Starting phenix.real_space_refine on Sat Mar 16 00:59:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om1_16965/03_2024/8om1_16965_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om1_16965/03_2024/8om1_16965.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om1_16965/03_2024/8om1_16965_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om1_16965/03_2024/8om1_16965_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om1_16965/03_2024/8om1_16965_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om1_16965/03_2024/8om1_16965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om1_16965/03_2024/8om1_16965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om1_16965/03_2024/8om1_16965_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om1_16965/03_2024/8om1_16965_updated.pdb" } resolution = 2.39 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= -0.004 sd= 0.927 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 42 5.49 5 Mg 1 5.21 5 S 494 5.16 5 Na 1 4.78 5 C 44165 2.51 5 N 11213 2.21 5 O 15311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 164": "OE1" <-> "OE2" 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 49": "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 PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D GLU 24": "OE1" <-> "OE2" 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 ASP 107": "OD1" <-> "OD2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" 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 248": "OE1" <-> "OE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ASP 114": "OD1" <-> "OD2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" 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 ASP 54": "OD1" <-> "OD2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 87": "OD1" <-> "OD2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F GLU 194": "OE1" <-> "OE2" 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 GLU 270": "OE1" <-> "OE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F GLU 388": "OE1" <-> "OE2" Residue "F ARG 423": "NH1" <-> "NH2" 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 91": "OE1" <-> "OE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ASP 170": "OD1" <-> "OD2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G GLU 194": "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 GLU 256": "OE1" <-> "OE2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "G GLU 311": "OE1" <-> "OE2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "G ASP 375": "OD1" <-> "OD2" Residue "G ARG 394": "NH1" <-> "NH2" Residue "G ARG 396": "NH1" <-> "NH2" Residue "G ASP 414": "OD1" <-> "OD2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G ASP 431": "OD1" <-> "OD2" 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 GLU 605": "OE1" <-> "OE2" Residue "G ASP 617": "OD1" <-> "OD2" Residue "G GLU 624": "OE1" <-> "OE2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H ARG 279": "NH1" <-> "NH2" Residue "I ASP 15": "OD1" <-> "OD2" Residue "I ASP 21": "OD1" <-> "OD2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I GLU 76": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I ASP 131": "OD1" <-> "OD2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "J TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 110": "OD1" <-> "OD2" Residue "J ASP 118": "OD1" <-> "OD2" Residue "J GLU 127": "OE1" <-> "OE2" Residue "J GLU 168": "OE1" <-> "OE2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 163": "OD1" <-> "OD2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L ASP 297": "OD1" <-> "OD2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 436": "NH1" <-> "NH2" Residue "L ASP 447": "OD1" <-> "OD2" Residue "L ARG 535": "NH1" <-> "NH2" Residue "L ASP 554": "OD1" <-> "OD2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "M TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 251": "OD1" <-> "OD2" Residue "M ASP 281": "OD1" <-> "OD2" Residue "M GLU 335": "OE1" <-> "OE2" Residue "M GLU 378": "OE1" <-> "OE2" Residue "M GLU 433": "OE1" <-> "OE2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O ASP 65": "OD1" <-> "OD2" Residue "O ARG 67": "NH1" <-> "NH2" 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 ASP 188": "OD1" <-> "OD2" Residue "O GLU 219": "OE1" <-> "OE2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "O GLU 239": "OE1" <-> "OE2" Residue "O ASP 252": "OD1" <-> "OD2" Residue "O GLU 311": "OE1" <-> "OE2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 72": "OE1" <-> "OE2" Residue "P ASP 79": "OD1" <-> "OD2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P ARG 186": "NH1" <-> "NH2" Residue "P ASP 222": "OD1" <-> "OD2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P ASP 302": "OD1" <-> "OD2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P ARG 322": "NH1" <-> "NH2" Residue "P GLU 330": "OE1" <-> "OE2" Residue "P GLU 332": "OE1" <-> "OE2" Residue "P GLU 333": "OE1" <-> "OE2" Residue "Q ASP 18": "OD1" <-> "OD2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q GLU 97": "OE1" <-> "OE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 30": "OD1" <-> "OD2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ASP 42": "OD1" <-> "OD2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S ARG 16": "NH1" <-> "NH2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "S ARG 39": "NH1" <-> "NH2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S ASP 84": "OD1" <-> "OD2" Residue "T ASP 9": "OD1" <-> "OD2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T GLU 28": "OE1" <-> "OE2" Residue "T GLU 49": "OE1" <-> "OE2" Residue "T TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 2": "OD1" <-> "OD2" Residue "U GLU 28": "OE1" <-> "OE2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U ASP 64": "OD1" <-> "OD2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "U ASP 82": "OD1" <-> "OD2" Residue "U ASP 85": "OD1" <-> "OD2" Residue "U GLU 88": "OE1" <-> "OE2" Residue "V GLU 21": "OE1" <-> "OE2" Residue "V ASP 56": "OD1" <-> "OD2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "V GLU 77": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "W ARG 25": "NH1" <-> "NH2" Residue "W ASP 26": "OD1" <-> "OD2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W GLU 36": "OE1" <-> "OE2" Residue "W TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 44": "OE1" <-> "OE2" Residue "W GLU 67": "OE1" <-> "OE2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W ARG 107": "NH1" <-> "NH2" Residue "W GLU 113": "OE1" <-> "OE2" Residue "W ARG 116": "NH1" <-> "NH2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 83": "OE1" <-> "OE2" Residue "X ASP 112": "OD1" <-> "OD2" 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 "X ASP 156": "OD1" <-> "OD2" Residue "Y GLU 12": "OE1" <-> "OE2" Residue "Y ASP 15": "OD1" <-> "OD2" Residue "Y TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 86": "OD1" <-> "OD2" Residue "Y PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 105": "NH1" <-> "NH2" Residue "Y GLU 132": "OE1" <-> "OE2" Residue "Y GLU 135": "OE1" <-> "OE2" Residue "Z TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 57": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z GLU 77": "OE1" <-> "OE2" Residue "Z ASP 79": "OD1" <-> "OD2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z ASP 99": "OD1" <-> "OD2" Residue "Z GLU 107": "OE1" <-> "OE2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "Z GLU 122": "OE1" <-> "OE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 35": "OE1" <-> "OE2" Residue "a ARG 37": "NH1" <-> "NH2" Residue "a ARG 40": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "b TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "c ARG 5": "NH1" <-> "NH2" Residue "c ASP 38": "OD1" <-> "OD2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "c GLU 49": "OE1" <-> "OE2" Residue "d GLU 9": "OE1" <-> "OE2" Residue "d ASP 16": "OD1" <-> "OD2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 55": "NH1" <-> "NH2" Residue "d PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 105": "OE1" <-> "OE2" Residue "d TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "d ARG 120": "NH1" <-> "NH2" Residue "e ASP 4": "OD1" <-> "OD2" Residue "e GLU 23": "OE1" <-> "OE2" Residue "e GLU 36": "OE1" <-> "OE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e GLU 41": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 58": "OE1" <-> "OE2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "e GLU 88": "OE1" <-> "OE2" Residue "e ARG 100": "NH1" <-> "NH2" Residue "e GLU 101": "OE1" <-> "OE2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "f ASP 30": "OD1" <-> "OD2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f GLU 51": "OE1" <-> "OE2" Residue "g GLU 26": "OE1" <-> "OE2" Residue "g GLU 29": "OE1" <-> "OE2" Residue "g ASP 32": "OD1" <-> "OD2" Residue "g GLU 33": "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 ARG 93": "NH1" <-> "NH2" Residue "g ASP 121": "OD1" <-> "OD2" Residue "h TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h GLU 51": "OE1" <-> "OE2" Residue "h GLU 54": "OE1" <-> "OE2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h GLU 97": "OE1" <-> "OE2" Residue "h GLU 99": "OE1" <-> "OE2" Residue "h GLU 107": "OE1" <-> "OE2" Residue "h GLU 109": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "h GLU 129": "OE1" <-> "OE2" Residue "h GLU 131": "OE1" <-> "OE2" Residue "i ARG 10": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 102": "NH1" <-> "NH2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "i PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 124": "OD1" <-> "OD2" Residue "j GLU 26": "OE1" <-> "OE2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "j ASP 61": "OD1" <-> "OD2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j ASP 69": "OD1" <-> "OD2" Residue "k GLU 20": "OE1" <-> "OE2" Residue "k ARG 25": "NH1" <-> "NH2" Residue "k GLU 30": "OE1" <-> "OE2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "k GLU 90": "OE1" <-> "OE2" Residue "k TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 14": "NH1" <-> "NH2" Residue "l GLU 17": "OE1" <-> "OE2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l ARG 29": "NH1" <-> "NH2" Residue "l GLU 34": "OE1" <-> "OE2" Residue "l ASP 38": "OD1" <-> "OD2" Residue "l GLU 74": "OE1" <-> "OE2" Residue "l ARG 85": "NH1" <-> "NH2" Residue "l ARG 87": "NH1" <-> "NH2" Residue "l TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 18": "OD1" <-> "OD2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m ARG 41": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 60": "OE1" <-> "OE2" Residue "m ARG 66": "NH1" <-> "NH2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "m PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 107": "OD1" <-> "OD2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "m ARG 113": "NH1" <-> "NH2" Residue "m GLU 117": "OE1" <-> "OE2" Residue "m ARG 122": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ASP 34": "OD1" <-> "OD2" Residue "n GLU 65": "OE1" <-> "OE2" Residue "n GLU 68": "OE1" <-> "OE2" Residue "n GLU 94": "OE1" <-> "OE2" Residue "n GLU 100": "OE1" <-> "OE2" Residue "n GLU 110": "OE1" <-> "OE2" Residue "n TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 