlier: 3.850A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS S 63 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.764A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2744 hydrogen bonds defined for protein. 7632 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: 20.00 Time building geometry restraints manager: 23.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 28006 1.40 - 1.62: 40542 1.62 - 1.85: 873 1.85 - 2.07: 0 2.07 - 2.30: 80 Bond restraints: 69501 Sorted by residual: bond pdb=" C6 GTP O 502 " pdb=" O6 GTP O 502 " ideal model delta sigma weight residual 1.230 1.395 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" C5 GTP O 502 " pdb=" N7 GTP O 502 " ideal model delta sigma weight residual 1.350 1.514 -0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" C4 FMN F 502 " pdb=" O4 FMN F 502 " ideal model delta sigma weight residual 1.230 1.391 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C2 FMN F 502 " pdb=" O2 FMN F 502 " ideal model delta sigma weight residual 1.230 1.389 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" C24 HQH D 601 " pdb=" N5 HQH D 601 " ideal model delta sigma weight residual 1.498 1.361 0.137 2.00e-02 2.50e+03 4.66e+01 ... (remaining 69496 not shown) Histogram of bond angle deviations from ideal: 73.02 - 85.26: 76 85.26 - 97.49: 3 97.49 - 109.73: 10674 109.73 - 121.97: 71449 121.97 - 134.21: 11901 Bond angle restraints: 94103 Sorted by residual: angle pdb=" O AME q 1 " pdb=" C AME q 1 " pdb=" N GLU q 2 " ideal model delta sigma weight residual 123.00 97.67 25.33 1.60e+00 3.91e-01 2.51e+02 angle pdb=" C14 HQH D 601 " pdb=" C9 HQH D 601 " pdb=" C7 HQH D 601 " ideal model delta sigma weight residual 68.20 114.00 -45.80 3.00e+00 1.11e-01 2.33e+02 angle pdb=" C18 HQH D 601 " pdb=" C11 HQH D 601 " pdb=" C22 HQH D 601 " ideal model delta sigma weight residual 74.50 117.37 -42.87 3.00e+00 1.11e-01 2.04e+02 angle pdb=" C13 HQH D 601 " pdb=" C20 HQH D 601 " pdb=" C17 HQH D 601 " ideal model delta sigma weight residual 85.93 126.05 -40.12 3.00e+00 1.11e-01 1.79e+02 angle pdb=" C16 HQH D 601 " pdb=" C9 HQH D 601 " pdb=" C7 HQH D 601 " ideal model delta sigma weight residual 85.85 123.90 -38.05 3.00e+00 1.11e-01 1.61e+02 ... (remaining 94098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 41332 35.34 - 70.68: 1035 70.68 - 106.02: 173 106.02 - 141.35: 37 141.35 - 176.69: 9 Dihedral angle restraints: 42586 sinusoidal: 18622 harmonic: 23964 Sorted by residual: dihedral pdb=" O2G GTP O 502 " pdb=" O3B GTP O 502 " pdb=" PG GTP O 502 " pdb=" PB GTP O 502 " ideal model delta sinusoidal sigma weight residual 177.30 0.61 176.69 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 81.97 175.62 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3B GTP O 502 " pdb=" O3A GTP O 502 " pdb=" PB GTP O 502 " pdb=" PA GTP O 502 " ideal model delta sinusoidal sigma weight residual 291.08 116.40 174.68 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 42583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.247: 10325 4.247 - 8.495: 0 8.495 - 12.742: 0 12.742 - 16.989: 0 16.989 - 21.236: 24 Chirality restraints: 10349 Sorted by residual: chirality pdb="FE2 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S3 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.68 21.24 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.66 -21.21 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.63 -21.19 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10346 not shown) Planarity restraints: 11699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 HQH D 601 " -0.067 2.00e-02 2.50e+03 1.93e-01 4.67e+02 pdb=" C18 HQH D 601 " 0.167 2.00e-02 2.50e+03 pdb=" C22 HQH D 601 " -0.009 2.00e-02 2.50e+03 pdb=" C6 HQH D 601 " 0.229 2.00e-02 2.50e+03 pdb=" C8 HQH D 601 " -0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AME q 1 " -0.102 2.00e-02 2.50e+03 1.74e-01 3.04e+02 pdb=" C AME q 1 " 0.302 2.00e-02 2.50e+03 pdb=" O AME q 1 " -0.106 2.00e-02 2.50e+03 pdb=" N GLU q 2 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SAC i 1 " -0.040 2.00e-02 2.50e+03 8.30e-02 6.88e+01 pdb=" C SAC i 1 " 0.143 2.00e-02 2.50e+03 pdb=" O SAC i 1 " -0.050 2.00e-02 2.50e+03 pdb=" N GLY i 2 " -0.053 2.00e-02 2.50e+03 ... (remaining 11696 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 485 2.48 - 3.08: 49535 3.08 - 3.69: 104608 3.69 - 4.29: 170582 4.29 - 4.90: 272874 Nonbonded interactions: 598084 Sorted by model distance: nonbonded pdb=" O ARG B 121 " pdb=" O HOH B 301 " model vdw 1.872 2.440 nonbonded pdb=" OE1 GLN P 86 " pdb=" O HOH P 601 " model vdw 1.920 2.440 nonbonded pdb=" OD2 ASP q 78 " pdb=" OG SER q 80 " model vdw 1.924 2.440 nonbonded pdb=" OE1 GLN G 110 " pdb=" O HOH G 901 " model vdw 1.929 2.440 nonbonded pdb=" OH TYR L 587 " pdb=" OE2 GLU N 117 " model vdw 1.931 2.440 ... (remaining 598079 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 6 through 83 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 29.090 Check model and map are aligned: 0.790 Set scattering table: 0.460 Process input model: 157.540 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.010 0.165 69501 Z= 0.635 Angle : 0.926 45.801 94103 Z= 0.425 Chirality : 1.019 21.236 10349 Planarity : 0.005 0.193 11699 Dihedral : 16.667 176.692 27103 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 0.38 % Allowed : 3.15 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.43 (0.09), residues: 8106 helix: -1.05 (0.07), residues: 4286 sheet: -0.65 (0.25), residues: 407 loop : -0.60 (0.11), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 254 HIS 0.008 0.001 HIS D 190 PHE 0.030 0.002 PHE M 151 TYR 0.024 0.002 TYR O 58 ARG 0.014 0.001 ARG l 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1356 time to evaluate : 6.187 Fit side-chains revert: symmetry clash REVERT: A 83 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7576 (mtpp) REVERT: B 45 ASP cc_start: 0.7749 (m-30) cc_final: 0.7530 (m-30) REVERT: B 79 MET cc_start: 0.8088 (ptt) cc_final: 0.7759 (ptt) REVERT: C 20 LYS cc_start: 0.8179 (tppp) cc_final: 0.7730 (ttpp) REVERT: C 78 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8910 (tp) REVERT: D 27 HIS cc_start: 0.7071 (p90) cc_final: 0.6866 (p90) REVERT: D 59 HIS cc_start: 0.8072 (m170) cc_final: 0.7857 (m-70) REVERT: D 75 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8035 (ttmt) REVERT: D 152 MET cc_start: 0.8557 (tpp) cc_final: 0.8161 (tpp) REVERT: E 10 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7155 (mtm-85) REVERT: E 40 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7018 (mt-10) REVERT: E 114 ASP cc_start: 0.7178 (t70) cc_final: 0.6917 (t0) REVERT: E 134 ASP cc_start: 0.7036 (m-30) cc_final: 0.6802 (m-30) REVERT: E 153 MET cc_start: 0.7705 (ppp) cc_final: 0.7459 (ppp) REVERT: F 317 MET cc_start: 0.8247 (mmp) cc_final: 0.7841 (mmm) REVERT: G 276 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7634 (mtt-85) REVERT: G 556 MET cc_start: 0.8051 (ptp) cc_final: 0.7827 (ptp) REVERT: G 622 ARG cc_start: 0.8435 (tpt170) cc_final: 0.8130 (tpt170) REVERT: H 62 ARG cc_start: 0.7071 (mtm180) cc_final: 0.6830 (mtp85) REVERT: H 163 GLN cc_start: 0.8231 (tt0) cc_final: 0.7991 (mt0) REVERT: I 16 MET cc_start: 0.7269 (tpt) cc_final: 0.6997 (tpt) REVERT: I 17 LYS cc_start: 0.7842 (tptp) cc_final: 0.7341 (tmmt) REVERT: I 131 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8519 (m-30) REVERT: I 174 ASP cc_start: 0.8466 (t0) cc_final: 0.8118 (t0) REVERT: J 91 PHE cc_start: 0.8251 (m-80) cc_final: 0.7857 (m-80) REVERT: L 23 MET cc_start: 0.8396 (mtp) cc_final: 0.8013 (mtp) REVERT: L 59 MET cc_start: 0.7983 (ttp) cc_final: 0.7772 (ttm) REVERT: L 78 MET cc_start: 0.7971 (ttm) cc_final: 0.7707 (ttm) REVERT: L 115 ASN cc_start: 0.7738 (p0) cc_final: 0.7229 (p0) REVERT: L 327 LEU cc_start: 0.8228 (tp) cc_final: 0.7902 (tm) REVERT: L 366 MET cc_start: 0.8759 (mtp) cc_final: 0.8412 (mtm) REVERT: M 98 MET cc_start: 0.8507 (mmp) cc_final: 0.7995 (mmp) REVERT: M 139 GLN cc_start: 0.7789 (mm110) cc_final: 0.7449 (mp10) REVERT: M 177 MET cc_start: 0.8014 (mtm) cc_final: 0.7494 (mtm) REVERT: N 282 MET cc_start: 0.8373 (mtp) cc_final: 0.8068 (mtm) REVERT: N 285 MET cc_start: 0.8398 (mmm) cc_final: 0.8186 (mmm) REVERT: O 67 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7452 (mtm-85) REVERT: O 213 LYS cc_start: 0.8553 (tptp) cc_final: 0.8023 (ttpp) REVERT: O 265 ASP cc_start: 0.7761 (t0) cc_final: 0.7359 (t70) REVERT: P 78 LYS cc_start: 0.7431 (mmtm) cc_final: 0.7136 (tptt) REVERT: P 123 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7119 (mt-10) REVERT: P 310 LEU cc_start: 0.9098 (tp) cc_final: 0.8889 (tp) REVERT: P 341 ASN cc_start: 0.7394 (p0) cc_final: 0.7156 (p0) REVERT: Q 45 MET cc_start: 0.9117 (mmm) cc_final: 0.8907 (mmm) REVERT: Q 104 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7470 (p0) REVERT: Q 107 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7961 (mm-30) REVERT: R 21 LYS cc_start: 0.8521 (mttt) cc_final: 0.8149 (mtmm) REVERT: R 92 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8033 (ttpt) REVERT: S 39 ARG cc_start: 0.7873 (mpt-90) cc_final: 0.7667 (mmt90) REVERT: U 12 LYS cc_start: 0.8406 (ttpp) cc_final: 0.8192 (tmmt) REVERT: U 29 LYS cc_start: 0.7034 (mptt) cc_final: 0.6822 (mptp) REVERT: U 57 GLU cc_start: 0.8157 (tp30) cc_final: 0.7908 (tp30) REVERT: V 85 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8027 (mmmm) REVERT: V 93 MET cc_start: 0.8826 (mmm) cc_final: 0.8586 (mmp) REVERT: V 109 ASN cc_start: 0.7814 (m-40) cc_final: 0.7470 (p0) REVERT: W 63 ASP cc_start: 0.7518 (m-30) cc_final: 0.6899 (m-30) REVERT: X 101 GLN cc_start: 0.7610 (tm-30) cc_final: 0.7262 (mp-120) REVERT: X 102 GLN cc_start: 0.8386 (mp10) cc_final: 0.8173 (mp10) REVERT: X 108 GLN cc_start: 0.8288 (tp40) cc_final: 0.8054 (tp-100) REVERT: X 123 GLN cc_start: 0.9069 (mt0) cc_final: 0.8775 (mt0) REVERT: X 131 LYS cc_start: 0.8443 (mtpp) cc_final: 0.8201 (ttpp) REVERT: Y 4 LYS cc_start: 0.7632 (tttm) cc_final: 0.7346 (ttmm) REVERT: Y 10 TYR cc_start: 0.8557 (t80) cc_final: 0.8161 (t80) REVERT: Y 21 ARG cc_start: 0.7219 (tpt170) cc_final: 0.6896 (tpt-90) REVERT: Y 119 MET cc_start: 0.7917 (mtp) cc_final: 0.7535 (mtp) REVERT: Z 43 ILE cc_start: 0.8987 (mm) cc_final: 0.8765 (mt) REVERT: Z 113 THR cc_start: 0.8339 (p) cc_final: 0.8069 (m) REVERT: a 35 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7736 (mt-10) REVERT: a 36 LYS cc_start: 0.8946 (tttm) cc_final: 0.8728 (tttm) REVERT: b 46 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7721 (tttt) REVERT: c 11 LYS cc_start: 0.7836 (mttm) cc_final: 0.7621 (mmmm) REVERT: c 44 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7724 (ttp-110) REVERT: d 9 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7370 (mm-30) REVERT: d 34 MET cc_start: 0.8403 (mmm) cc_final: 0.8202 (mmp) REVERT: d 44 MET cc_start: 0.7412 (tpt) cc_final: 0.7050 (tpp) REVERT: d 50 MET cc_start: 0.8325 (mtp) cc_final: 0.7956 (mtp) REVERT: d 55 ARG cc_start: 0.7002 (mtt90) cc_final: 0.6760 (mtt90) REVERT: d 95 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7694 (mptt) REVERT: e 27 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7874 (mmtm) REVERT: e 36 GLU cc_start: 0.7891 (tt0) cc_final: 0.7669 (tt0) REVERT: f 27 ARG cc_start: 0.8330 (mtm110) cc_final: 0.7984 (mtm110) REVERT: f 41 MET cc_start: 0.7408 (mmm) cc_final: 0.6936 (mmt) REVERT: g 29 GLU cc_start: 0.7208 (tt0) cc_final: 0.6965 (mt-10) REVERT: g 57 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8211 (mtt180) REVERT: g 107 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6970 (tp30) REVERT: g 108 SER cc_start: 0.7913 (m) cc_final: 0.7705 (t) REVERT: h 25 MET cc_start: 0.8318 (ttp) cc_final: 0.7973 (ttm) REVERT: h 100 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8738 (mtmm) REVERT: i 26 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7247 (mt-10) REVERT: j 40 PHE cc_start: 0.8562 (t80) cc_final: 0.8251 (t80) REVERT: k 25 ARG cc_start: 0.7659 (mtm-85) cc_final: 0.7417 (mtt180) REVERT: l 70 MET cc_start: 0.8264 (mmm) cc_final: 0.7993 (mmt) REVERT: m 35 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7988 (mtt-85) REVERT: m 57 SER cc_start: 0.8669 (p) cc_final: 0.8436 (p) REVERT: m 105 LYS cc_start: 0.8273 (tptp) cc_final: 0.7749 (tptp) REVERT: m 109 ASP cc_start: 0.7629 (m-30) cc_final: 0.7296 (m-30) REVERT: m 110 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6604 (ttp-170) REVERT: n 8 TYR cc_start: 0.8302 (p90) cc_final: 0.8080 (p90) REVERT: n 51 LYS cc_start: 0.7860 (tttp) cc_final: 0.7393 (tttm) REVERT: n 61 GLN cc_start: 0.7455 (tm-30) cc_final: 0.7112 (tm-30) REVERT: o 10 TRP cc_start: 0.4870 (m-10) cc_final: 0.4663 (m-10) REVERT: o 43 GLN cc_start: 0.8359 (tp40) cc_final: 0.8049 (tp-100) REVERT: o 47 ASP cc_start: 0.7403 (m-30) cc_final: 0.7128 (m-30) REVERT: o 53 GLN cc_start: 0.7942 (tt0) cc_final: 0.7721 (tt0) REVERT: o 67 LYS cc_start: 0.8068 (tptm) cc_final: 0.7811 (tptm) REVERT: o 90 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7972 (mm-30) REVERT: p 164 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6940 (mt-10) REVERT: q 8 LYS cc_start: 0.7579 (mmpt) cc_final: 0.7068 (mttm) REVERT: q 13 GLN cc_start: 0.8543 (mt0) cc_final: 0.8044 (mt0) REVERT: r 57 ASP cc_start: 0.7733 (t0) cc_final: 0.7402 (t0) REVERT: r 92 LYS cc_start: 0.7754 (ttmm) cc_final: 0.7473 (tppt) outliers start: 27 outliers final: 16 residues processed: 1379 average time/residue: 1.6971 time to fit residues: 2969.6338 Evaluate side-chains 1156 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1137 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain Y residue 35 ILE Chi-restraints excluded: chain f residue 40 SER Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain s residue 62 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 676 optimal weight: 0.9990 chunk 607 optimal weight: 8.9990 chunk 336 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 409 optimal weight: 0.9990 chunk 324 optimal weight: 1.9990 chunk 627 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 chunk 381 optimal weight: 2.9990 chunk 467 optimal weight: 0.5980 chunk 727 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 172 GLN B 181 GLN E 99 HIS E 121 GLN E 150 ASN ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS F 398 GLN F 431 GLN ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN K 91 GLN L 579 ASN M 44 GLN M 184 HIS M 427 GLN N 223 ASN P 44 GLN P 184 ASN S 21 HIS S 24 GLN W 128 HIS a 68 ASN e 97 HIS f 9 HIS g 55 ASN ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 62 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 73 ASN n 77 GLN p 22 GLN s 36 GLN s 38 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.265 69501 Z= 0.484 Angle : 1.585 51.182 94103 Z= 1.018 Chirality : 0.304 6.397 10349 Planarity : 0.005 0.056 11699 Dihedral : 14.395 177.538 10899 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.20 % Favored : 97.79 % Rotamer: Outliers : 2.03 % Allowed : 8.70 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: 0.04 (0.09), residues: 8106 helix: 0.41 (0.08), residues: 4291 sheet: -0.34 (0.26), residues: 393 loop : -0.26 (0.11), residues: 3422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 254 HIS 0.006 0.001 HIS F 356 PHE 0.023 0.002 PHE L 335 TYR 0.023 0.001 TYR F 43 ARG 0.005 0.000 ARG M 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1356 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1210 time to evaluate : 6.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.8232 (m100) cc_final: 0.7950 (m100) REVERT: A 66 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7749 (t0) REVERT: A 83 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7648 (mtpp) REVERT: B 45 ASP cc_start: 0.7562 (m-30) cc_final: 0.7326 (m-30) REVERT: B 79 MET cc_start: 0.8032 (ptt) cc_final: 0.7829 (ptt) REVERT: C 20 LYS cc_start: 0.8012 (tppp) cc_final: 0.7589 (ttpp) REVERT: D 59 HIS cc_start: 0.8091 (m170) cc_final: 0.7862 (m-70) REVERT: D 75 LYS cc_start: 0.8445 (ttpt) cc_final: 0.7866 (ttmt) REVERT: D 152 MET cc_start: 0.8765 (tpp) cc_final: 0.8392 (tpp) REVERT: D 290 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7456 (mtm110) REVERT: E 10 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7133 (mtm-85) REVERT: E 153 MET cc_start: 0.7864 (ppp) cc_final: 0.7592 (ppp) REVERT: F 249 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7604 (mtt90) REVERT: F 278 GLU cc_start: 0.7237 (tt0) cc_final: 0.6881 (tt0) REVERT: F 317 MET cc_start: 0.8154 (mmp) cc_final: 0.7833 (mmm) REVERT: G 121 MET cc_start: 0.8553 (mmm) cc_final: 0.8136 (mmm) REVERT: G 150 MET cc_start: 0.8780 (mmm) cc_final: 0.8565 (mmm) REVERT: G 276 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7674 (mtt-85) REVERT: G 306 MET cc_start: 0.7866 (mmt) cc_final: 0.7440 (mmt) REVERT: G 387 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6411 (mt-10) REVERT: G 436 ARG cc_start: 0.6592 (mtm-85) cc_final: 0.5829 (mtm-85) REVERT: G 568 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: G 638 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6533 (pt0) REVERT: H 62 ARG cc_start: 0.7053 (mtm180) cc_final: 0.6821 (mtp85) REVERT: H 152 SER cc_start: 0.8916 (t) cc_final: 0.8406 (m) REVERT: H 163 GLN cc_start: 0.8239 (tt0) cc_final: 0.8038 (mt0) REVERT: H 183 MET cc_start: 0.8138 (mtp) cc_final: 0.7922 (mtp) REVERT: H 230 ASN cc_start: 0.8104 (m-40) cc_final: 0.7723 (t0) REVERT: I 131 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: I 174 ASP cc_start: 0.8366 (t0) cc_final: 0.7978 (t0) REVERT: K 27 MET cc_start: 0.8463 (tpp) cc_final: 0.8148 (tpp) REVERT: L 23 MET cc_start: 0.8276 (mtp) cc_final: 0.7940 (mtp) REVERT: L 42 PHE cc_start: 0.8191 (m-80) cc_final: 0.7956 (m-80) REVERT: L 78 MET cc_start: 0.7965 (ttm) cc_final: 0.7725 (ttm) REVERT: L 115 ASN cc_start: 0.7205 (p0) cc_final: 0.6997 (p0) REVERT: L 297 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6948 (t70) REVERT: L 305 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8840 (p) REVERT: L 482 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7469 (ptt) REVERT: L 539 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7380 (tpt) REVERT: M 117 MET cc_start: 0.8206 (ttt) cc_final: 0.7962 (ttt) REVERT: M 139 GLN cc_start: 0.7832 (mm110) cc_final: 0.7424 (mp10) REVERT: M 168 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: M 177 MET cc_start: 0.7789 (mtm) cc_final: 0.7422 (mtm) REVERT: O 20 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.6050 (pt0) REVERT: O 67 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.7376 (mtm-85) REVERT: O 81 LYS cc_start: 0.8639 (mttt) cc_final: 0.8249 (mtmt) REVERT: O 213 LYS cc_start: 0.8576 (tptp) cc_final: 0.8113 (ttpp) REVERT: O 265 ASP cc_start: 0.7565 (t0) cc_final: 0.7095 (t70) REVERT: P 123 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7003 (mt-10) REVERT: P 265 TRP cc_start: 0.7606 (t60) cc_final: 0.7185 (t60) REVERT: Q 36 ARG cc_start: 0.8379 (ttt-90) cc_final: 0.8056 (ttt180) REVERT: Q 45 MET cc_start: 0.9057 (mmm) cc_final: 0.8852 (mmt) REVERT: R 3 GLN cc_start: 0.8349 (mm110) cc_final: 0.8114 (mm110) REVERT: R 21 LYS cc_start: 0.8582 (mttt) cc_final: 0.8177 (mtmm) REVERT: R 92 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7986 (ttmm) REVERT: S 74 LYS cc_start: 0.7985 (mtpm) cc_final: 0.7671 (mtpt) REVERT: U 57 GLU cc_start: 0.8042 (tp30) cc_final: 0.7706 (tp30) REVERT: V 85 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8093 (mmmm) REVERT: V 109 ASN cc_start: 0.7781 (m-40) cc_final: 0.7420 (p0) REVERT: W 59 LYS cc_start: 0.8085 (tmtm) cc_final: 0.7848 (tmtm) REVERT: X 83 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7175 (mt-10) REVERT: X 108 GLN cc_start: 0.8241 (tp40) cc_final: 0.8014 (tp-100) REVERT: Y 6 PHE cc_start: 0.8312 (t80) cc_final: 0.7858 (t80) REVERT: Y 9 SER cc_start: 0.7844 (t) cc_final: 0.7463 (p) REVERT: Y 10 TYR cc_start: 0.8528 (t80) cc_final: 0.8215 (t80) REVERT: Y 21 ARG cc_start: 0.6962 (tpt170) cc_final: 0.6635 (tpt-90) REVERT: Y 32 ILE cc_start: 0.8095 (mt) cc_final: 0.7849 (mm) REVERT: Y 60 TYR cc_start: 0.8082 (m-10) cc_final: 0.7761 (m-10) REVERT: Y 119 MET cc_start: 0.7720 (mtp) cc_final: 0.7424 (mtp) REVERT: a 35 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7684 (mt-10) REVERT: a 36 LYS cc_start: 0.8843 (tttm) cc_final: 0.8541 (tttm) REVERT: b 30 ILE cc_start: 0.8811 (mm) cc_final: 0.8547 (mt) REVERT: b 46 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7774 (tttt) REVERT: c 44 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7670 (ttp-110) REVERT: d 9 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7326 (mm-30) REVERT: d 50 MET cc_start: 0.8276 (mtp) cc_final: 0.7870 (mtp) REVERT: d 60 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7777 (mtm-85) REVERT: d 95 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7757 (mptt) REVERT: d 111 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6906 (mp0) REVERT: e 83 GLU cc_start: 0.7656 (tp30) cc_final: 0.7429 (mm-30) REVERT: f 41 MET cc_start: 0.7189 (mmm) cc_final: 0.6916 (mmt) REVERT: g 107 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6982 (tp30) REVERT: g 108 SER cc_start: 0.8065 (m) cc_final: 0.7818 (t) REVERT: h 98 SER cc_start: 0.8627 (t) cc_final: 0.8385 (p) REVERT: h 107 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: h 129 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: i 6 ASP cc_start: 0.7727 (m-30) cc_final: 0.7373 (m-30) REVERT: i 26 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7406 (mt-10) REVERT: j 40 PHE cc_start: 0.8603 (t80) cc_final: 0.8314 (t80) REVERT: l 24 LYS cc_start: 0.8474 (tttp) cc_final: 0.8188 (tttt) REVERT: m 4 LYS cc_start: 0.6153 (tppp) cc_final: 0.5876 (tppp) REVERT: m 34 GLU cc_start: 0.7275 (mt-10) cc_final: 0.7020 (mt-10) REVERT: m 35 ARG cc_start: 0.8342 (mtt180) cc_final: 0.8102 (mtt-85) REVERT: m 57 SER cc_start: 0.8743 (p) cc_final: 0.8420 (p) REVERT: m 105 LYS cc_start: 0.8180 (tptp) cc_final: 0.7843 (tptp) REVERT: m 109 ASP cc_start: 0.7559 (m-30) cc_final: 0.7343 (m-30) REVERT: m 110 ARG cc_start: 0.7103 (ttp80) cc_final: 0.6649 (ttp-170) REVERT: n 8 TYR cc_start: 0.8241 (p90) cc_final: 0.8022 (p90) REVERT: n 61 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7045 (tm-30) REVERT: n 64 ARG cc_start: 0.7582 (mtp-110) cc_final: 0.7158 (mtp85) REVERT: n 89 SER cc_start: 0.8803 (m) cc_final: 0.8592 (m) REVERT: o 7 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.6705 (tmm-80) REVERT: o 15 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6567 (mm-30) REVERT: o 43 GLN cc_start: 0.8354 (tp40) cc_final: 0.8116 (tp40) REVERT: o 47 ASP cc_start: 0.7339 (m-30) cc_final: 0.7114 (m-30) REVERT: o 53 GLN cc_start: 0.7828 (tt0) cc_final: 0.7624 (tt0) REVERT: o 67 LYS cc_start: 0.7894 (tptm) cc_final: 0.7454 (ttpp) REVERT: o 90 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8118 (mm-30) REVERT: p 5 ASP cc_start: 0.8024 (t0) cc_final: 0.7524 (t0) REVERT: p 126 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.6873 (tppt) REVERT: q 8 LYS cc_start: 0.7707 (mmpt) cc_final: 0.7437 (mmpt) REVERT: q 13 GLN cc_start: 0.8548 (mt0) cc_final: 0.8050 (mt0) REVERT: q 25 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.6869 (ttp-170) REVERT: q 96 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: r 57 ASP cc_start: 0.7560 (t0) cc_final: 0.7319 (t0) REVERT: r 92 LYS cc_start: 0.7763 (ttmm) cc_final: 0.7446 (tppt) outliers start: 146 outliers final: 44 residues processed: 1266 average time/residue: 1.6889 time to fit residues: 2761.1554 Evaluate side-chains 1184 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1122 time to evaluate : 6.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 568 GLU Chi-restraints excluded: chain G residue 638 GLU Chi-restraints excluded: chain G residue 655 GLU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 297 ASP Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 539 MET Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 382 THR Chi-restraints excluded: chain N residue 332 MET Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 49 SER Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 107 GLU Chi-restraints excluded: chain h residue 129 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 126 LYS Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 404 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 605 optimal weight: 5.9990 chunk 495 optimal weight: 0.0030 chunk 200 optimal weight: 0.3980 chunk 728 optimal weight: 4.9990 chunk 787 optimal weight: 0.9990 chunk 648 optimal weight: 8.9990 chunk 722 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 584 optimal weight: 6.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 GLN F 437 HIS G 546 GLN I 22 ASN K 7 ASN L 579 ASN ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN S 24 GLN X 72 GLN Z 84 GLN f 9 HIS ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN l 62 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 73 ASN n 77 GLN o 75 ASN p 22 GLN q 116 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 69501 Z= 0.475 Angle : 1.554 50.540 94103 Z= 1.003 Chirality : 0.308 6.452 10349 Planarity : 0.004 0.055 11699 Dihedral : 12.363 170.052 10886 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.54 % Favored : 97.45 % Rotamer: Outliers : 2.17 % Allowed : 10.70 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: 0.65 (0.09), residues: 8106 helix: 0.99 (0.08), residues: 4290 sheet: -0.07 (0.26), residues: 383 loop : -0.08 (0.11), residues: 3433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 157 HIS 0.005 0.001 HIS L 264 PHE 0.022 0.001 PHE L 335 TYR 0.019 0.001 TYR Y 24 ARG 0.008 0.000 ARG G 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1335 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1179 time to evaluate : 6.