121": "NH1" <-> "NH2" Residue "n ASP 133": "OD1" <-> "OD2" Residue "n GLU 141": "OE1" <-> "OE2" Residue "n ARG 157": "NH1" <-> "NH2" Residue "n ARG 158": "NH1" <-> "NH2" Residue "n GLU 159": "OE1" <-> "OE2" Residue "n ARG 174": "NH1" <-> "NH2" Residue "o ARG 7": "NH1" <-> "NH2" Residue "o GLU 15": "OE1" <-> "OE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o ARG 33": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ASP 85": "OD1" <-> "OD2" Residue "o TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o GLU 104": "OE1" <-> "OE2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o ARG 110": "NH1" <-> "NH2" Residue "p ARG 15": "NH1" <-> "NH2" Residue "p TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p ARG 53": "NH1" <-> "NH2" Residue "p TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 65": "NH1" <-> "NH2" Residue "p GLU 78": "OE1" <-> "OE2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 127": "OE1" <-> "OE2" Residue "q GLU 2": "OE1" <-> "OE2" Residue "q ASP 32": "OD1" <-> "OD2" Residue "q ARG 34": "NH1" <-> "NH2" Residue "q GLU 41": "OE1" <-> "OE2" Residue "q ASP 51": "OD1" <-> "OD2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "q GLU 85": "OE1" <-> "OE2" Residue "q ARG 131": "NH1" <-> "NH2" Residue "r ARG 11": "NH1" <-> "NH2" Residue "r ARG 26": "NH1" <-> "NH2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r ARG 33": "NH1" <-> "NH2" Residue "r GLU 104": "OE1" <-> "OE2" Residue "s ASP 47": "OD1" <-> "OD2" Residue "s ASP 51": "OD1" <-> "OD2" Residue "s ARG 56": "NH1" <-> "NH2" Residue "s ARG 64": "NH1" <-> "NH2" Residue "s GLU 65": "OE1" <-> "OE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 71256 Number of models: 1 Model: "" Number of chains: 118 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: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1259 Classifications: {'peptide': 157} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'WYK:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: 5301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5301 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 31, 'TRANS': 657} 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: 4809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4809 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 26, 'TRANS': 580} 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: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1021 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 685 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} 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: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 706 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "V" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 105} 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: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} 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: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 482 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "g" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 850 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1166 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} 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': 2, 'PTRANS': 10, '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: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 566 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 6, 'TRANS': 59} 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: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1323 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 18, 'TRANS': 138} 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: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1541 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "o" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1019 Classifications: {'peptide': 119} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 111} Chain: "p" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1439 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "q" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1212 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} 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: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 809 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 11, 'TRANS': 89} 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: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 104 Unusual residues: {'LMT': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'CDL:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'3PE': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 71 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "L" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 288 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 3, 'PC1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 73 Chain: "M" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "N" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 142 Unusual residues: {'3PE': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' MG': 1, '3PE': 1, 'DGT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "Y" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 143 Unusual residues: {'3PE': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "Z" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "d" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "f" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "h" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 171 Unusual residues: {'CDL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 61 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: "p" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "q" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "r" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "D" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 257 Classifications: {'water': 257} Link IDs: {None: 256} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "G" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 300 Classifications: {'water': 300} Link IDs: {None: 299} Chain: "H" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "I" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "K" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "M" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 190 Classifications: {'water': 190} Link IDs: {None: 189} Chain: "N" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Chain: "P" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 149 Classifications: {'water': 149} Link IDs: {None: 148} Chain: "Q" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "W" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "X" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "a" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "b" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "e" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "f" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "h" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "i" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "l" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "m" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "n" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "p" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "r" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "s" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1700 SG CYS B 129 96.791 91.704 199.993 1.00 10.62 S ATOM 1202 SG CYS B 65 90.634 93.662 201.687 1.00 12.11 S ATOM 1196 SG CYS B 64 91.475 87.957 198.688 1.00 12.26 S ATOM 1930 SG CYS B 159 94.356 89.006 204.562 1.00 10.80 S ATOM 8192 SG CYS E 103 113.998 43.521 255.896 1.00 29.00 S ATOM 8226 SG CYS E 108 112.549 40.748 257.730 1.00 29.84 S ATOM 8510 SG CYS E 144 116.830 40.499 252.691 1.00 27.91 S ATOM 8533 SG CYS E 148 115.574 37.515 253.696 1.00 30.15 S ATOM 11751 SG CYS F 362 120.109 50.710 232.665 1.00 15.36 S ATOM 11771 SG CYS F 365 117.098 49.840 237.332 1.00 16.16 S ATOM 12093 SG CYS F 405 121.992 45.659 236.735 1.00 18.29 S ATOM 11732 SG CYS F 359 123.477 51.640 238.305 1.00 18.05 S ATOM 13197 SG CYS G 114 116.035 69.151 223.215 1.00 13.04 S ATOM 13136 SG CYS G 105 109.984 71.262 224.950 1.00 11.84 S ATOM 13157 SG CYS G 108 115.349 74.020 227.383 1.00 12.81 S ATOM 13529 SG CYS G 156 124.592 63.468 228.661 1.00 14.51 S ATOM 13506 SG CYS G 153 121.278 65.543 234.130 1.00 14.02 S ATOM 13553 SG CYS G 159 127.539 66.884 233.106 1.00 16.72 S ATOM 13882 SG CYS G 203 123.067 69.413 229.052 1.00 14.45 S ATOM 12643 SG CYS G 41 125.453 56.867 226.448 1.00 14.27 S ATOM 12729 SG CYS G 52 121.697 57.063 225.146 1.00 13.72 S ATOM 12754 SG CYS G 55 123.603 52.714 221.869 1.00 15.05 S ATOM 12855 SG CYS G 69 126.779 53.555 223.281 1.00 16.46 S ATOM 21229 SG CYS I 128 101.016 82.335 223.793 1.00 11.61 S ATOM 20899 SG CYS I 85 104.454 85.127 219.025 1.00 11.03 S ATOM 20857 SG CYS I 79 105.663 86.867 225.130 1.00 12.08 S ATOM 20876 SG CYS I 82 106.666 80.541 222.704 1.00 12.19 S ATOM 21179 SG CYS I 121 97.478 83.388 210.641 1.00 9.70 S ATOM 21153 SG CYS I 118 97.468 89.944 211.474 1.00 10.01 S ATOM 21200 SG CYS I 124 98.585 85.530 216.185 1.00 10.67 S ATOM 20927 SG CYS I 89 102.974 86.512 211.269 1.00 10.54 S ATOM 41684 SG CYS R 59 102.308 77.826 238.994 1.00 16.60 S ATOM 41860 SG CYS R 84 105.327 78.805 237.042 1.00 16.76 S ATOM 41882 SG CYS R 87 102.608 81.164 237.709 1.00 15.47 S Time building chain proxies: 29.29, per 1000 atoms: 0.41 Number of scatterers: 71256 At special positions: 0 Unit cell: (186.755, 189.502, 288.372, 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 42 15.00 Mg 1 11.99 Na 1 11.00 O 15311 8.00 N 11213 7.00 C 44165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.98 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " 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="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 159 " 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="FE4 SF4 F 501 " - pdb=" SG CYS F 359 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 362 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 405 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " 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="FE1 SF4 I 201 " - pdb=" SG CYS I 128 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 85 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 79 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 82 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 118 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 89 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 124 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 121 " 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 59 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " Number of angles added : 3 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15520 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 359 helices and 29 sheets defined 53.7% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.35 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 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 72 removed outlier: 3.598A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 4.395A 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 removed outlier: 3.724A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 104 through 115 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 127 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 179 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: 4.604A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.529A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.936A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C 137 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 3.920A 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: 3.912A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.826A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 Proline residue: D 101 - end of helix removed outlier: 3.813A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.649A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.896A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.567A 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: 4.641A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 293 through 317 removed outlier: 3.502A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 405 removed outlier: 4.689A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.612A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.264A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.608A pdb=" N GLN E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.548A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.777A 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 178 Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 45 through 63 removed outlier: 3.822A pdb=" N GLY F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Proline residue: F 53 - end of helix Processing helix chain 'F' and resid 75 through 82 removed outlier: 3.641A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 removed outlier: 3.517A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 129 Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 189 through 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 229 Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 276 through 283 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.335A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.749A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 437 Proline residue: F 414 - end of helix removed outlier: 3.660A pdb=" N ARG F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Proline residue: F 424 - end of helix Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.634A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.567A pdb=" N ILE G 202 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 275 removed outlier: 5.338A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.794A 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: 3.586A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 362 Processing helix chain 'G' and resid 369 through 372 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 removed outlier: 3.708A pdb=" N ILE G 432 " --> pdb=" O LEU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 445 removed outlier: 3.696A pdb=" N LEU G 443 " --> pdb=" O CYS G 440 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS G 444 " --> pdb=" O GLU G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 461 through 481 removed outlier: 4.630A pdb=" N ALA G 464 " --> pdb=" O ASP G 461 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 470 " --> pdb=" O LEU G 467 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL G 479 " --> pdb=" O LYS G 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR G 481 " --> pdb=" O ARG G 478 " (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 534 through 536 No H-bonds generated for 'chain 'G' and resid 534 through 536' 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 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.572A pdb=" N VAL G 631 " --> pdb=" O PRO G 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 628 through 631' Processing helix chain 'G' and resid 642 through 651 removed outlier: 3.836A pdb=" N LEU G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 679 No H-bonds generated for 'chain 'G' and resid 676 through 679' Processing helix chain 'G' and resid 682 through 690 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix removed outlier: 3.620A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.173A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.880A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.125A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 4.013A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 192 Proline residue: H 180 - end of helix Processing helix chain 'H' and resid 204 through 207 No H-bonds generated for 'chain 'H' and resid 204 through 207' Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 217 through 242 removed outlier: 3.747A 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: 3.564A 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 28 Processing helix chain 'I' and resid 30 through 43 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 177 removed outlier: 5.917A pdb=" N ALA I 165 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU I 176 " --> pdb=" O GLN I 172 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) 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: 3.514A pdb=" N ALA J 72 " --> pdb=" O GLY J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 109 Processing helix chain 'J' and resid 137 through 145 removed outlier: 4.641A pdb=" N MET J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 170 removed outlier: 3.720A 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 50 Processing helix chain 'K' and resid 54 through 85 Proline residue: K 58 - end of helix removed outlier: 3.628A pdb=" N PHE K 66 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.514A 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: 3.943A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.569A pdb=" N MET L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.753A pdb=" N LYS L 28 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 57 removed outlier: 4.022A 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: 3.702A pdb=" N TRP L 106 " --> pdb=" O GLN L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 155 removed outlier: 3.660A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 192 removed outlier: 4.208A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.070A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.335A 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 232 through 238 removed outlier: 4.023A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.383A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.552A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.522A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR L 294 " --> pdb=" O ILE L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.975A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.869A 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: 5.376A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.556A 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: 6.386A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.264A 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 508 removed outlier: 3.748A pdb=" N THR L 508 " --> pdb=" O LEU L 504 " (cutoff:3.500A) 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: 3.718A pdb=" N ILE L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE L 536 " --> pdb=" O ILE L 533 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.577A pdb=" N SER L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU L 542 " --> pdb=" O MET L 539 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU L 544 " --> pdb=" O SER L 541 " (cutoff:3.500A) removed outlier: 3.730A 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 578 Processing helix chain 'L' and resid 584 through 604 Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.196A 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: 3.687A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.547A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) 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: 4.573A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.491A 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: 3.543A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE M 158 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.507A 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: 4.920A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.620A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 249 removed outlier: 4.259A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.766A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 4.001A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.682A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.773A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 3.755A 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: 3.588A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER M 407 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET M 408 " --> pdb=" O MET M 405 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.980A 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 removed outlier: 3.541A pdb=" N ILE M 454 " --> pdb=" O PRO M 451 " (cutoff:3.500A) No H-bonds generated for '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 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: 4.289A 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 148 removed outlier: 4.536A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.501A pdb=" N TYR N 146 " --> pdb=" O ILE N 143 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.931A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 194 removed outlier: 3.547A pdb=" N ILE N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Proline residue: N 214 - end of helix removed outlier: 4.348A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.786A pdb=" N LEU N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 4.263A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE N 244 " --> pdb=" O LEU N 241 " (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: 3.720A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN N 289 " --> pdb=" O MET N 285 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU N 290 " --> pdb=" O ALA N 286 " (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: 3.977A 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 35 through 46 Processing helix chain 'O' and resid 58 through 61 No H-bonds generated for 'chain 'O' and resid 58 through 61' Processing helix chain 'O' and resid 71 through 73 No H-bonds generated for 'chain 'O' and resid 71 through 73' 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 removed outlier: 3.735A pdb=" N GLU O 136 " --> pdb=" O VAL O 133 " (cutoff:3.500A) 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 216 removed outlier: 