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.8291 (m100) cc_final: 0.8049 (m100) REVERT: A 83 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7649 (mtpp) REVERT: B 45 ASP cc_start: 0.7438 (m-30) cc_final: 0.7224 (m-30) REVERT: B 180 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: C 20 LYS cc_start: 0.8025 (tppp) cc_final: 0.7642 (ttpp) REVERT: D 59 HIS cc_start: 0.8072 (m170) cc_final: 0.7861 (m-70) REVERT: D 75 LYS cc_start: 0.8374 (ttpt) cc_final: 0.7768 (ttmt) REVERT: D 107 ASP cc_start: 0.8451 (t0) cc_final: 0.7900 (t70) REVERT: D 110 SER cc_start: 0.8588 (m) cc_final: 0.8349 (p) REVERT: D 152 MET cc_start: 0.8728 (tpp) cc_final: 0.8416 (tpp) REVERT: D 405 MET cc_start: 0.8734 (mtp) cc_final: 0.8404 (mtm) REVERT: E 10 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.7059 (mtm-85) REVERT: F 101 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: F 317 MET cc_start: 0.8162 (mmp) cc_final: 0.7829 (mmm) REVERT: G 276 ARG cc_start: 0.7931 (mtp85) cc_final: 0.7699 (mtt-85) REVERT: G 387 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6401 (mt-10) REVERT: G 436 ARG cc_start: 0.6647 (mtm-85) cc_final: 0.5841 (mtm-85) REVERT: G 624 GLU cc_start: 0.7933 (tt0) cc_final: 0.7691 (tt0) REVERT: G 638 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6423 (pt0) REVERT: H 62 ARG cc_start: 0.7063 (mtm180) cc_final: 0.6849 (mtp85) REVERT: H 163 GLN cc_start: 0.8258 (tt0) cc_final: 0.8030 (mt0) REVERT: H 183 MET cc_start: 0.8105 (mtp) cc_final: 0.7854 (mtp) REVERT: H 230 ASN cc_start: 0.8043 (m-40) cc_final: 0.7703 (t0) REVERT: I 131 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8431 (m-30) REVERT: K 57 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7835 (mtt) REVERT: L 23 MET cc_start: 0.8256 (mtp) cc_final: 0.7947 (mtp) REVERT: L 42 PHE cc_start: 0.8167 (m-80) cc_final: 0.7939 (m-80) REVERT: L 78 MET cc_start: 0.7970 (ttm) cc_final: 0.7742 (ttm) REVERT: L 297 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6817 (t70) REVERT: L 468 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8226 (mt) REVERT: M 139 GLN cc_start: 0.7955 (mm110) cc_final: 0.7495 (mp10) REVERT: M 168 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: M 177 MET cc_start: 0.7776 (mtm) cc_final: 0.7377 (mtm) REVERT: N 282 MET cc_start: 0.8431 (mtp) cc_final: 0.7948 (mtm) REVERT: O 20 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6033 (pt0) REVERT: O 213 LYS cc_start: 0.8544 (tptp) cc_final: 0.8077 (ttpp) REVERT: O 265 ASP cc_start: 0.7448 (t0) cc_final: 0.6942 (t70) REVERT: P 50 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8019 (ptt180) REVERT: P 123 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6926 (mt-10) REVERT: P 127 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7091 (pt0) REVERT: P 265 TRP cc_start: 0.7524 (t60) cc_final: 0.7212 (t60) REVERT: Q 45 MET cc_start: 0.9052 (mmm) cc_final: 0.8788 (mmt) REVERT: R 21 LYS cc_start: 0.8566 (mttt) cc_final: 0.8159 (mtmm) REVERT: R 37 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: R 51 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6902 (mt-10) REVERT: R 92 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7937 (ttpt) REVERT: U 57 GLU cc_start: 0.8036 (tp30) cc_final: 0.7718 (tp30) REVERT: V 53 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6897 (tt0) REVERT: V 85 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8091 (mmmm) REVERT: V 93 MET cc_start: 0.8834 (mmm) cc_final: 0.8428 (mmp) REVERT: V 109 ASN cc_start: 0.7759 (m-40) cc_final: 0.7310 (p0) REVERT: X 107 ASP cc_start: 0.8611 (m-30) cc_final: 0.8356 (m-30) REVERT: X 109 CYS cc_start: 0.5349 (t) cc_final: 0.4971 (t) REVERT: Y 6 PHE cc_start: 0.8292 (t80) cc_final: 0.7919 (t80) REVERT: Y 32 ILE cc_start: 0.8074 (mt) cc_final: 0.7799 (mm) REVERT: Y 60 TYR cc_start: 0.8177 (m-10) cc_final: 0.7786 (m-10) REVERT: Y 119 MET cc_start: 0.7835 (mtp) cc_final: 0.7517 (mtp) REVERT: a 35 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7691 (mt-10) REVERT: a 36 LYS cc_start: 0.8835 (tttm) cc_final: 0.8558 (tttm) REVERT: b 10 ASN cc_start: 0.7032 (t0) cc_final: 0.6695 (t0) REVERT: b 30 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8486 (mt) REVERT: b 33 MET cc_start: 0.7714 (mtt) cc_final: 0.7507 (mtt) REVERT: c 36 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7365 (t0) REVERT: d 9 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7315 (mm-30) REVERT: d 34 MET cc_start: 0.8388 (mmm) cc_final: 0.8180 (mmp) REVERT: d 44 MET cc_start: 0.7335 (tpp) cc_final: 0.7033 (tpp) REVERT: d 50 MET cc_start: 0.8271 (mtp) cc_final: 0.7880 (mtp) REVERT: d 91 PHE cc_start: 0.8698 (m-10) cc_final: 0.8370 (m-10) REVERT: d 95 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7775 (mptt) REVERT: d 111 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6805 (mp0) REVERT: f 41 MET cc_start: 0.7180 (mmm) cc_final: 0.6755 (mmt) REVERT: g 31 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6143 (pp20) REVERT: g 107 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7081 (tp30) REVERT: g 108 SER cc_start: 0.8147 (m) cc_final: 0.7878 (t) REVERT: h 107 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7535 (tp30) REVERT: h 129 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: j 40 PHE cc_start: 0.8612 (t80) cc_final: 0.8363 (t80) REVERT: k 25 ARG cc_start: 0.7504 (mpp-170) cc_final: 0.7196 (mtt180) REVERT: l 24 LYS cc_start: 0.8394 (tttp) cc_final: 0.8112 (tttt) REVERT: m 18 ASP cc_start: 0.7524 (t0) cc_final: 0.7198 (t70) REVERT: m 34 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6955 (mt-10) REVERT: m 35 ARG cc_start: 0.8320 (mtt180) cc_final: 0.8071 (mtt-85) REVERT: m 57 SER cc_start: 0.8712 (p) cc_final: 0.8380 (p) REVERT: m 105 LYS cc_start: 0.8193 (tptp) cc_final: 0.7888 (tptp) REVERT: m 109 ASP cc_start: 0.7455 (m-30) cc_final: 0.7244 (m-30) REVERT: m 110 ARG cc_start: 0.7058 (ttp80) cc_final: 0.6468 (ttp-170) REVERT: n 56 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6307 (tpp) REVERT: n 61 GLN cc_start: 0.7464 (tm-30) cc_final: 0.6985 (tm-30) REVERT: n 64 ARG cc_start: 0.7503 (mtp-110) cc_final: 0.7189 (mtp85) REVERT: n 89 SER cc_start: 0.8839 (m) cc_final: 0.8617 (m) REVERT: o 7 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6567 (tmm-80) REVERT: o 13 SER cc_start: 0.7546 (p) cc_final: 0.7199 (t) REVERT: o 15 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6653 (mm-30) REVERT: o 53 GLN cc_start: 0.7804 (tt0) cc_final: 0.7602 (tt0) REVERT: o 67 LYS cc_start: 0.7819 (tptm) cc_final: 0.7173 (ttpp) REVERT: o 71 ASP cc_start: 0.7862 (m-30) cc_final: 0.7544 (m-30) REVERT: o 90 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8062 (mm-30) REVERT: p 5 ASP cc_start: 0.8082 (t0) cc_final: 0.7603 (t0) REVERT: q 25 ARG cc_start: 0.7535 (ttm-80) cc_final: 0.6959 (ttp-170) REVERT: q 96 ASP cc_start: 0.7676 (m-30) cc_final: 0.7464 (m-30) REVERT: r 57 ASP cc_start: 0.7527 (t0) cc_final: 0.7283 (t0) REVERT: r 92 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7544 (tppt) outliers start: 156 outliers final: 50 residues processed: 1246 average time/residue: 1.6124 time to fit residues: 2584.5414 Evaluate side-chains 1183 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1112 time to evaluate : 6.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 638 GLU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 297 ASP Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 292 SER Chi-restraints excluded: chain M residue 382 THR Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 49 SER Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain c residue 36 ASN Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 107 GLU Chi-restraints excluded: chain h residue 129 GLU Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 719 optimal weight: 6.9990 chunk 547 optimal weight: 4.9990 chunk 378 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 347 optimal weight: 6.9990 chunk 489 optimal weight: 5.9990 chunk 731 optimal weight: 8.9990 chunk 774 optimal weight: 2.9990 chunk 382 optimal weight: 3.9990 chunk 693 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN F 431 GLN ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN J 107 ASN K 7 ASN L 109 HIS L 403 ASN L 446 ASN L 579 ASN ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN O 287 HIS R 3 GLN S 24 GLN Z 84 GLN Z 102 ASN f 9 HIS h 108 GLN ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 8 GLN l 27 ASN l 62 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 77 GLN p 22 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 69501 Z= 0.522 Angle : 1.573 50.588 94103 Z= 1.010 Chirality : 0.309 6.471 10349 Planarity : 0.005 0.065 11699 Dihedral : 11.955 171.747 10879 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.55 % Favored : 97.43 % Rotamer: Outliers : 3.04 % Allowed : 11.54 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: 0.66 (0.09), residues: 8106 helix: 0.98 (0.08), residues: 4284 sheet: 0.07 (0.26), residues: 380 loop : -0.08 (0.11), residues: 3442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 157 HIS 0.005 0.001 HIS D 347 PHE 0.024 0.002 PHE M 151 TYR 0.020 0.002 TYR Y 24 ARG 0.007 0.001 ARG G 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1331 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1112 time to evaluate : 6.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7607 (mtpp) REVERT: A 109 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8228 (mppt) REVERT: B 45 ASP cc_start: 0.7538 (m-30) cc_final: 0.7316 (m-30) REVERT: B 180 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: C 20 LYS cc_start: 0.8033 (tppp) cc_final: 0.7736 (ttpp) REVERT: D 59 HIS cc_start: 0.8100 (m170) cc_final: 0.7881 (m-70) REVERT: D 75 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7891 (ttmt) REVERT: D 152 MET cc_start: 0.8730 (tpp) cc_final: 0.8423 (tpp) REVERT: D 290 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7327 (mtm110) REVERT: D 405 MET cc_start: 0.8793 (mtp) cc_final: 0.8369 (mtm) REVERT: E 10 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7173 (mtm-85) REVERT: F 32 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7241 (mtm180) REVERT: F 317 MET cc_start: 0.8219 (mmp) cc_final: 0.7873 (mmm) REVERT: G 122 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7803 (mpp) REVERT: G 276 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7781 (mtt-85) REVERT: G 306 MET cc_start: 0.7922 (mmt) cc_final: 0.7610 (mmt) REVERT: G 387 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6416 (mt-10) REVERT: G 436 ARG cc_start: 0.6610 (mtm-85) cc_final: 0.5805 (mtm-85) REVERT: G 568 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: G 613 TYR cc_start: 0.8505 (p90) cc_final: 0.7670 (p90) REVERT: G 624 GLU cc_start: 0.8017 (tt0) cc_final: 0.7750 (tt0) REVERT: H 62 ARG cc_start: 0.7091 (mtm180) cc_final: 0.6808 (mtp85) REVERT: H 163 GLN cc_start: 0.8244 (tt0) cc_final: 0.7895 (mt0) REVERT: H 183 MET cc_start: 0.8176 (mtp) cc_final: 0.7765 (mtp) REVERT: H 230 ASN cc_start: 0.8136 (m-40) cc_final: 0.7756 (t0) REVERT: I 131 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8437 (m-30) REVERT: K 57 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7969 (mtt) REVERT: L 23 MET cc_start: 0.8263 (mtp) cc_final: 0.7969 (mtp) REVERT: L 42 PHE cc_start: 0.8179 (m-80) cc_final: 0.7952 (m-80) REVERT: L 62 MET cc_start: 0.8324 (ttt) cc_final: 0.7997 (ttp) REVERT: L 78 MET cc_start: 0.7941 (ttm) cc_final: 0.7716 (ttm) REVERT: L 297 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6757 (t70) REVERT: L 468 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8197 (mt) REVERT: M 138 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7952 (t0) REVERT: M 139 GLN cc_start: 0.7921 (mm110) cc_final: 0.7606 (mt0) REVERT: M 168 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: M 177 MET cc_start: 0.7869 (mtm) cc_final: 0.7491 (mtm) REVERT: N 156 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6435 (mmt) REVERT: O 20 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.6031 (pt0) REVERT: O 213 LYS cc_start: 0.8551 (tptp) cc_final: 0.8007 (ttpp) REVERT: O 265 ASP cc_start: 0.7474 (t0) cc_final: 0.6978 (t70) REVERT: P 50 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8374 (ptt180) REVERT: P 123 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6937 (mt-10) REVERT: P 127 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: P 265 TRP cc_start: 0.7541 (t60) cc_final: 0.7180 (t60) REVERT: Q 45 MET cc_start: 0.9048 (mmm) cc_final: 0.8775 (mmt) REVERT: R 3 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7830 (mm110) REVERT: R 21 LYS cc_start: 0.8607 (mttt) cc_final: 0.8211 (mtmm) REVERT: R 37 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: R 92 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7904 (ttpt) REVERT: S 25 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7159 (mtt90) REVERT: T 19 LEU cc_start: 0.7949 (mt) cc_final: 0.7738 (mt) REVERT: U 20 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8000 (mttt) REVERT: V 53 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: V 85 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8085 (mmmm) REVERT: V 93 MET cc_start: 0.8845 (mmm) cc_final: 0.8416 (mmp) REVERT: V 109 ASN cc_start: 0.7816 (m-40) cc_final: 0.7445 (p0) REVERT: W 89 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8099 (mtpp) REVERT: X 131 