3.782A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 228 No H-bonds generated for 'chain 'O' and resid 225 through 228' Processing helix chain 'O' and resid 231 through 239 Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 263 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 280 through 282 No H-bonds generated for 'chain 'O' and resid 280 through 282' Processing helix chain 'O' and resid 286 through 298 removed outlier: 3.505A pdb=" N GLU O 298 " --> pdb=" O ASN O 294 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' Processing helix chain 'P' and resid 3 through 5 No H-bonds generated for 'chain 'P' and resid 3 through 5' Processing helix chain 'P' and resid 29 through 41 removed outlier: 4.163A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 4.800A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU P 61 " --> pdb=" O HIS P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 85 Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 123 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 188 removed outlier: 3.604A pdb=" N TYR P 185 " --> pdb=" O HIS P 181 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 4.700A 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 Processing helix chain 'P' and resid 281 through 288 removed outlier: 3.508A 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: 5.722A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL P 317 " --> pdb=" O LYS P 313 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.202A 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: 4.014A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 98 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 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: 4.852A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN S 38 " --> pdb=" O PHE S 35 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR S 40 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL S 41 " --> pdb=" O GLN S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 removed outlier: 3.967A pdb=" N VAL S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 21 removed outlier: 3.618A pdb=" N ARG T 14 " --> pdb=" O GLY T 10 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 67 No H-bonds generated for 'chain 'T' and resid 64 through 67' Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 removed outlier: 3.513A 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: 3.515A pdb=" N GLU U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.688A 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: 3.989A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.765A pdb=" N LYS V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 51 removed outlier: 3.531A 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 72 removed outlier: 4.168A pdb=" N ASN W 72 " --> pdb=" O MET W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 96 Processing helix chain 'W' and resid 102 through 109 removed outlier: 4.236A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) removed outlier: 4.593A 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 10 through 12 No H-bonds generated for 'chain 'X' and resid 10 through 12' Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 34 Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 76 removed outlier: 3.965A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY X 64 " --> pdb=" O LEU X 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE X 70 " --> pdb=" O LEU X 67 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG X 71 " --> pdb=" O ASN X 68 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER X 75 " --> pdb=" O GLN X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 removed outlier: 3.569A pdb=" N TYR X 90 " --> pdb=" O THR X 86 " (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 Processing helix chain 'Y' and resid 2 through 11 removed outlier: 3.513A pdb=" N PHE Y 7 " --> pdb=" O VAL Y 3 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR Y 10 " --> pdb=" O PHE Y 6 " (cutoff:3.500A) removed outlier: 4.837A 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 50 through 82 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 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 137 Processing helix chain 'a' and resid 2 through 30 Proline residue: a 7 - end of helix removed outlier: 3.584A pdb=" N ALA a 10 " --> pdb=" O PRO a 7 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.532A pdb=" N SER a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE a 26 " --> pdb=" O THR a 23 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS a 27 " --> pdb=" O ALA a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 54 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 2 through 14 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 4.425A pdb=" N SER b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.639A 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 Processing helix chain 'd' and resid 16 through 20 removed outlier: 3.613A pdb=" N SER d 20 " --> pdb=" O GLU d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 97 removed outlier: 3.608A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'e' and resid 48 through 54 removed outlier: 3.847A 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 87 Processing helix chain 'f' and resid 3 through 33 removed outlier: 3.583A pdb=" N GLU f 8 " --> pdb=" O GLN f 4 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL f 11 " --> pdb=" O ARG f 7 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N HIS f 12 " --> pdb=" O GLU f 8 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE f 13 " --> pdb=" O HIS f 9 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU f 14 " --> pdb=" O TRP f 10 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL f 15 " --> pdb=" O VAL f 11 " (cutoff:3.500A) Proline residue: f 16 - end of helix removed outlier: 3.767A pdb=" N LEU f 33 " --> pdb=" O ASP f 29 " (cutoff:3.500A) 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 100 removed outlier: 5.959A pdb=" N GLU g 85 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP g 86 " --> pdb=" O MET g 83 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG g 88 " --> pdb=" O GLU g 85 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU g 92 " --> pdb=" O ARG g 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG g 98 " --> pdb=" O VAL g 95 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL g 100 " --> pdb=" O TYR g 97 " (cutoff:3.500A) 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 46 removed outlier: 4.320A 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 removed outlier: 3.549A pdb=" N GLN h 108 " --> pdb=" O ARG h 104 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 25 Processing helix chain 'i' and resid 64 through 73 Processing helix chain 'i' and resid 75 through 88 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 44 through 48 Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' 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 24 through 26 No H-bonds generated for 'chain 'k' and resid 24 through 26' Processing helix chain 'k' and resid 33 through 44 removed outlier: 4.006A pdb=" N ARG k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) 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 25 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 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 51 Processing helix chain 'm' and resid 62 through 70 Processing helix chain 'm' and resid 73 through 78 Proline residue: m 77 - end of helix No H-bonds generated for 'chain 'm' and resid 73 through 78' Processing helix chain 'm' and resid 83 through 116 Proline residue: m 96 - end of helix Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 57 through 73 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 141 removed outlier: 3.980A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.858A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.912A 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 72 Processing helix chain 'o' and resid 80 through 118 Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 58 removed outlier: 3.580A pdb=" N LYS p 57 " --> pdb=" O ARG p 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN p 58 " --> pdb=" O GLN p 54 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 6.567A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 171 Processing helix chain 'q' and resid 3 through 15 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: 4.219A 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 19 through 21 No H-bonds generated for 'chain 'r' and resid 19 through 21' Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 'r' and resid 59 through 61 No H-bonds generated for 'chain 'r' and resid 59 through 61' Processing helix chain 's' and resid 36 through 39 Processing helix chain 's' and resid 44 through 55 removed outlier: 4.800A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N PHE s 55 " --> pdb=" O ASP s 51 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.548A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.150A 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: 6.889A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ILE C 52 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.480A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 Processing sheet with id= F, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.566A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 220 through 224 removed outlier: 7.015A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.337A 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 146 through 148 Processing sheet with id= K, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= L, first strand: chain 'G' and resid 223 through 228 removed outlier: 6.179A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= N, first strand: chain 'G' and resid 342 through 345 removed outlier: 4.735A pdb=" N ASN G 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.277A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU G 378 " --> pdb=" O VAL G 452 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 67 through 69 Processing sheet with id= R, first strand: chain 'I' and resid 94 through 100 removed outlier: 5.884A pdb=" N GLU I 99 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N THR I 108 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= T, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.773A pdb=" N MET L 78 " --> pdb=" O THR L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 122 through 125 removed outlier: 6.762A pdb=" N ALA O 168 " --> pdb=" O THR O 26 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP O 28 " --> pdb=" O ALA O 168 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE O 170 " --> pdb=" O ASP O 28 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU O 219 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N TYR O 171 " --> pdb=" O GLU O 219 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU O 221 " --> pdb=" O TYR O 171 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP O 173 " --> pdb=" O LEU O 221 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR O 223 " --> pdb=" O ASP O 173 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.584A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.698A 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: 3.535A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS S 63 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN S 72 " --> pdb=" O TYR S 68 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.446A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2895 hydrogen bonds defined for protein. 7899 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: 24.06 Time building geometry restraints manager: 27.11 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: 28134 1.40 - 1.63: 40918 1.63 - 1.86: 885 1.86 - 2.09: 0 2.09 - 2.32: 80 Bond restraints: 70017 Sorted by residual: bond pdb=" C2' DGT O 502 " pdb=" C3' DGT O 502 " ideal model delta sigma weight residual 1.284 1.503 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C6 DGT O 502 " pdb=" O6 DGT O 502 " ideal model delta sigma weight residual 1.181 1.393 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CZ WYK B 87 " pdb=" NH2 WYK B 87 " ideal model delta sigma weight residual 1.453 1.243 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C5 DGT O 502 " pdb=" N7 DGT O 502 " ideal model delta sigma weight residual 1.338 1.520 -0.182 2.00e-02 2.50e+03 8.28e+01 bond pdb=" C4 FMN F 502 " pdb=" O4 FMN F 502 " ideal model delta sigma weight residual 1.230 1.390 -0.160 2.00e-02 2.50e+03 6.42e+01 ... (remaining 70012 not shown) Histogram of bond angle deviations from ideal: 73.00 - 85.88: 76 85.88 - 98.75: 5 98.75 - 111.63: 33231 111.63 - 124.51: 59605 124.51 - 137.38: 1815 Bond angle restraints: 94732 Sorted by residual: angle pdb=" C51 CDL h 202 " pdb=" CB5 CDL h 202 " pdb=" OB6 CDL h 202 " ideal model delta sigma weight residual 111.33 120.87 -9.54 1.32e+00 5.72e-01 5.21e+01 angle pdb=" C11 CDL q 201 " pdb=" CA5 CDL q 201 " pdb=" OA6 CDL q 201 " ideal model delta sigma weight residual 111.33 120.52 -9.19 1.32e+00 5.72e-01 4.83e+01 angle pdb=" C11 CDL L 703 " pdb=" CA5 CDL L 703 " pdb=" OA6 CDL L 703 " ideal model delta sigma weight residual 111.33 120.45 -9.12 1.32e+00 5.72e-01 4.76e+01 angle pdb=" C11 CDL K 101 " pdb=" CA5 CDL K 101 " pdb=" OA6 CDL K 101 " ideal model delta sigma weight residual 111.33 120.22 -8.89 1.32e+00 5.72e-01 4.53e+01 angle pdb=" C51 CDL h 201 " pdb=" CB5 CDL h 201 " pdb=" OB6 CDL h 201 " ideal model delta sigma weight residual 111.33 120.10 -8.77 1.32e+00 5.72e-01 4.40e+01 ... (remaining 94727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.95: 41089 34.95 - 69.89: 1639 69.89 - 104.84: 221 104.84 - 139.79: 40 139.79 - 174.73: 5 Dihedral angle restraints: 42994 sinusoidal: 18939 harmonic: 24055 Sorted by residual: 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 82.86 174.73 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' FMN F 502 " pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " pdb=" O1P FMN F 502 " ideal model delta sinusoidal sigma weight residual 75.26 -51.72 126.97 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" CA SER H 67 " pdb=" C SER H 67 " pdb=" N MET H 68 " pdb=" CA MET H 68 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 42991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.325: 10368 4.325 - 8.650: 0 8.650 - 12.975: 0 12.975 - 17.300: 0 17.300 - 21.625: 24 Chirality restraints: 10392 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 -11.07 21.62 2.00e-01 2.50e+01 1.17e+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 10.90 -21.45 2.00e-01 2.50e+01 1.15e+04 chirality pdb="FE4 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.89 21.44 2.00e-01 2.50e+01 1.15e+04 ... (remaining 10389 not shown) Planarity restraints: 11748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N SAC i 1 " 0.317 2.00e-02 2.50e+03 1.91e-01 4.58e+02 pdb=" CA SAC i 1 " -0.229 2.00e-02 2.50e+03 pdb=" C1A SAC i 1 " 0.064 2.00e-02 2.50e+03 pdb=" C2A SAC i 1 " -0.162 2.00e-02 2.50e+03 pdb=" OAC SAC i 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AME q 1 " -0.013 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C AME q 1 " 0.048 2.00e-02 2.50e+03 pdb=" O AME q 1 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU q 2 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR q 142 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO q 143 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO q 143 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO q 143 " -0.032 5.00e-02 4.00e+02 ... (remaining 11745 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 1184 2.53 - 3.12: 56383 3.12 - 3.72: 125242 3.72 - 4.31: 190830 4.31 - 4.90: 289432 Nonbonded interactions: 663071 Sorted by model distance: nonbonded pdb=" OE2 GLU N 34 " pdb=" O HOH N 501 " model vdw 1.939 2.440 nonbonded pdb=" O HOH I 363 " pdb=" O HOH q 324 " model vdw 1.946 2.440 nonbonded pdb=" O2B LMT L 701 " pdb=" O3' LMT L 701 " model vdw 1.953 2.440 nonbonded pdb=" O HOH B 353 " pdb=" O HOH P 725 " model vdw 1.961 2.440 nonbonded pdb=" O HOH G 956 " pdb=" O HOH G1115 " model vdw 1.966 2.440 ... (remaining 663066 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.270 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: 0.080 Extract box with map and model: 66.450 Check model and map are aligned: 0.820 Set scattering table: 0.530 Process input model: 172.770 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 265.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.219 70017 Z= 0.539 Angle : 0.937 15.898 94732 Z= 0.431 Chirality : 1.029 21.625 10392 Planarity : 0.005 0.191 11748 Dihedral : 18.681 174.733 27459 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 0.91 % Allowed : 12.42 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.11 (0.09), residues: 8136 helix: 0.26 (0.07), residues: 4317 sheet: -0.14 (0.23), residues: 430 loop : 0.08 (0.11), residues: 3389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 254 HIS 0.010 0.002 HIS C 160 PHE 0.030 0.003 PHE N 292 TYR 0.026 0.003 TYR H 282 ARG 0.023 0.001 ARG c 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1041 time to evaluate : 7.751 Fit side-chains REVERT: H 61 MET cc_start: 0.6846 (mmm) cc_final: 0.6553 (tpp) REVERT: H 62 ARG cc_start: 0.6656 (ttt180) cc_final: 0.6206 (tpp80) REVERT: H 253 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: L 23 MET cc_start: 0.7909 (mtt) cc_final: 0.7563 (mtt) REVERT: M 114 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: M 207 MET cc_start: 0.8265 (mmm) cc_final: 0.7972 (mmm) REVERT: Q 16 LYS cc_start: 0.7626 (mmtm) cc_final: 0.7271 (ptmm) REVERT: q 25 ARG cc_start: 0.7893 (ttt90) cc_final: 0.7582 (ttt90) outliers start: 66 outliers final: 50 residues processed: 1094 average time/residue: 1.7348 time to fit residues: 2429.6623 Evaluate side-chains 1032 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 980 time to evaluate : 6.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain I residue 15 ASP Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 512 SER Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 255 LYS Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain X residue 77 CYS Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain e residue 72 MET Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain n residue 175 GLU Chi-restraints excluded: chain s residue 51 ASP Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 677 optimal weight: 1.9990 chunk 607 optimal weight: 0.8980 chunk 337 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 410 optimal weight: 2.9990 chunk 324 optimal weight: 0.9990 chunk 628 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 382 optimal weight: 0.9980 chunk 467 optimal weight: 2.9990 chunk 728 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN D 114 ASN E 150 ASN F 431 GLN G 313 ASN H 292 ASN I 22 ASN L 361 ASN Q 9 GLN S 72 GLN W 110 HIS X 94 GLN b 61 ASN i 127 HIS j 42 HIS m 51 ASN n 25 HIS n 123 GLN o 84 HIS p 27 ASN p 171 GLN q 101 ASN r 24 GLN r 28 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 70017 Z= 0.501 Angle : 1.554 50.558 94732 Z= 1.005 Chirality : 0.312 6.587 10392 Planarity : 0.005 0.052 11748 Dihedral : 14.374 172.618 11259 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.68 % Favored : 98.29 % Rotamer: Outliers : 1.72 % Allowed : 12.09 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.05 (0.09), residues: 8136 helix: 1.24 (0.08), residues: 4342 sheet: 0.06 (0.24), residues: 408 loop : 0.23 (0.11), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 144 HIS 0.006 0.001 HIS n 50 PHE 0.026 0.002 PHE N 292 TYR 0.021 0.001 TYR C 28 ARG 0.008 0.000 ARG E 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1046 time to evaluate : 6.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 430 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: H 62 ARG cc_start: 0.6590 (ttt180) cc_final: 0.6139 (tpp80) REVERT: H 227 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7131 (tp30) REVERT: L 23 MET cc_start: 0.7818 (mtt) cc_final: 0.7474 (mtt) REVERT: L 52 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8647 (mp) REVERT: M 47 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7497 (pp20) REVERT: M 207 MET cc_start: 0.8219 (mmm) cc_final: 0.7957 (mmm) REVERT: O 72 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: Q 16 LYS cc_start: 0.7575 (mmtm) cc_final: 0.7249 (ptmm) REVERT: U 75 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: X 161 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7522 (tttm) REVERT: a 67 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: f 8 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: l 98 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6603 (m-30) REVERT: o 80 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8220 (mmtt) REVERT: q 25 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7612 (ttt90) REVERT: r 112 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7305 (mp) outliers start: 124 outliers final: 43 residues processed: 1117 average time/residue: 1.6799 time to fit residues: 2422.5298 Evaluate side-chains 1043 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 988 time to evaluate : 7.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 316 GLU Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 75 GLU Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain e residue 4 ASP Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain l residue 98 ASP Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain p residue 129 GLU Chi-restraints excluded: chain r residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 404 optimal weight: 6.9990 chunk 226 optimal weight: 4.9990 chunk 606 optimal weight: 3.9990 chunk 495 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 729 optimal weight: 0.8980 chunk 788 optimal weight: 4.9990 chunk 649 optimal weight: 0.8980 chunk 723 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 585 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 181 GLN E 101 GLN E 150 ASN F 250 ASN F 326 GLN F 431 GLN G 313 ASN I 22 ASN M 304 GLN N 2 ASN N 87 GLN N 150 ASN P 240 HIS S 47 HIS S 72 GLN W 60 GLN b 61 ASN f 9 HIS g 25 GLN m 51 ASN n 123 GLN p 27 ASN p 171 GLN q 101 ASN r 24 GLN r 28 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 70017 Z= 0.511 Angle : 1.540 50.820 94732 Z= 1.000 Chirality : 0.309 6.497 10392 Planarity : 0.004 0.045 11748 Dihedral : 12.596 170.471 11203 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.88 % Favored : 98.11 % Rotamer: Outliers : 1.95 % Allowed : 12.56 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.37 (0.09), residues: 8136 helix: 1.54 (0.08), residues: 4333 sheet: 0.17 (0.24), residues: 407 loop : 0.30 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 254 HIS 0.006 0.001 HIS C 160 PHE 0.030 0.001 PHE N 292 TYR 0.021 0.001 TYR C 28 ARG 0.009 0.000 ARG c 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1025 time to evaluate : 6.