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7995 (ttmm) REVERT: Y 10 TYR cc_start: 0.8573 (t80) cc_final: 0.8319 (t80) REVERT: Y 32 ILE cc_start: 0.8162 (mt) cc_final: 0.7896 (mm) REVERT: Y 119 MET cc_start: 0.7880 (mtp) cc_final: 0.7666 (mtp) REVERT: a 35 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7590 (mt-10) REVERT: a 36 LYS cc_start: 0.8854 (tttm) cc_final: 0.8604 (tttm) REVERT: b 10 ASN cc_start: 0.6983 (t0) cc_final: 0.6615 (t0) REVERT: b 30 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8484 (mt) REVERT: d 9 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7321 (mm-30) REVERT: d 34 MET cc_start: 0.8414 (mmm) cc_final: 0.8202 (mmp) REVERT: d 44 MET cc_start: 0.7376 (tpp) cc_final: 0.6994 (tpp) REVERT: d 91 PHE cc_start: 0.8704 (m-10) cc_final: 0.8415 (m-10) REVERT: d 95 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7779 (mptt) REVERT: e 5 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8707 (OUTLIER) REVERT: e 83 GLU cc_start: 0.7718 (tp30) cc_final: 0.7405 (tp30) REVERT: f 41 MET cc_start: 0.7290 (mmm) cc_final: 0.6942 (mmt) REVERT: g 31 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6277 (pp20) REVERT: g 107 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7047 (tp30) REVERT: g 108 SER cc_start: 0.8124 (m) cc_final: 0.7893 (t) REVERT: h 107 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7551 (tp30) REVERT: h 129 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6715 (mt-10) REVERT: i 26 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7383 (mt-10) REVERT: i 110 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7204 (tt) REVERT: j 40 PHE cc_start: 0.8593 (t80) cc_final: 0.8337 (t80) REVERT: l 24 LYS cc_start: 0.8439 (tttp) cc_final: 0.8127 (tttt) REVERT: l 41 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7583 (mmm) REVERT: l 67 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: m 18 ASP cc_start: 0.7478 (t0) cc_final: 0.7212 (t70) REVERT: m 34 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6984 (mt-10) REVERT: m 35 ARG cc_start: 0.8323 (mtt180) cc_final: 0.8067 (mtt-85) REVERT: m 57 SER cc_start: 0.8731 (p) cc_final: 0.8386 (p) REVERT: m 105 LYS cc_start: 0.8185 (tptp) cc_final: 0.7859 (tptp) REVERT: m 109 ASP cc_start: 0.7538 (m-30) cc_final: 0.7311 (m-30) REVERT: m 110 ARG cc_start: 0.7113 (ttp80) cc_final: 0.6619 (ttp-170) REVERT: n 53 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6207 (tm-30) REVERT: n 56 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.6288 (tpp) REVERT: n 61 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7062 (tm-30) REVERT: n 64 ARG cc_start: 0.7517 (mtp-110) cc_final: 0.7225 (mtm110) REVERT: o 7 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6583 (tmm-80) REVERT: o 13 SER cc_start: 0.7410 (p) cc_final: 0.7112 (t) REVERT: o 15 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6673 (mm-30) REVERT: o 53 GLN cc_start: 0.7787 (tt0) cc_final: 0.7584 (tt0) REVERT: o 67 LYS cc_start: 0.7863 (tptm) cc_final: 0.7487 (ttpp) REVERT: o 90 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8108 (mm-30) REVERT: p 5 ASP cc_start: 0.8121 (t0) cc_final: 0.7574 (t0) REVERT: q 25 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.6966 (ttp-170) REVERT: q 96 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: r 9 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8341 (mtpt) outliers start: 219 outliers final: 99 residues processed: 1219 average time/residue: 1.6062 time to fit residues: 2516.7525 Evaluate side-chains 1222 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1091 time to evaluate : 6.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 568 GLU Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 638 GLU Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 297 ASP Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 292 SER Chi-restraints excluded: chain M residue 382 THR Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 156 MET Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain W residue 89 LYS Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 49 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 62 MET Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain g residue 21 THR Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain h residue 32 THR Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 107 GLU Chi-restraints excluded: chain h residue 129 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 41 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain n residue 158 ARG Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 35 GLU Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 102 MET Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 644 optimal weight: 9.9990 chunk 439 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 576 optimal weight: 20.0000 chunk 319 optimal weight: 0.9990 chunk 660 optimal weight: 0.9990 chunk 535 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 395 optimal weight: 6.9990 chunk 694 optimal weight: 20.0000 chunk 195 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN E 121 GLN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN F 431 GLN ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN I 22 ASN L 579 ASN M 144 ASN S 24 GLN Z 84 GLN f 9 HIS ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN l 62 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 77 GLN o 75 ASN p 22 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 69501 Z= 0.494 Angle : 1.559 50.622 94103 Z= 1.005 Chirality : 0.308 6.425 10349 Planarity : 0.004 0.057 11699 Dihedral : 11.566 174.960 10876 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.42 % Favored : 97.57 % Rotamer: Outliers : 2.96 % Allowed : 12.50 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: 0.78 (0.09), residues: 8106 helix: 1.11 (0.08), residues: 4284 sheet: 0.10 (0.26), residues: 379 loop : -0.06 (0.11), residues: 3443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.005 0.001 HIS L 264 PHE 0.023 0.002 PHE N 292 TYR 0.019 0.001 TYR L 422 ARG 0.006 0.000 ARG G 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1115 time to evaluate : 6.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.8236 (m100) cc_final: 0.7981 (m100) REVERT: A 83 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7530 (mtpp) REVERT: A 109 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8243 (mppt) REVERT: B 45 ASP cc_start: 0.7502 (m-30) cc_final: 0.7288 (m-30) REVERT: B 180 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: C 20 LYS cc_start: 0.8023 (tppp) cc_final: 0.7626 (ttpp) REVERT: C 61 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8554 (mp) REVERT: D 59 HIS cc_start: 0.8100 (m170) cc_final: 0.7886 (m-70) REVERT: D 290 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7351 (mtm110) REVERT: E 10 ARG cc_start: 0.7625 (mtm-85) cc_final: 0.7152 (mtm-85) REVERT: F 32 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7247 (mtm180) REVERT: F 317 MET cc_start: 0.8206 (mmp) cc_final: 0.7913 (mmm) REVERT: G 71 MET cc_start: 0.8757 (tpp) cc_final: 0.8529 (tpp) REVERT: G 122 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7800 (mpp) REVERT: G 276 ARG cc_start: 0.7980 (mtp85) cc_final: 0.7767 (mtt-85) REVERT: G 306 MET cc_start: 0.7945 (mmt) cc_final: 0.7659 (mmt) REVERT: G 387 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6419 (mt-10) REVERT: G 436 ARG cc_start: 0.6636 (mtm-85) cc_final: 0.5841 (mtm-85) REVERT: G 568 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: G 613 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7661 (p90) REVERT: G 624 GLU cc_start: 0.7976 (tt0) cc_final: 0.7757 (tt0) REVERT: H 62 ARG cc_start: 0.7119 (mtm180) cc_final: 0.6858 (mtp85) REVERT: H 163 GLN cc_start: 0.8261 (tt0) cc_final: 0.7937 (mt0) REVERT: H 183 MET cc_start: 0.8139 (mtp) cc_final: 0.7720 (mtp) REVERT: H 230 ASN cc_start: 0.8050 (m-40) cc_final: 0.7697 (t0) REVERT: H 253 GLU cc_start: 0.8053 (mp0) cc_final: 0.7742 (mp0) REVERT: K 57 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7909 (mtt) REVERT: L 23 MET cc_start: 0.8212 (mtp) cc_final: 0.7942 (mtp) REVERT: L 42 PHE cc_start: 0.8169 (m-80) cc_final: 0.7932 (m-80) REVERT: L 62 MET cc_start: 0.8319 (ttt) cc_final: 0.8007 (ttp) REVERT: L 78 MET cc_start: 0.7959 (ttm) cc_final: 0.7751 (ttm) REVERT: L 297 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6798 (t70) REVERT: L 405 ASN cc_start: 0.8067 (t0) cc_final: 0.7591 (m-40) REVERT: L 468 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8175 (mt) REVERT: L 511 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7997 (mm) REVERT: M 138 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.7940 (t0) REVERT: M 168 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: M 177 MET cc_start: 0.7821 (mtm) cc_final: 0.7328 (mtm) REVERT: M 441 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7437 (mmt) REVERT: N 156 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6439 (mmt) REVERT: N 217 MET cc_start: 0.8486 (mtp) cc_final: 0.8101 (mtt) REVERT: O 20 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6018 (pt0) REVERT: O 213 LYS cc_start: 0.8566 (tptp) cc_final: 0.8071 (ttpp) REVERT: O 265 ASP cc_start: 0.7447 (t0) cc_final: 0.6954 (t70) REVERT: O 311 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: P 50 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8133 (ptt180) REVERT: P 123 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6933 (mt-10) REVERT: P 127 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7124 (pt0) REVERT: Q 45 MET cc_start: 0.9055 (mmm) cc_final: 0.8751 (mmt) REVERT: Q 109 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7449 (mttt) REVERT: R 3 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7631 (mp-120) REVERT: R 21 LYS cc_start: 0.8603 (mttt) cc_final: 0.8176 (mtmm) REVERT: R 37 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: R 92 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7913 (ttpt) REVERT: S 25 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7174 (mtt90) REVERT: S 74 LYS cc_start: 0.7997 (mtpm) cc_final: 0.7675 (mtpt) REVERT: U 20 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7998 (mttt) REVERT: V 53 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6929 (tt0) REVERT: V 85 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8035 (mmmm) REVERT: V 109 ASN cc_start: 0.7793 (m-40) cc_final: 0.7391 (p0) REVERT: W 43 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7031 (mtp180) REVERT: W 59 LYS cc_start: 0.8171 (tmtm) cc_final: 0.7753 (tmtm) REVERT: X 107 ASP cc_start: 0.8762 (m-30) cc_final: 0.8483 (m-30) REVERT: X 131 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7950 (ttmm) REVERT: Y 32 ILE cc_start: 0.8134 (mt) cc_final: 0.7855 (mm) REVERT: Y 60 TYR cc_start: 0.8122 (m-10) cc_final: 0.7755 (m-10) REVERT: Y 119 MET cc_start: 0.7812 (mtp) cc_final: 0.7510 (mtp) REVERT: a 35 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7565 (mt-10) REVERT: b 10 ASN cc_start: 0.6965 (t0) cc_final: 0.6579 (t0) REVERT: b 30 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8450 (mt) REVERT: b 33 MET cc_start: 0.7770 (mtt) cc_final: 0.7567 (mtt) REVERT: d 9 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7316 (mm-30) REVERT: d 25 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7431 (mtpt) REVERT: d 34 MET cc_start: 0.8388 (mmm) cc_final: 0.8186 (mmp) REVERT: d 44 MET cc_start: 0.7377 (tpp) cc_final: 0.7035 (tpp) REVERT: d 91 PHE cc_start: 0.8689 (m-10) cc_final: 0.8436 (m-10) REVERT: d 95 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7774 (mptt) REVERT: d 106 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7672 (mmmm) REVERT: d 107 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7466 (mmpt) REVERT: d 111 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: f 41 MET cc_start: 0.7257 (mmm) cc_final: 0.6923 (mmt) REVERT: f 46 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: g 31 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6077 (pp20) REVERT: g 107 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7012 (tp30) REVERT: g 108 SER cc_start: 0.8155 (m) cc_final: 0.7935 (t) REVERT: h 107 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7570 (tp30) REVERT: h 129 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6701 (mt-10) REVERT: i 26 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: i 110 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7265 (tt) REVERT: j 40 PHE cc_start: 0.8589 (t80) cc_final: 0.8358 (t80) REVERT: l 24 LYS cc_start: 0.8453 (tttp) cc_final: 0.8156 (tttt) REVERT: l 67 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: m 4 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6399 (tppp) REVERT: m 18 ASP cc_start: 0.7470 (t0) cc_final: 0.7203 (t70) REVERT: m 34 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6947 (mt-10) REVERT: m 57 SER cc_start: 0.8726 (p) cc_final: 0.8392 (p) REVERT: m 105 LYS cc_start: 0.8207 (tptp) cc_final: 0.7914 (tptp) REVERT: m 109 ASP cc_start: 0.7524 (m-30) cc_final: 0.7320 (m-30) REVERT: m 110 ARG cc_start: 0.7107 (ttp80) cc_final: 0.6476 (ttp-170) REVERT: n 89 SER cc_start: 0.8881 (m) cc_final: 0.8666 (m) REVERT: o 7 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.6529 (tmm-80) REVERT: o 15 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6690 (mm-30) REVERT: o 53 GLN cc_start: 0.7804 (tt0) cc_final: 0.7604 (tt0) REVERT: o 67 LYS cc_start: 0.7858 (tptm) cc_final: 0.7478 (ttpp) REVERT: o 90 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8064 (mm-30) REVERT: r 9 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8341 (mtpt) outliers start: 213 outliers final: 100 residues processed: 1208 average time/residue: 1.6212 time to fit residues: 2515.0404 Evaluate side-chains 1222 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1082 time to evaluate : 6.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 61 LYS Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 568 GLU Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain G residue 638 GLU Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 297 ASP Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 292 SER Chi-restraints excluded: chain M residue 441 MET Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 156 MET Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 311 GLU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 109 LYS Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain W residue 43 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 49 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 62 MET Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 46 GLU Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 107 GLU Chi-restraints excluded: chain h residue 129 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 26 GLU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 70 MET Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain m residue 4 LYS Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain n residue 158 ARG Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 35 GLU Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 102 MET Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 30 ILE Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 260 optimal weight: 2.9990 chunk 697 optimal weight: 7.9990 chunk 153 optimal weight: 0.0020 chunk 454 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 774 optimal weight: 0.0170 chunk 643 optimal weight: 0.8980 chunk 358 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 256 optimal weight: 4.9990 chunk 406 optimal weight: 0.9980 overall best weight: 0.5426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 ASN E 121 GLN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN F 431 GLN F 437 HIS I 22 ASN K 7 ASN L 248 HIS L 579 ASN M 144 ASN Z 84 GLN f 9 HIS ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 62 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 75 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 69501 Z= 0.464 Angle : 1.543 50.602 94103 Z= 0.999 Chirality : 0.306 6.364 10349 Planarity : 0.004 0.052 11699 Dihedral : 10.857 170.703 10874 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.90 % Favored : 98.09 % Rotamer: Outliers : 2.06 % Allowed : 14.03 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: 1.12 (0.09), residues: 8106 helix: 1.41 (0.08), residues: 4270 sheet: 0.13 (0.26), residues: 387 loop : 0.09 (0.11), residues: 3449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 85 HIS 0.005 0.001 HIS L 264 PHE 0.022 0.001 PHE L 335 TYR 0.018 0.001 TYR L 422 ARG 0.009 0.000 ARG M 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1173 time to evaluate : 6.112 Fit side-chains revert: symmetry clash REVERT: A 23 TRP cc_start: 0.8193 (m100) cc_final: 0.7934 (m100) REVERT: A 83 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7412 (mtpp) REVERT: A 109 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8233 (mppt) REVERT: B 180 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: C 20 LYS cc_start: 0.8008 (tppp) cc_final: 0.7616 (ttpp) REVERT: C 61 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8562 (mp) REVERT: D 59 HIS cc_start: 0.7986 (m170) cc_final: 0.7779 (m-70) REVERT: D 75 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7959 (ttmt) REVERT: D 112 MET cc_start: 0.8615 (mmt) cc_final: 0.8024 (mtt) REVERT: D 249 ASP cc_start: 0.7683 (m-30) cc_final: 0.7457 (m-30) REVERT: D 290 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7343 (mtm110) REVERT: D 405 MET cc_start: 0.8688 (mtp) cc_final: 0.8340 (mtm) REVERT: E 10 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7197 (mtm-85) REVERT: F 32 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7210 (mtm180) REVERT: F 317 MET cc_start: 0.8146 (mmp) cc_final: 0.7764 (mmm) REVERT: G 21 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: G 276 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7683 (mtt-85) REVERT: G 387 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6413 (mt-10) REVERT: G 431 ASP cc_start: 0.7006 (m-30) cc_final: 0.6733 (m-30) REVERT: G 436 ARG cc_start: 0.6634 (mtm-85) cc_final: 0.5790 (mtm-85) REVERT: G 568 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: G 613 TYR cc_start: 0.8488 (p90) cc_final: 0.7611 (p90) REVERT: H 62 ARG cc_start: 0.7123 (mtm180) cc_final: 0.6898 (mtp85) REVERT: H 163 GLN cc_start: 0.8300 (tt0) cc_final: 0.7981 (mt0) REVERT: H 230 ASN cc_start: 0.7883 (m-40) cc_final: 0.7602 (t0) REVERT: H 253 GLU cc_start: 0.8064 (mp0) cc_final: 0.7758 (mp0) REVERT: I 22 ASN cc_start: 0.7633 (m-40) cc_final: 0.7178 (m110) REVERT: J 76 GLU cc_start: 0.7708 (pm20) cc_final: 0.7479 (pm20) REVERT: J 171 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7366 (ttp-170) REVERT: K 70 GLU cc_start: 0.7062 (mp0) cc_final: 0.6810 (mp0) REVERT: L 23 MET cc_start: 0.8133 (mtp) cc_final: 0.7860 (mtp) REVERT: L 42 PHE cc_start: 0.8156 (m-80) cc_final: 0.7919 (m-80) REVERT: L 62 MET cc_start: 0.8279 (ttt) cc_final: 0.7980 (ttp) REVERT: L 341 MET cc_start: 0.8176 (mtp) cc_final: 0.7866 (mtp) REVERT: L 405 ASN cc_start: 0.7726 (t0) cc_final: 0.7475 (m-40) REVERT: L 468 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8132 (mt) REVERT: L 573 MET cc_start: 0.8397 (mmm) cc_final: 0.8170 (mmm) REVERT: M 138 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8014 (t0) REVERT: M 177 MET cc_start: 0.7816 (mtm) cc_final: 0.7371 (mtm) REVERT: M 222 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6842 (mm-30) REVERT: M 441 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7622 (mmt) REVERT: N 215 MET cc_start: 0.8365 (tpt) cc_final: 0.8088 (mmm) REVERT: N 217 MET cc_start: 0.8462 (mtp) cc_final: 0.8055 (mtt) REVERT: O 20 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5922 (pt0) REVERT: O 213 LYS cc_start: 0.8560 (tptp) cc_final: 0.8042 (ttpp) REVERT: O 217 MET cc_start: 0.7935 (ptt) cc_final: 0.7731 (pmm) REVERT: O 265 ASP cc_start: 0.7351 (t0) cc_final: 0.6848 (t70) REVERT: O 311 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6915 (mt-10) REVERT: P 50 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7953 (ptt180) REVERT: P 123 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6918 (mt-10) REVERT: P 127 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: Q 45 MET cc_start: 0.9006 (mmm) cc_final: 0.8736 (mmt) REVERT: Q 109 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7380 (mttt) REVERT: R 21 LYS cc_start: 0.8474 (mttt) cc_final: 0.8134 (mppt) REVERT: R 37 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7068 (mt-10) REVERT: R 51 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6891 (mt-10) REVERT: R 92 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7871 (ttpt) REVERT: S 25 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7185 (mtt90) REVERT: S 74 LYS cc_start: 0.7998 (mtpm) cc_final: 0.7688 (mtpt) REVERT: T 16 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7278 (tm) REVERT: U 17 TYR cc_start: 0.8784 (t80) cc_final: 0.8281 (t80) REVERT: U 20 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8000 (mttt) REVERT: V 53 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6893 (tt0) REVERT: V 85 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8069 (mmmm) REVERT: W 59 LYS cc_start: 0.8143 (tmtm) cc_final: 0.7706 (tmtm) REVERT: W 89 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8100 (mtpp) REVERT: X 99 CYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7704 (m) REVERT: X 107 ASP cc_start: 0.8754 (m-30) cc_final: 0.8478 (m-30) REVERT: Y 32 ILE cc_start: 0.8019 (mt) cc_final: 0.7755 (mm) REVERT: Y 60 TYR cc_start: 0.8151 (m-10) cc_final: 0.7833 (m-10) REVERT: a 35 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7605 (mt-10) REVERT: b 10 ASN cc_start: 0.7043 (t0) cc_final: 0.6663 (t0) REVERT: b 30 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8357 (mt) REVERT: c 27 MET cc_start: 0.7843 (mtm) cc_final: 0.7596 (mtm) REVERT: d 44 MET cc_start: 0.7378 (tpp) cc_final: 0.7030 (tpp) REVERT: d 50 MET cc_start: 0.8312 (mtp) cc_final: 0.7981 (mtp) REVERT: d 91 PHE cc_start: 0.8601 (m-10) cc_final: 0.8381 (m-10) REVERT: d 95 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7792 (mttt) REVERT: d 107 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7476 (mmpt) REVERT: d 111 GLU cc_start: 0.7164 (mp0) cc_final: 0.6470 (mp0) REVERT: e 73 ARG cc_start: 0.7400 (tpp-160) cc_final: 0.6843 (mmm-85) REVERT: e 83 GLU cc_start: 0.7746 (tp30) cc_final: 0.7524 (tp30) REVERT: f 41 MET cc_start: 0.7217 (mmm) cc_final: 0.6861 (mmt) REVERT: g 107 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7006 (tp30) REVERT: h 107 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: h 129 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: i 26 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7211 (mt-10) REVERT: i 110 LEU cc_start: 0.7504 (mt) cc_final: 0.7289 (tt) REVERT: j 40 PHE cc_start: 0.8560 (t80) cc_final: 0.8355 (t80) REVERT: l 24 LYS cc_start: 0.8420 (tttp) cc_final: 0.8124 (tttt) REVERT: l 70 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7642 (mmt) REVERT: m 18 ASP cc_start: 0.7537 (t0) cc_final: 0.7234 (t70) REVERT: m 34 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6965 (mt-10) REVERT: m 57 SER cc_start: 0.8693 (p) cc_final: 0.8360 (p) REVERT: m 105 LYS cc_start: 0.8234 (tptp) cc_final: 0.7962 (tptp) REVERT: m 109 ASP cc_start: 0.7398 (m-30) cc_final: 0.7196 (m-30) REVERT: m 110 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6444 (ttp-170) REVERT: n 61 GLN cc_start: 0.7353 (tm-30) cc_final: 0.6820 (tm-30) REVERT: n 64 ARG cc_start: 0.7564 (mtp-110) cc_final: 0.7263 (mtm110) REVERT: n 89 SER cc_start: 0.8871 (m) cc_final: 0.8666 (m) REVERT: o 7 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7695 (ttt-90) REVERT: o 13 SER cc_start: 0.7250 (p) cc_final: 0.7015 (t) REVERT: o 53 GLN cc_start: 0.7689 (tt0) cc_final: 0.7474 (tt0) REVERT: o 67 LYS cc_start: 0.7815 (tptm) cc_final: 0.7436 (ttpp) REVERT: p 5 ASP cc_start: 0.7892 (t0) cc_final: 0.7408 (t0) REVERT: p 92 ARG cc_start: 0.7333 (mtp85) cc_final: 0.6846 (mtt-85) REVERT: q 25 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.6898 (ttp-110) outliers start: 148 outliers final: 51 residues processed: 1245 average time/residue: 1.6012 time to fit residues: 2582.8687 Evaluate side-chains 1185 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1105 time to evaluate : 6.