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 396 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8658 (ttt-90) REVERT: G 613 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.6587 (p90) REVERT: H 62 ARG cc_start: 0.6538 (ttt180) cc_final: 0.6117 (tpp80) REVERT: H 227 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: L 52 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8652 (mp) REVERT: M 114 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: M 207 MET cc_start: 0.8180 (mmm) cc_final: 0.7961 (mmm) REVERT: O 72 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: Q 16 LYS cc_start: 0.7567 (mmtm) cc_final: 0.7255 (ptmm) REVERT: V 63 ASP cc_start: 0.7874 (t0) cc_final: 0.7620 (t70) REVERT: X 57 LYS cc_start: 0.8239 (mtmp) cc_final: 0.8012 (mptt) REVERT: X 156 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: X 161 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7484 (tttm) REVERT: d 54 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7669 (mtm) REVERT: d 95 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8232 (ttpp) REVERT: f 8 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6505 (tt0) REVERT: f 56 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7221 (tttm) REVERT: l 98 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6652 (m-30) REVERT: l 130 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8960 (tptt) REVERT: q 25 ARG cc_start: 0.7851 (ttt90) cc_final: 0.7489 (ttt90) REVERT: r 112 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7299 (mp) outliers start: 141 outliers final: 55 residues processed: 1117 average time/residue: 1.6820 time to fit residues: 2425.1992 Evaluate side-chains 1047 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 977 time to evaluate : 6.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 396 ARG Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain G residue 653 ASN Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 316 GLU Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 95 LYS Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 98 ASP Chi-restraints excluded: chain l residue 130 LYS Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 144 SER Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 58 CYS Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 129 GLU Chi-restraints excluded: chain r residue 112 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 720 optimal weight: 5.9990 chunk 548 optimal weight: 4.9990 chunk 378 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 348 optimal weight: 5.9990 chunk 489 optimal weight: 7.9990 chunk 732 optimal weight: 4.9990 chunk 775 optimal weight: 6.9990 chunk 382 optimal weight: 6.9990 chunk 693 optimal weight: 0.1980 chunk 208 optimal weight: 7.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN E 101 GLN E 150 ASN F 257 ASN F 431 GLN G 313 ASN H 163 GLN I 22 ASN L 361 ASN L 579 ASN N 87 GLN S 72 GLN b 61 ASN d 61 GLN f 9 HIS i 13 GLN m 51 ASN n 123 GLN p 27 ASN p 171 GLN q 52 ASN ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 24 GLN r 28 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.247 70017 Z= 0.604 Angle : 1.580 50.496 94732 Z= 1.015 Chirality : 0.316 6.675 10392 Planarity : 0.005 0.054 11748 Dihedral : 12.803 172.192 11196 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.04 % Favored : 97.95 % Rotamer: Outliers : 2.45 % Allowed : 12.71 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.13 (0.09), residues: 8136 helix: 1.34 (0.08), residues: 4333 sheet: 0.02 (0.24), residues: 408 loop : 0.21 (0.11), residues: 3395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP O 254 HIS 0.009 0.002 HIS C 160 PHE 0.032 0.002 PHE N 292 TYR 0.029 0.002 TYR D 364 ARG 0.008 0.001 ARG c 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 983 time to evaluate : 6.545 Fit side-chains revert: symmetry clash REVERT: B 184 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8347 (tttm) REVERT: C 31 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: G 31 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: G 430 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: G 613 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.6576 (p90) REVERT: H 62 ARG cc_start: 0.6630 (ttt180) cc_final: 0.6160 (tpp80) REVERT: H 206 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: H 227 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: I 17 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7892 (ttmm) REVERT: I 124 CYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7123 (p) REVERT: J 127 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6908 (mm-30) REVERT: L 52 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8705 (mp) REVERT: M 47 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7583 (pp20) REVERT: M 114 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: M 304 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7550 (mt0) REVERT: O 2 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6639 (ttt180) REVERT: O 72 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: Q 15 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6392 (pp20) REVERT: Q 16 LYS cc_start: 0.7579 (mmtm) cc_final: 0.6866 (ptmm) REVERT: R 70 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8541 (tttm) REVERT: U 75 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6964 (mm-30) REVERT: V 63 ASP cc_start: 0.7878 (t0) cc_final: 0.7613 (t70) REVERT: X 57 LYS cc_start: 0.8264 (mtmp) cc_final: 0.8053 (mptt) REVERT: X 156 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: X 161 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7587 (tttm) REVERT: a 67 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: d 54 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7554 (mmm) REVERT: f 8 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6585 (tt0) REVERT: f 56 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7261 (tttm) REVERT: l 98 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: q 25 ARG cc_start: 0.7906 (ttt90) cc_final: 0.7587 (ttt90) REVERT: q 67 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: q 144 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7335 (p90) REVERT: r 92 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7867 (mmtm) REVERT: r 112 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7338 (mp) outliers start: 177 outliers final: 73 residues processed: 1084 average time/residue: 1.7001 time to fit residues: 2372.8365 Evaluate side-chains 1064 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 961 time to evaluate : 6.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 15 ASP Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 127 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 154 LYS Chi-restraints excluded: chain P residue 316 GLU Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 75 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 77 CYS Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain e residue 4 ASP Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain f residue 44 GLN Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 98 ASP Chi-restraints excluded: chain m residue 3 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 144 SER Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 58 CYS Chi-restraints excluded: chain p residue 14 SER Chi-restraints excluded: chain p residue 129 GLU Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain q residue 144 TYR Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain r residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 645 optimal weight: 2.9990 chunk 440 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 577 optimal weight: 0.1980 chunk 319 optimal weight: 2.9990 chunk 661 optimal weight: 4.9990 chunk 535 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 395 optimal weight: 5.9990 chunk 695 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN E 101 GLN E 150 ASN F 431 GLN G 313 ASN H 163 GLN I 22 ASN J 85 ASN L 361 ASN O 184 GLN R 94 HIS S 72 GLN X 94 GLN b 61 ASN d 61 GLN f 9 HIS m 51 ASN m 78 ASN n 123 GLN p 27 ASN p 171 GLN q 101 ASN r 24 GLN r 28 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 70017 Z= 0.520 Angle : 1.544 50.533 94732 Z= 1.002 Chirality : 0.310 6.514 10392 Planarity : 0.004 0.045 11748 Dihedral : 12.246 170.927 11194 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.89 % Favored : 98.09 % Rotamer: Outliers : 1.98 % Allowed : 13.31 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.34 (0.09), residues: 8136 helix: 1.53 (0.08), residues: 4326 sheet: 0.11 (0.24), residues: 411 loop : 0.27 (0.11), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 254 HIS 0.006 0.001 HIS C 160 PHE 0.031 0.002 PHE N 292 TYR 0.021 0.002 TYR C 28 ARG 0.007 0.000 ARG d 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1002 time to evaluate : 7.875 Fit side-chains revert: symmetry clash REVERT: C 31 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: G 31 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: G 430 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: G 613 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.6586 (p90) REVERT: H 62 ARG cc_start: 0.6580 (ttt180) cc_final: 0.6136 (tpp80) REVERT: H 206 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: H 227 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7079 (tp30) REVERT: I 17 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7865 (ttmm) REVERT: I 124 CYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7088 (p) REVERT: L 52 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8663 (mp) REVERT: M 47 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: M 114 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: O 2 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6610 (ttt180) REVERT: O 72 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: Q 16 LYS cc_start: 0.7575 (mmtm) cc_final: 0.7254 (ptmm) REVERT: V 63 ASP cc_start: 0.7854 (t0) cc_final: 0.7607 (t70) REVERT: X 156 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: X 161 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7507 (tttm) REVERT: a 40 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7683 (mmm160) REVERT: f 8 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6564 (tt0) REVERT: f 56 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7218 (tttm) REVERT: k 19 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7668 (ttm) REVERT: l 98 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: q 25 ARG cc_start: 0.7872 (ttt90) cc_final: 0.7503 (ttt90) REVERT: q 67 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: r 92 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7782 (mmtm) REVERT: r 112 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7264 (mp) outliers start: 143 outliers final: 63 residues processed: 1092 average time/residue: 1.6855 time to fit residues: 2377.5981 Evaluate side-chains 1057 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 971 time to evaluate : 6.