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 568 GLU Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 441 MET Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 311 GLU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain Q residue 109 LYS Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain W residue 89 LYS Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 107 GLU Chi-restraints excluded: chain h residue 129 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 MET Chi-restraints excluded: chain n residue 158 ARG Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 747 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 441 optimal weight: 8.9990 chunk 565 optimal weight: 5.9990 chunk 438 optimal weight: 6.9990 chunk 652 optimal weight: 1.9990 chunk 432 optimal weight: 10.0000 chunk 772 optimal weight: 10.0000 chunk 483 optimal weight: 5.9990 chunk 470 optimal weight: 6.9990 chunk 356 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN C 211 GLN E 121 GLN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN F 431 GLN ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 HIS L 579 ASN M 220 HIS P 36 ASN R 3 GLN Z 84 GLN ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 62 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 77 GLN ** o 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.244 69501 Z= 0.547 Angle : 1.580 50.783 94103 Z= 1.013 Chirality : 0.310 6.498 10349 Planarity : 0.005 0.062 11699 Dihedral : 11.239 177.475 10872 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.65 % Favored : 97.34 % Rotamer: Outliers : 2.90 % Allowed : 13.68 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: 0.85 (0.09), residues: 8106 helix: 1.14 (0.08), residues: 4281 sheet: 0.18 (0.26), residues: 382 loop : -0.00 (0.11), residues: 3443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 254 HIS 0.006 0.001 HIS D 347 PHE 0.024 0.002 PHE M 151 TYR 0.022 0.002 TYR I 120 ARG 0.009 0.001 ARG M 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1098 time to evaluate : 6.314 Fit side-chains REVERT: A 83 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7499 (mtpp) REVERT: A 109 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8242 (mppt) REVERT: B 180 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: C 20 LYS cc_start: 0.8023 (tppp) cc_final: 0.7613 (ttpp) REVERT: C 61 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8561 (mp) REVERT: C 112 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6953 (p0) REVERT: D 59 HIS cc_start: 0.8117 (m170) cc_final: 0.7885 (m-70) REVERT: D 75 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7870 (ttmt) REVERT: D 112 MET cc_start: 0.8663 (mmt) cc_final: 0.7918 (mtt) REVERT: D 290 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7328 (mtm110) REVERT: D 405 MET cc_start: 0.8759 (mtp) cc_final: 0.8368 (mtm) REVERT: E 10 ARG cc_start: 0.7591 (mtm-85) cc_final: 0.7112 (mtm-85) REVERT: F 32 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7226 (mtm180) REVERT: F 314 THR cc_start: 0.7493 (OUTLIER) cc_final: 0.7275 (t) REVERT: F 317 MET cc_start: 0.8253 (mmp) cc_final: 0.7814 (mmm) REVERT: F 437 HIS cc_start: 0.5486 (m170) cc_final: 0.5198 (m170) REVERT: G 21 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6612 (pm20) REVERT: G 122 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7819 (mpp) REVERT: G 276 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7787 (mtt-85) REVERT: G 387 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6405 (mt-10) REVERT: G 436 ARG cc_start: 0.6668 (mtm-85) cc_final: 0.5696 (mtm-85) REVERT: G 445 ASP cc_start: 0.5764 (m-30) cc_final: 0.5309 (m-30) REVERT: G 568 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: G 613 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7643 (p90) REVERT: H 62 ARG cc_start: 0.7121 (mtm180) cc_final: 0.6863 (mtp85) REVERT: H 163 GLN cc_start: 0.8259 (tt0) cc_final: 0.7872 (mt0) REVERT: H 230 ASN cc_start: 0.8105 (m-40) cc_final: 0.7733 (t0) REVERT: H 302 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8090 (mtp) REVERT: H 318 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7373 (mtp) REVERT: I 131 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8489 (m-30) REVERT: L 23 MET cc_start: 0.8223 (mtp) cc_final: 0.7981 (mtp) REVERT: L 42 PHE cc_start: 0.8176 (m-80) cc_final: 0.7927 (m-80) REVERT: L 62 MET cc_start: 0.8311 (ttt) cc_final: 0.8012 (ttp) REVERT: L 405 ASN cc_start: 0.8133 (t0) cc_final: 0.7677 (m-40) REVERT: L 468 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8217 (mt) REVERT: L 511 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8012 (mm) REVERT: M 138 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.7960 (t0) REVERT: M 139 GLN cc_start: 0.7964 (mm110) cc_final: 0.7582 (mt0) REVERT: M 168 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: M 177 MET cc_start: 0.7868 (mtm) cc_final: 0.7413 (mtm) REVERT: N 282 MET cc_start: 0.8307 (mtp) cc_final: 0.7946 (mtm) REVERT: O 20 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5937 (pt0) REVERT: O 213 LYS cc_start: 0.8594 (tptp) cc_final: 0.8052 (ttpp) REVERT: O 265 ASP cc_start: 0.7460 (t0) cc_final: 0.6959 (t70) REVERT: O 311 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: P 50 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8516 (ptt180) REVERT: P 123 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6918 (mt-10) REVERT: P 127 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: P 265 TRP cc_start: 0.7553 (t60) cc_final: 0.7197 (t60) REVERT: Q 109 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7453 (mttt) REVERT: R 3 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7542 (mp-120) REVERT: R 21 LYS cc_start: 0.8632 (mttt) cc_final: 0.8241 (mtmm) REVERT: R 37 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: R 92 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7933 (ttpt) REVERT: S 25 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7164 (mtt90) REVERT: S 42 GLU cc_start: 0.7704 (tp30) cc_final: 0.7442 (tp30) REVERT: S 74 LYS cc_start: 0.7985 (mtpm) cc_final: 0.7648 (mtpt) REVERT: T 16 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7416 (tm) REVERT: U 20 LYS cc_start: 0.8429 (mtpt) cc_final: 0.7999 (mttt) REVERT: V 53 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7019 (tt0) REVERT: V 85 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8053 (mmmm) REVERT: V 109 ASN cc_start: 0.7814 (m-40) cc_final: 0.7457 (p0) REVERT: W 43 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7019 (mtp180) REVERT: W 59 LYS cc_start: 0.8203 (tmtm) cc_final: 0.7960 (tmtm) REVERT: W 89 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8101 (mtpp) REVERT: X 99 CYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7781 (m) REVERT: X 107 ASP cc_start: 0.8763 (m-30) cc_final: 0.8497 (m-30) REVERT: X 131 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7968 (ttmm) REVERT: Y 18 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7194 (mt0) REVERT: Y 32 ILE cc_start: 0.8161 (mt) cc_final: 0.7884 (mm) REVERT: a 35 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7553 (mt-10) REVERT: b 30 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8449 (mt) REVERT: c 36 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7494 (t0) REVERT: d 44 MET cc_start: 0.7422 (tpp) cc_final: 0.7003 (tpp) REVERT: d 91 PHE cc_start: 0.8648 (m-10) cc_final: 0.8438 (m-10) REVERT: d 95 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7769 (mttt) REVERT: d 106 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7709 (mmmm) REVERT: d 107 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7442 (mmpt) REVERT: f 41 MET cc_start: 0.7305 (mmm) cc_final: 0.6970 (mmt) REVERT: g 31 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6179 (pp20) REVERT: g 107 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7114 (tp30) REVERT: h 100 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8250 (mtmm) REVERT: h 107 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: h 129 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6727 (mt-10) REVERT: i 110 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7242 (tt) REVERT: j 40 PHE cc_start: 0.8556 (t80) cc_final: 0.8341 (t80) REVERT: k 54 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: l 24 LYS cc_start: 0.8438 (tttp) cc_final: 0.8135 (tttt) REVERT: m 18 ASP cc_start: 0.7473 (t0) cc_final: 0.7224 (t70) REVERT: m 34 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6948 (mt-10) REVERT: m 57 SER cc_start: 0.8736 (p) cc_final: 0.8392 (p) REVERT: m 105 LYS cc_start: 0.8193 (tptp) cc_final: 0.7916 (tptp) REVERT: m 109 ASP cc_start: 0.7529 (m-30) cc_final: 0.7323 (m-30) REVERT: m 110 ARG cc_start: 0.7055 (ttp80) cc_final: 0.6429 (ttp-170) REVERT: n 58 ARG cc_start: 0.6666 (tpt-90) cc_final: 0.5930 (tpt-90) REVERT: n 61 GLN cc_start: 0.7350 (tm-30) cc_final: 0.6965 (tm-30) REVERT: o 7 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6551 (tmm-80) REVERT: o 67 LYS cc_start: 0.7843 (tptm) cc_final: 0.7453 (ttpp) REVERT: p 38 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7970 (mm) outliers start: 209 outliers final: 106 residues processed: 1204 average time/residue: 1.6059 time to fit residues: 2481.6279 Evaluate side-chains 1233 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1083 time to evaluate : 6.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 61 LYS Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 568 GLU Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain G residue 638 GLU Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 461 SER Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 292 SER Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 311 GLU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 109 LYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain W residue 43 ARG Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain W residue 89 LYS Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 18 GLN Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain c residue 36 ASN Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 21 THR Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 107 GLU Chi-restraints excluded: chain h residue 129 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 54 GLU Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 MET Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain n residue 158 ARG Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 35 GLU Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 39 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain s residue 28 ASP Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 477 optimal weight: 0.5980 chunk 308 optimal weight: 2.9990 chunk 461 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 490 optimal weight: 0.9990 chunk 525 optimal weight: 9.9990 chunk 381 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 606 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN F 431 GLN F 437 HIS I 22 ASN L 109 HIS L 579 ASN P 36 ASN Z 84 GLN f 9 HIS ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN l 62 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 77 GLN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 69501 Z= 0.475 Angle : 1.553 50.584 94103 Z= 1.003 Chirality : 0.307 6.388 10349 Planarity : 0.004 0.054 11699 Dihedral : 10.893 174.858 10872 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.08 % Favored : 97.89 % Rotamer: Outliers : 2.29 % Allowed : 14.85 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: 1.03 (0.09), residues: 8106 helix: 1.32 (0.08), residues: 4279 sheet: 0.17 (0.26), residues: 387 loop : 0.06 (0.11), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 157 HIS 0.006 0.001 HIS F 437 PHE 0.022 0.001 PHE N 292 TYR 0.019 0.001 TYR J 108 ARG 0.008 0.000 ARG M 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1097 time to evaluate : 6.351 Fit side-chains revert: symmetry clash REVERT: A 23 TRP cc_start: 0.8210 (m100) cc_final: 0.7914 (m100) REVERT: A 83 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7416 (mtpp) REVERT: A 109 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8259 (mppt) REVERT: B 180 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: C 20 LYS cc_start: 0.8003 (tppp) cc_final: 0.7604 (ttpp) REVERT: C 61 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8538 (mp) REVERT: D 59 HIS cc_start: 0.8076 (m170) cc_final: 0.7866 (m-70) REVERT: D 75 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7851 (ttmt) REVERT: D 112 MET cc_start: 0.8574 (mmt) cc_final: 0.7995 (mtt) REVERT: D 290 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7340 (mtm110) REVERT: D 405 MET cc_start: 0.8761 (mtp) cc_final: 0.8341 (mtm) REVERT: E 10 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.7132 (mtm-85) REVERT: F 32 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7229 (mtm180) REVERT: F 317 MET cc_start: 0.8195 (mmp) cc_final: 0.7810 (mmm) REVERT: F 437 HIS cc_start: 0.5554 (OUTLIER) cc_final: 0.5067 (m170) REVERT: G 21 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6515 (pm20) REVERT: G 276 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7723 (mtt-85) REVERT: G 387 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6387 (mt-10) REVERT: G 436 ARG cc_start: 0.6597 (mtm-85) cc_final: 0.5802 (mtm-85) REVERT: G 568 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: H 62 ARG cc_start: 0.7134 (mtm180) cc_final: 0.6904 (mtp85) REVERT: H 163 GLN cc_start: 0.8278 (tt0) cc_final: 0.7923 (mt0) REVERT: H 230 ASN cc_start: 0.7987 (m-40) cc_final: 0.7665 (t0) REVERT: H 253 GLU cc_start: 0.8053 (mp0) cc_final: 0.7742 (mp0) REVERT: H 318 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7265 (mtp) REVERT: I 22 ASN cc_start: 0.7628 (m-40) cc_final: 0.7165 (m110) REVERT: I 131 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8440 (m-30) REVERT: J 109 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.5678 (m-80) REVERT: L 23 MET cc_start: 0.8180 (mtp) cc_final: 0.7935 (mtp) REVERT: L 42 PHE cc_start: 0.8169 (m-80) cc_final: 0.7924 (m-80) REVERT: L 62 MET cc_start: 0.8305 (ttt) cc_final: 0.8011 (ttp) REVERT: L 341 MET cc_start: 0.8158 (mtp) cc_final: 0.7956 (ttm) REVERT: L 405 ASN cc_start: 0.7933 (t0) cc_final: 0.7575 (m-40) REVERT: L 468 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8148 (mt) REVERT: M 138 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.7988 (t0) REVERT: M 168 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8269 (tp40) REVERT: M 177 MET cc_start: 0.7840 (mtm) cc_final: 0.7400 (mtm) REVERT: N 217 MET cc_start: 0.8548 (mtp) cc_final: 0.8147 (mtt) REVERT: N 282 MET cc_start: 0.8335 (mtp) cc_final: 0.7923 (mtm) REVERT: O 20 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5913 (pt0) REVERT: O 213 LYS cc_start: 0.8574 (tptp) cc_final: 0.8088 (ttpp) REVERT: O 265 ASP cc_start: 0.7421 (t0) cc_final: 0.6916 (t70) REVERT: O 311 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: P 50 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8085 (ptt180) REVERT: P 123 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6870 (mt-10) REVERT: P 127 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: Q 109 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7431 (mttt) REVERT: R 3 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7515 (mp-120) REVERT: R 21 LYS cc_start: 0.8595 (mttt) cc_final: 0.8211 (mtmm) REVERT: R 37 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7038 (mt-10) REVERT: R 92 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7920 (ttpt) REVERT: S 25 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7166 (mtt90) REVERT: S 42 GLU cc_start: 0.7699 (tp30) cc_final: 0.7413 (tp30) REVERT: S 74 LYS cc_start: 0.7994 (mtpm) cc_final: 0.7671 (mtpt) REVERT: T 16 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7305 (tm) REVERT: U 20 LYS cc_start: 0.8426 (mtpt) cc_final: 0.7968 (mttt) REVERT: V 53 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6911 (tt0) REVERT: V 85 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8021 (mmmm) REVERT: V 109 ASN cc_start: 0.7790 (m-40) cc_final: 0.7326 (p0) REVERT: W 59 LYS cc_start: 0.8147 (tmtm) cc_final: 0.7907 (tmtm) REVERT: W 89 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8088 (mtpp) REVERT: X 99 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7725 (m) REVERT: X 107 ASP cc_start: 0.8831 (m-30) cc_final: 0.8499 (m-30) REVERT: Y 32 ILE cc_start: 0.8127 (mt) cc_final: 0.7832 (mm) REVERT: Y 60 TYR cc_start: 0.7995 (m-10) cc_final: 0.7769 (m-10) REVERT: a 35 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7577 (mt-10) REVERT: b 10 ASN cc_start: 0.7068 (t0) cc_final: 0.6757 (t0) REVERT: b 30 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8355 (mt) REVERT: c 36 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7478 (t0) REVERT: d 44 MET cc_start: 0.7412 (tpp) cc_final: 0.6972 (tpp) REVERT: d 91 PHE cc_start: 0.8606 (m-10) cc_final: 0.8397 (m-10) REVERT: d 95 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7787 (mttt) REVERT: d 106 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7688 (mmmm) REVERT: d 107 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7429 (mmpt) REVERT: f 41 MET cc_start: 0.7259 (mmm) cc_final: 0.6819 (mmt) REVERT: g 31 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5986 (pp20) REVERT: g 107 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7061 (tp30) REVERT: h 100 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8221 (mtmm) REVERT: h 107 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: h 129 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6680 (mt-10) REVERT: i 110 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7271 (tt) REVERT: j 40 PHE cc_start: 0.8556 (t80) cc_final: 0.8340 (t80) REVERT: k 54 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: l 24 LYS cc_start: 0.8459 (tttp) cc_final: 0.8167 (tttt) REVERT: m 18 ASP cc_start: 0.7459 (t0) cc_final: 0.7187 (t70) REVERT: m 29 ARG cc_start: 0.7417 (mmt90) cc_final: 0.7199 (mpt-90) REVERT: m 34 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6948 (mt-10) REVERT: m 57 SER cc_start: 0.8727 (p) cc_final: 0.8394 (p) REVERT: m 105 LYS cc_start: 0.8182 (tptp) cc_final: 0.7900 (tptp) REVERT: m 110 ARG cc_start: 0.7070 (ttp80) cc_final: 0.6467 (ttp-170) REVERT: n 58 ARG cc_start: 0.6684 (tpt-90) cc_final: 0.5955 (tpt-90) REVERT: n 61 GLN cc_start: 0.7341 (tm-30) cc_final: 0.6910 (tm-30) REVERT: n 89 SER cc_start: 0.8941 (m) cc_final: 0.8706 (m) REVERT: o 7 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7678 (ttt-90) REVERT: o 67 LYS cc_start: 0.7807 (tptm) cc_final: 0.7405 (ttpp) REVERT: o 104 GLU cc_start: 0.8028 (tp30) cc_final: 0.7726 (tm-30) REVERT: p 38 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7923 (mm) REVERT: q 25 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.6904 (ttp-170) outliers start: 165 outliers final: 75 residues processed: 1183 average time/residue: 1.6192 time to fit residues: 2460.3777 Evaluate side-chains 1196 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1083 time to evaluate : 6.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 61 LYS Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 568 GLU Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 292 SER Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 311 GLU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain Q residue 109 LYS Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain W residue 89 LYS Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 131 LEU Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain c residue 36 ASN Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 86 MET Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 107 GLU Chi-restraints excluded: chain h residue 129 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain k residue 54 GLU Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 MET Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain n residue 158 ARG Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 702 optimal weight: 8.9990 chunk 739 optimal weight: 2.9990 chunk 674 optimal weight: 10.0000 chunk 719 optimal weight: 9.9990 chunk 433 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 564 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 650 optimal weight: 0.4980 chunk 680 optimal weight: 7.9990 chunk 716 optimal weight: 0.0020 overall best weight: 3.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN F 431 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 HIS L 579 ASN P 36 ASN Z 84 GLN h 108 GLN ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 62 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 77 GLN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 69501 Z= 0.526 Angle : 1.574 50.580 94103 Z= 1.011 Chirality : 0.310 6.459 10349 Planarity : 0.005 0.061 11699 Dihedral : 11.049 178.954 10872 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.63 % Favored : 97.36 % Rotamer: Outliers : 2.46 % Allowed : 14.93 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: 0.88 (0.09), residues: 8106 helix: 1.19 (0.08), residues: 4264 sheet: 0.18 (0.26), residues: 380 loop : -0.01 (0.11), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 157 HIS 0.016 0.001 HIS F 437 PHE 0.023 0.002 PHE N 292 TYR 0.021 0.002 TYR J 108 ARG 0.008 0.001 ARG F 438 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1085 time to evaluate : 6.165 Fit side-chains revert: symmetry clash REVERT: A 83 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7483 (mtpp) REVERT: A 109 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8268 (mppt) REVERT: B 126 MET cc_start: 0.8456 (ttp) cc_final: 0.8149 (ppp) REVERT: B 180 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: C 20 LYS cc_start: 0.8013 (tppp) cc_final: 0.7595 (ttpp) REVERT: C 61 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8573 (mp) REVERT: D 59 HIS cc_start: 0.8088 (m170) cc_final: 0.7866 (m-70) REVERT: D 75 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7912 (ttmt) REVERT: D 112 MET cc_start: 0.8622 (mmt) cc_final: 0.8007 (mtt) REVERT: D 290 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7337 (mtm110) REVERT: E 10 ARG cc_start: 0.7597 (mtm-85) cc_final: 0.7111 (mtm-85) REVERT: F 32 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7252 (mtm180) REVERT: F 317 MET cc_start: 0.8240 (mmp) cc_final: 0.7842 (mmm) REVERT: F 437 HIS cc_start: 0.5201 (m170) cc_final: 0.4975 (m170) REVERT: G 21 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6556 (pm20) REVERT: G 122 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7831 (mpp) REVERT: G 276 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7783 (mtt-85) REVERT: G 387 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6390 (mt-10) REVERT: G 436 ARG cc_start: 0.6651 (mtm-85) cc_final: 0.5721 (mtm-85) REVERT: G 445 ASP cc_start: 0.5754 (m-30) cc_final: 0.5293 (m-30) REVERT: G 568 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: G 622 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7841 (tpt-90) REVERT: H 62 ARG cc_start: 0.7142 (mtm180) cc_final: 0.6890 (mtp85) REVERT: H 163 GLN cc_start: 0.8269 (tt0) cc_final: 0.7901 (mt0) REVERT: H 230 ASN cc_start: 0.8092 (m-40) cc_final: 0.7735 (t0) REVERT: H 318 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7347 (mtp) REVERT: I 22 ASN cc_start: 0.7642 (m-40) cc_final: 0.7166 (m110) REVERT: I 131 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8479 (m-30) REVERT: J 109 TYR cc_start: 0.5940 (OUTLIER) cc_final: 0.5695 (m-80) REVERT: L 23 MET cc_start: 0.8215 (mtp) cc_final: 0.7974 (mtp) REVERT: L 42 PHE cc_start: 0.8158 (m-80) cc_final: 0.7913 (m-80) REVERT: L 62 MET cc_start: 0.8288 (ttt) cc_final: 0.8009 (ttp) REVERT: L 405 ASN cc_start: 0.8021 (t0) cc_final: 0.7596 (m-40) REVERT: L 468 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8213 (mt) REVERT: L 511 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8022 (mm) REVERT: M 138 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.7963 (t0) REVERT: M 177 MET cc_start: 0.7862 (mtm) cc_final: 0.7407 (mtm) REVERT: M 222 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: M 441 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7790 (mmt) REVERT: N 148 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8290 (mt) REVERT: N 217 MET cc_start: 0.8559 (mtp) cc_final: 0.8198 (mtt) REVERT: N 282 MET cc_start: 0.8289 (mtp) cc_final: 0.7950 (mtm) REVERT: O 20 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5969 (pt0) REVERT: O 213 LYS cc_start: 0.8574 (tptp) cc_final: 0.8035 (ttpp) REVERT: O 265 ASP cc_start: 0.7449 (t0) cc_final: 0.6939 (t70) REVERT: O 311 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: P 50 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8422 (ptt180) REVERT: P 123 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6871 (mt-10) REVERT: P 127 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7226 (pt0) REVERT: P 265 TRP cc_start: 0.7572 (t60) cc_final: 0.7216 (t60) REVERT: R 3 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7487 (mp-120) REVERT: R 21 LYS cc_start: 0.8654 (mttt) cc_final: 0.8272 (mtmm) REVERT: R 37 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: R 92 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7902 (ttpt) REVERT: S 25 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7197 (mtt90) REVERT: S 42 GLU cc_start: 0.7706 (tp30) cc_final: 0.7423 (tp30) REVERT: T 16 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7339 (tm) REVERT: U 20 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7949 (mttt) REVERT: V 53 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: V 85 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8033 (mmmm) REVERT: V 109 ASN cc_start: 0.7811 (m-40) cc_final: 0.7397 (p0) REVERT: W 59 LYS cc_start: 0.8175 (tmtm) cc_final: 0.7921 (tmtm) REVERT: W 89 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8097 (mtpp) REVERT: X 99 CYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7751 (m) REVERT: X 107 ASP cc_start: 0.8805 (m-30) cc_final: 0.8481 (m-30) REVERT: X 131 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7974 (ttmm) REVERT: Y 32 ILE cc_start: 0.8121 (mt) cc_final: 0.7850 (mm) REVERT: a 35 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7537 (mt-10) REVERT: b 30 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8338 (mt) REVERT: c 36 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7485 (t0) REVERT: d 44 MET cc_start: 0.7432 (tpp) cc_final: 0.7006 (tpp) REVERT: d 95 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7786 (mttt) REVERT: d 106 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7696 (mmmm) REVERT: d 107 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7447 (mmpt) REVERT: f 41 MET cc_start: 0.7324 (mmm) cc_final: 0.6989 (mmt) REVERT: g 31 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6062 (pp20) REVERT: g 107 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7074 (tp30) REVERT: h 100 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8246 (mtmm) REVERT: h 107 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7609 (tp30) REVERT: h 129 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: i 110 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7220 (tt) REVERT: j 40 PHE cc_start: 0.8579 (t80) cc_final: 0.8361 (t80) REVERT: k 19 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.4408 (mmp) REVERT: k 54 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: l 24 LYS cc_start: 0.8431 (tttp) cc_final: 0.8136 (tttt) REVERT: m 29 ARG cc_start: 0.7448 (mmt90) cc_final: 0.7212 (mmt90) REVERT: m 34 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7023 (mt-10) REVERT: m 57 SER cc_start: 0.8736 (p) cc_final: 0.8391 (p) REVERT: m 105 LYS cc_start: 0.8137 (tptp) cc_final: 0.7934 (tptp) REVERT: m 110 ARG cc_start: 0.7083 (ttp80) cc_final: 0.6447 (ttp-170) REVERT: o 7 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.6550 (tmm-80) REVERT: o 68 CYS cc_start: 0.4620 (t) cc_final: 0.4246 (t) REVERT: p 38 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7938 (mm) REVERT: p 162 MET cc_start: 0.7902 (mtp) cc_final: 0.7649 (mtp) outliers start: 177 outliers final: 97 residues processed: 1181 average time/residue: 1.6408 time to fit residues: 2484.2537 Evaluate side-chains 1218 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1079 time to evaluate : 6.