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 479 VAL Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 15 ASP Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 316 GLU Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain X residue 77 CYS Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain a residue 40 ARG Chi-restraints excluded: chain e residue 72 MET Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 98 ASP Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 119 LYS Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 144 SER Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 58 CYS Chi-restraints excluded: chain p residue 14 SER Chi-restraints excluded: chain p residue 129 GLU Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain r residue 112 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 260 optimal weight: 0.9990 chunk 698 optimal weight: 0.0370 chunk 153 optimal weight: 0.0980 chunk 455 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 775 optimal weight: 5.9990 chunk 644 optimal weight: 0.6980 chunk 359 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 256 optimal weight: 7.9990 chunk 407 optimal weight: 6.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN D 280 GLN D 421 GLN E 101 GLN E 150 ASN F 250 ASN F 431 GLN G 313 ASN H 163 GLN I 22 ASN J 85 ASN L 361 ASN N 87 GLN O 184 GLN R 94 HIS S 72 GLN X 94 GLN b 61 ASN d 61 GLN f 9 HIS m 51 ASN n 123 GLN p 27 ASN q 101 ASN r 24 GLN r 28 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 70017 Z= 0.499 Angle : 1.526 50.585 94732 Z= 0.995 Chirality : 0.306 6.424 10392 Planarity : 0.004 0.045 11748 Dihedral : 11.422 168.518 11194 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.70 % Favored : 98.29 % Rotamer: Outliers : 1.63 % Allowed : 13.75 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.58 (0.09), residues: 8136 helix: 1.74 (0.08), residues: 4347 sheet: 0.11 (0.24), residues: 425 loop : 0.37 (0.11), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 254 HIS 0.005 0.001 HIS n 50 PHE 0.029 0.001 PHE N 292 TYR 0.021 0.001 TYR L 422 ARG 0.008 0.000 ARG d 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1027 time to evaluate : 6.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 10 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7979 (ptp-110) REVERT: E 114 ASP cc_start: 0.7580 (m-30) cc_final: 0.7376 (m-30) REVERT: G 31 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: G 231 MET cc_start: 0.8838 (mmp) cc_final: 0.8585 (mmp) REVERT: G 613 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.6652 (p90) REVERT: H 62 ARG cc_start: 0.6507 (ttt180) cc_final: 0.6078 (tpp80) REVERT: H 206 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: H 227 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7084 (tp30) REVERT: L 52 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8640 (mp) REVERT: M 47 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7530 (pp20) REVERT: M 114 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: M 304 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7673 (mm-40) REVERT: O 72 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: Q 16 LYS cc_start: 0.7525 (mmtm) cc_final: 0.7239 (ptmm) REVERT: V 63 ASP cc_start: 0.7814 (t0) cc_final: 0.7575 (t70) REVERT: X 156 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.7111 (m-30) REVERT: X 161 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7424 (tttm) REVERT: d 95 LYS cc_start: 0.8436 (tttm) cc_final: 0.8217 (ttpp) REVERT: e 63 GLU cc_start: 0.7807 (tt0) cc_final: 0.7601 (tt0) REVERT: f 8 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6500 (tt0) REVERT: k 19 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7660 (ttm) REVERT: l 98 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6666 (m-30) REVERT: p 107 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7742 (mt-10) REVERT: q 67 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: r 92 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7815 (mmtm) REVERT: s 68 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.4792 (mpt90) outliers start: 118 outliers final: 42 residues processed: 1101 average time/residue: 1.6672 time to fit residues: 2367.7146 Evaluate side-chains 1035 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 975 time to evaluate : 6.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 98 ASP Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 3 SER Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 144 SER Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain p residue 14 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 129 GLU Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain s residue 68 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 748 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 442 optimal weight: 4.9990 chunk 566 optimal weight: 0.4980 chunk 439 optimal weight: 6.9990 chunk 653 optimal weight: 1.9990 chunk 433 optimal weight: 0.3980 chunk 772 optimal weight: 4.9990 chunk 483 optimal weight: 4.9990 chunk 471 optimal weight: 0.5980 chunk 356 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN E 101 GLN F 431 GLN G 313 ASN H 163 GLN I 22 ASN J 85 ASN L 361 ASN N 87 GLN O 184 GLN R 94 HIS S 72 GLN X 94 GLN b 61 ASN d 61 GLN f 9 HIS m 51 ASN n 123 GLN p 171 GLN q 101 ASN r 24 GLN r 28 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 70017 Z= 0.500 Angle : 1.526 50.608 94732 Z= 0.995 Chirality : 0.307 6.432 10392 Planarity : 0.004 0.049 11748 Dihedral : 11.125 168.821 11191 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.23 % Rotamer: Outliers : 1.48 % Allowed : 14.22 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.67 (0.09), residues: 8136 helix: 1.83 (0.08), residues: 4333 sheet: 0.15 (0.24), residues: 426 loop : 0.41 (0.11), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 144 HIS 0.005 0.001 HIS n 50 PHE 0.029 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.009 0.000 ARG d 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1000 time to evaluate : 6.493 Fit side-chains revert: symmetry clash REVERT: B 184 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8329 (tttm) REVERT: C 31 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: E 10 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7946 (ptp-110) REVERT: F 279 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8615 (tp) REVERT: G 31 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: G 231 MET cc_start: 0.8833 (mmp) cc_final: 0.8542 (mmp) REVERT: G 283 MET cc_start: 0.8664 (mmm) cc_final: 0.7617 (mtm) REVERT: G 613 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.6599 (p90) REVERT: H 227 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: L 52 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8616 (mp) REVERT: M 47 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7539 (pp20) REVERT: M 114 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: M 304 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7483 (mt0) REVERT: O 72 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: Q 16 LYS cc_start: 0.7524 (mmtm) cc_final: 0.7250 (ptmm) REVERT: V 63 ASP cc_start: 0.7805 (t0) cc_final: 0.7566 (t70) REVERT: X 156 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: X 161 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7432 (tttm) REVERT: d 54 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7626 (mtm) REVERT: f 8 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6503 (tt0) REVERT: k 19 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7620 (ttm) REVERT: l 98 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6710 (m-30) REVERT: l 136 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8252 (t0) REVERT: p 107 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7736 (mt-10) REVERT: q 67 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: r 92 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7812 (mmtm) outliers start: 107 outliers final: 44 residues processed: 1068 average time/residue: 1.6888 time to fit residues: 2324.0146 Evaluate side-chains 1044 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 979 time to evaluate : 6.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 77 CYS Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 98 ASP Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain l residue 136 ASN Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 129 GLU Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain r residue 92 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 478 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 461 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 491 optimal weight: 0.9990 chunk 526 optimal weight: 4.9990 chunk 382 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 607 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN E 101 GLN F 431 GLN G 313 ASN I 22 ASN J 85 ASN L 361 ASN N 87 GLN O 184 GLN R 94 HIS S 72 GLN X 94 GLN b 61 ASN d 61 GLN f 9 HIS m 51 ASN n 123 GLN r 24 GLN r 28 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 70017 Z= 0.512 Angle : 1.537 50.495 94732 Z= 0.999 Chirality : 0.309 6.512 10392 Planarity : 0.004 0.051 11748 Dihedral : 11.156 169.805 11185 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.76 % Favored : 98.22 % Rotamer: Outliers : 1.48 % Allowed : 14.32 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.09), residues: 8136 helix: 1.77 (0.08), residues: 4336 sheet: 0.18 (0.25), residues: 419 loop : 0.39 (0.11), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 254 HIS 0.005 0.001 HIS D 157 PHE 0.030 0.002 PHE N 292 TYR 0.019 0.001 TYR I 120 ARG 0.008 0.000 ARG d 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 988 time to evaluate : 6.562 Fit side-chains revert: symmetry clash REVERT: B 184 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8334 (tttm) REVERT: C 31 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: E 10 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7896 (ptp-110) REVERT: G 31 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: G 231 MET cc_start: 0.8837 (mmp) cc_final: 0.8541 (mmp) REVERT: G 283 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7748 (mtm) REVERT: G 430 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: G 613 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.6563 (p90) REVERT: H 62 ARG cc_start: 0.6530 (ttt180) cc_final: 0.6093 (tpp80) REVERT: H 227 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: L 52 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8629 (mp) REVERT: L 539 MET cc_start: 0.8034 (tmm) cc_final: 0.7659 (tpt) REVERT: M 47 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7546 (pp20) REVERT: M 114 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: M 207 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7619 (mmm) REVERT: M 304 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: O 72 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: Q 16 LYS cc_start: 0.7525 (mmtm) cc_final: 0.7236 (ptmm) REVERT: V 63 ASP cc_start: 0.7827 (t0) cc_final: 0.7582 (t70) REVERT: X 156 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: X 161 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7459 (tttm) REVERT: a 40 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7607 (mmm160) REVERT: d 54 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7653 (mtm) REVERT: f 8 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6555 (tt0) REVERT: f 56 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7090 (tttm) REVERT: k 19 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7550 (ttm) REVERT: l 98 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6679 (m-30) REVERT: p 107 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7729 (mt-10) REVERT: q 67 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: r 92 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7848 (mmtm) outliers start: 107 outliers final: 55 residues processed: 1052 average time/residue: 1.7127 time to fit residues: 2317.9704 Evaluate side-chains 1055 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 976 time to evaluate : 6.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 77 CYS Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain a residue 40 ARG Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 98 ASP Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 3 SER Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 46 MET Chi-restraints excluded: chain o residue 58 CYS Chi-restraints excluded: chain p residue 14 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 129 GLU Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain r residue 92 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 703 optimal weight: 0.0010 chunk 740 optimal weight: 0.9980 chunk 675 optimal weight: 2.9990 chunk 720 optimal weight: 0.5980 chunk 433 optimal weight: 0.5980 chunk 313 optimal weight: 7.9990 chunk 565 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 650 optimal weight: 0.6980 chunk 681 optimal weight: 0.6980 chunk 717 optimal weight: 0.3980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN E 101 GLN F 250 ASN F 431 GLN G 313 ASN H 292 ASN I 22 ASN M 304 GLN N 87 GLN O 184 GLN R 94 HIS S 72 GLN X 94 GLN b 61 ASN d 61 GLN f 9 HIS m 51 ASN n 123 GLN q 12 GLN r 24 GLN r 28 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 70017 Z= 0.498 Angle : 1.523 50.568 94732 Z= 0.994 Chirality : 0.307 6.437 10392 Planarity : 0.004 0.054 11748 Dihedral : 10.709 168.215 11185 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.70 % Favored : 98.28 % Rotamer: Outliers : 1.27 % Allowed : 14.58 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.76 (0.09), residues: 8136 helix: 1.91 (0.08), residues: 4340 sheet: 0.17 (0.24), residues: 428 loop : 0.45 (0.11), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 144 HIS 0.005 0.001 HIS n 50 PHE 0.030 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.009 0.000 ARG d 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1010 time to evaluate : 6.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 10 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7822 (ptp-110) REVERT: F 279 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8530 (tp) REVERT: G 31 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: G 231 MET cc_start: 0.8822 (mmp) cc_final: 0.8536 (mmp) REVERT: G 283 MET cc_start: 0.8648 (mmm) cc_final: 0.7788 (mtm) REVERT: G 430 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: G 613 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.6586 (p90) REVERT: H 227 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: L 28 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7633 (ptpt) REVERT: L 52 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8630 (mp) REVERT: M 47 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7605 (pp20) REVERT: M 114 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: M 207 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7477 (mmm) REVERT: O 72 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: Q 16 LYS cc_start: 0.7516 (mmtm) cc_final: 0.7249 (ptmm) REVERT: V 63 ASP cc_start: 0.7798 (t0) cc_final: 0.7564 (t70) REVERT: X 57 LYS cc_start: 0.8092 (mtmp) cc_final: 0.7879 (mptt) REVERT: X 161 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7400 (tttm) REVERT: d 1 MET cc_start: 0.8071 (ptt) cc_final: 0.7707 (ptt) REVERT: d 54 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7446 (mmm) REVERT: f 8 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6483 (tt0) REVERT: l 98 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6645 (m-30) REVERT: q 67 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: r 92 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7796 (mmtm) REVERT: s 68 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.4855 (mpt90) outliers start: 92 outliers final: 44 residues processed: 1065 average time/residue: 1.6990 time to fit residues: 2329.1103 Evaluate side-chains 1049 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 986 time to evaluate : 6.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain g residue 29 GLU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 98 ASP Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 3 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 58 CYS Chi-restraints excluded: chain p residue 14 SER Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain s residue 68 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 473 optimal weight: 10.0000 chunk 761 optimal weight: 0.9980 chunk 464 optimal weight: 2.9990 chunk 361 optimal weight: 7.9990 chunk 529 optimal weight: 0.3980 chunk 798 optimal weight: 0.0050 chunk 735 optimal weight: 2.9990 chunk 636 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 491 optimal weight: 0.9990 chunk 390 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN E 101 GLN F 431 GLN G 313 ASN I 22 ASN J 85 ASN N 87 GLN N 274 ASN O 184 GLN R 94 HIS S 72 GLN b 61 ASN f 9 HIS m 51 ASN n 123 GLN p 171 GLN q 12 GLN q 52 ASN r 24 GLN r 28 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 70017 Z= 0.500 Angle : 1.526 50.516 94732 Z= 0.994 Chirality : 0.307 6.434 10392 Planarity : 0.004 0.054 11748 Dihedral : 10.580 168.644 11185 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.70 % Favored : 98.28 % Rotamer: Outliers : 1.04 % Allowed : 15.09 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.78 (0.09), residues: 8136 helix: 1.92 (0.08), residues: 4333 sheet: 0.18 (0.24), residues: 430 loop : 0.47 (0.11), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.005 0.001 HIS n 50 PHE 0.029 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.008 0.000 ARG d 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16272 Ramachandran restraints generated. 8136 Oldfield, 0 Emsley, 8136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 994 time to evaluate : 9.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 184 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8315 (tttm) REVERT: E 10 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7784 (ptp-110) REVERT: F 279 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8519 (tp) REVERT: G 31 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: G 231 MET cc_start: 0.8816 (mmp) cc_final: 0.8505 (mmp) REVERT: G 283 MET cc_start: 0.8665 (mmm) cc_final: 0.7797 (mtm) REVERT: G 430 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: G 613 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.6556 (p90) REVERT: H 181 MET cc_start: 0.7787 (mtm) cc_final: 0.7489 (mtm) REVERT: H 227 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: L 52 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8630 (mp) REVERT: M 47 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7546 (pp20) REVERT: M 114 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: M 207 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7549 (mmm) REVERT: O 72 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7214 (mt-10) REVERT: Q 16 LYS cc_start: 0.7516 (mmtm) cc_final: 0.7260 (ptmm) REVERT: V 63 ASP cc_start: 0.7799 (t0) cc_final: 0.7561 (t70) REVERT: X 57 LYS cc_start: 0.8090 (mtmp) cc_final: 0.7879 (mptt) REVERT: X 161 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7390 (tttm) REVERT: d 54 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7427 (mmm) REVERT: f 8 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6546 (tt0) REVERT: k 19 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7512 (ttm) REVERT: l 98 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6654 (m-30) REVERT: q 67 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: r 92 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7804 (mmtm) REVERT: s 68 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.4833 (mpt90) outliers start: 75 outliers final: 42 residues processed: 1045 average time/residue: 1.7597 time to fit residues: 2382.8295 Evaluate side-chains 1049 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 987 time to evaluate : 6.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 77 CYS Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 98 ASP Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 58 CYS Chi-restraints excluded: chain p residue 14 SER Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain s residue 68 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 505 optimal weight: 3.9990 chunk 677 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 586 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 637 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 654 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN E 101 GLN F 431 GLN G 313 ASN H 292 ASN I 22 ASN N 87 GLN O 184 GLN R 94 HIS S 72 GLN X 94 GLN b 61 ASN f 9 HIS m 51 ASN n 123 GLN p 171 GLN q 12 GLN q 52 ASN r 24 GLN r 28 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100738 restraints weight = 54454.771| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 0.70 r_work: 0.3068 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 70017 Z= 0.510 Angle : 1.536 50.496 94732 Z= 0.998 Chirality : 0.309 6.478 10392 Planarity : 0.004 0.054 11748 Dihedral : 10.707 169.391 11185 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.75 % Favored : 98.23 % Rotamer: Outliers : 1.25 % Allowed : 14.89 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.68 (0.09), residues: 8136 helix: 1.83 (0.08), residues: 4336 sheet: 0.21 (0.25), residues: 419 loop : 0.42 (0.11), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 254 HIS 0.006 0.001 HIS C 160 PHE 0.029 0.001 PHE N 292 TYR 0.019 0.001 TYR I 120 ARG 0.007 0.000 ARG d 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31896.37 seconds wall clock time: 553 minutes 14.43 seconds (33194.43 seconds total)