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 61 LYS Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 568 GLU Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain G residue 622 ARG Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 461 SER Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 292 SER Chi-restraints excluded: chain M residue 441 MET Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 311 GLU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain W residue 89 LYS Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 131 LEU Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 143 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain c residue 36 ASN Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 86 MET Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 21 THR Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 107 GLU Chi-restraints excluded: chain h residue 129 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain k residue 54 GLU Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 MET Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain n residue 158 ARG Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain s residue 28 ASP Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 472 optimal weight: 8.9990 chunk 760 optimal weight: 6.9990 chunk 464 optimal weight: 0.9990 chunk 360 optimal weight: 4.9990 chunk 528 optimal weight: 3.9990 chunk 798 optimal weight: 9.9990 chunk 734 optimal weight: 6.9990 chunk 635 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 490 optimal weight: 0.9990 chunk 389 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN F 431 GLN L 109 HIS L 579 ASN Z 84 GLN h 108 GLN i 127 HIS l 62 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN o 75 ASN o 84 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 69501 Z= 0.486 Angle : 1.559 50.591 94103 Z= 1.005 Chirality : 0.308 6.456 10349 Planarity : 0.004 0.055 11699 Dihedral : 10.862 176.676 10872 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.32 % Favored : 97.67 % Rotamer: Outliers : 2.18 % Allowed : 15.39 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: 1.00 (0.09), residues: 8106 helix: 1.27 (0.08), residues: 4274 sheet: 0.27 (0.27), residues: 378 loop : 0.06 (0.11), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 157 HIS 0.007 0.001 HIS F 437 PHE 0.022 0.001 PHE N 292 TYR 0.021 0.001 TYR J 108 ARG 0.010 0.000 ARG G 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16212 Ramachandran restraints generated. 8106 Oldfield, 0 Emsley, 8106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1091 time to evaluate : 6.134 Fit side-chains REVERT: A 23 TRP cc_start: 0.8205 (m100) cc_final: 0.7987 (m100) REVERT: A 83 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7420 (mtpp) REVERT: A 109 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8266 (mppt) REVERT: B 180 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: C 20 LYS cc_start: 0.8024 (tppp) cc_final: 0.7622 (ttpp) REVERT: C 61 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8547 (mp) REVERT: D 59 HIS cc_start: 0.8072 (m170) cc_final: 0.7855 (m-70) REVERT: D 112 MET cc_start: 0.8565 (mmt) cc_final: 0.8014 (mtt) REVERT: D 290 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7342 (mtm110) REVERT: D 405 MET cc_start: 0.8645 (mtp) cc_final: 0.8364 (mtp) REVERT: E 10 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.7123 (mtm-85) REVERT: F 32 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7246 (mtm180) REVERT: F 317 MET cc_start: 0.8214 (mmp) cc_final: 0.7827 (mmm) REVERT: F 437 HIS cc_start: 0.5432 (m170) cc_final: 0.5111 (m170) REVERT: G 21 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: G 276 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7765 (mtt-85) REVERT: G 387 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: G 436 ARG cc_start: 0.6600 (mtm-85) cc_final: 0.5804 (mtm-85) REVERT: G 445 ASP cc_start: 0.5726 (m-30) cc_final: 0.5277 (m-30) REVERT: G 568 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: H 62 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6886 (mtp85) REVERT: H 163 GLN cc_start: 0.8272 (tt0) cc_final: 0.7916 (mt0) REVERT: H 230 ASN cc_start: 0.8006 (m-40) cc_final: 0.7664 (t0) REVERT: H 253 GLU cc_start: 0.8059 (mp0) cc_final: 0.7747 (mp0) REVERT: H 318 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7276 (mtp) REVERT: I 22 ASN cc_start: 0.7601 (m-40) cc_final: 0.7147 (m110) REVERT: I 131 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: J 109 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.5786 (m-80) REVERT: L 23 MET cc_start: 0.8186 (mtp) cc_final: 0.7942 (mtp) REVERT: L 42 PHE cc_start: 0.8179 (m-80) cc_final: 0.7941 (m-80) REVERT: L 62 MET cc_start: 0.8279 (ttt) cc_final: 0.8007 (ttp) REVERT: L 405 ASN cc_start: 0.7988 (t0) cc_final: 0.7610 (m-40) REVERT: L 468 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8166 (mt) REVERT: M 138 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7996 (t0) REVERT: M 139 GLN cc_start: 0.8007 (mm110) cc_final: 0.7602 (mt0) REVERT: M 177 MET cc_start: 0.7848 (mtm) cc_final: 0.7406 (mtm) REVERT: M 222 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: M 441 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7846 (mmt) REVERT: N 148 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8315 (mt) REVERT: N 217 MET cc_start: 0.8562 (mtp) cc_final: 0.8147 (mtt) REVERT: O 20 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5972 (pt0) REVERT: O 213 LYS cc_start: 0.8580 (tptp) cc_final: 0.8094 (ttpp) REVERT: O 265 ASP cc_start: 0.7380 (t0) cc_final: 0.6872 (t70) REVERT: O 311 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6988 (mt-10) REVERT: P 50 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8100 (ptt180) REVERT: P 123 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6867 (mt-10) REVERT: P 127 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: R 3 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7472 (mp-120) REVERT: R 21 LYS cc_start: 0.8561 (mttt) cc_final: 0.8156 (mtmm) REVERT: R 37 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7035 (mt-10) REVERT: R 92 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7921 (ttpt) REVERT: S 25 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7119 (mtt90) REVERT: S 42 GLU cc_start: 0.7704 (tp30) cc_final: 0.7423 (tp30) REVERT: S 77 SER cc_start: 0.8484 (t) cc_final: 0.8101 (m) REVERT: T 16 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7250 (tm) REVERT: U 20 LYS cc_start: 0.8429 (mtpt) cc_final: 0.7963 (mttt) REVERT: V 33 ILE cc_start: 0.8750 (tp) cc_final: 0.8450 (tt) REVERT: V 53 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: V 85 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8015 (mmmm) REVERT: V 109 ASN cc_start: 0.7786 (m-40) cc_final: 0.7361 (p0) REVERT: W 59 LYS cc_start: 0.8150 (tmtm) cc_final: 0.7898 (tmtm) REVERT: W 89 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8086 (mtpp) REVERT: X 99 CYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7734 (m) REVERT: X 107 ASP cc_start: 0.8800 (m-30) cc_final: 0.8507 (m-30) REVERT: X 131 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7924 (ttmm) REVERT: Y 18 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7218 (mt0) REVERT: Y 32 ILE cc_start: 0.8130 (mt) cc_final: 0.7840 (mm) REVERT: Y 60 TYR cc_start: 0.7918 (m-10) cc_final: 0.7668 (m-10) REVERT: a 35 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7553 (mt-10) REVERT: b 15 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7364 (mm-30) REVERT: b 30 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8289 (mt) REVERT: c 36 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7476 (t0) REVERT: d 44 MET cc_start: 0.7479 (tpp) cc_final: 0.7136 (tpp) REVERT: d 95 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7788 (mttt) REVERT: d 106 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7683 (mmmm) REVERT: d 107 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7444 (mmpt) REVERT: e 5 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8620 (OUTLIER) REVERT: e 73 ARG cc_start: 0.7541 (tpp-160) cc_final: 0.6937 (mmm-85) REVERT: f 41 MET cc_start: 0.7284 (mmm) cc_final: 0.6949 (mmt) REVERT: g 31 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6047 (pp20) REVERT: g 107 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7076 (tp30) REVERT: h 100 LYS cc_start: 0.8455 (mtpt) cc_final: 0.8239 (mtmm) REVERT: h 107 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: h 129 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: i 110 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7261 (tt) REVERT: j 40 PHE cc_start: 0.8577 (t80) cc_final: 0.8360 (t80) REVERT: k 19 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.4469 (mmp) REVERT: k 54 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: l 24 LYS cc_start: 0.8419 (tttp) cc_final: 0.8129 (tttt) REVERT: m 29 ARG cc_start: 0.7401 (mmt90) cc_final: 0.7175 (mpt-90) REVERT: m 34 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6975 (mt-10) REVERT: m 57 SER cc_start: 0.8726 (p) cc_final: 0.8388 (p) REVERT: m 105 LYS cc_start: 0.8128 (tptp) cc_final: 0.7910 (tptp) REVERT: m 110 ARG cc_start: 0.7006 (ttp80) cc_final: 0.6414 (ttp-170) REVERT: o 7 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6508 (tmm-80) REVERT: o 67 LYS cc_start: 0.7620 (tptm) cc_final: 0.7311 (ttpp) REVERT: p 38 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7919 (mm) REVERT: p 162 MET cc_start: 0.7932 (mtp) cc_final: 0.7718 (mtp) REVERT: q 25 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.6930 (ttp-110) outliers start: 157 outliers final: 95 residues processed: 1175 average time/residue: 1.6477 time to fit residues: 2486.4149 Evaluate side-chains 1207 residues out of total 7200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1073 time to evaluate : 6.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 61 LYS Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 568 GLU Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain G residue 638 GLU Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 292 SER Chi-restraints excluded: chain M residue 441 MET Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 311 GLU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain T residue 24 LYS Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain W residue 89 LYS Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 18 GLN Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 131 LEU Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 143 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain c residue 36 ASN Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 86 MET Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 21 THR Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 107 GLU Chi-restraints excluded: chain h residue 129 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain k residue 54 GLU Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 MET Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain n residue 158 ARG Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 102 MET Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 504 optimal weight: 9.9990 chunk 676 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 585 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 636 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 653 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN F 431 GLN K 7 ASN L 109 HIS L 579 ASN Z 84 GLN h 108 GLN l 62 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 77 GLN o 53 GLN o 75 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.094075 restraints weight = 74479.706| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.07 r_work: 0.2922 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 69501 Z= 0.497 Angle : 1.564 50.587 94103 Z= 1.007 Chirality : 0.308 6.458 10349 Planarity : 0.004 0.058 11699 Dihedral : 10.843 177.647 10872 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.54 % Favored : 97.45 % Rotamer: Outliers : 2.29 % Allowed : 15.28 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: 0.97 (0.09), residues: 8106 helix: 1.24 (0.08), residues: 4278 sheet: 0.26 (0.27), residues: 380 loop : 0.05 (0.11), residues: 3448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 157 HIS 0.005 0.001 HIS L 264 PHE 0.022 0.002 PHE N 292 TYR 0.023 0.002 TYR F 43 ARG 0.010 0.000 ARG G 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33101.94 seconds wall clock time: 572 minutes 31.10 seconds (34351.10 seconds total)