Starting phenix.real_space_refine on Thu Mar 14 21:40:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4c_14292/03_2024/7r4c_14292_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4c_14292/03_2024/7r4c_14292.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4c_14292/03_2024/7r4c_14292_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4c_14292/03_2024/7r4c_14292_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4c_14292/03_2024/7r4c_14292_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4c_14292/03_2024/7r4c_14292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4c_14292/03_2024/7r4c_14292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4c_14292/03_2024/7r4c_14292_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4c_14292/03_2024/7r4c_14292_updated.pdb" } resolution = 2.3 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= 0.010 sd= 1.072 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: 11 Type Number sf(0) Gaussians I 2 10.91 5 K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 35 5.49 5 Mg 1 5.21 5 S 465 5.16 5 Cl 2 4.86 5 C 42991 2.51 5 N 10995 2.21 5 O 13524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 66": "OD1" <-> "OD2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D ASP 7": "OD1" <-> "OD2" Residue "D TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F GLU 428": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "G ASP 14": "OD1" <-> "OD2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 339": "OD1" <-> "OD2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ASP 414": "OD1" <-> "OD2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G ASP 558": "OD1" <-> "OD2" Residue "G GLU 605": "OE1" <-> "OE2" Residue "G ASP 617": "OD1" <-> "OD2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G ASP 675": "OD1" <-> "OD2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ASP 13": "OD1" <-> "OD2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "J TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 197": "OD1" <-> "OD2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 393": "OD1" <-> "OD2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L ASP 554": "OD1" <-> "OD2" Residue "L PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 335": "OE1" <-> "OE2" Residue "M ARG 346": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "M TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N GLU 347": "OE1" <-> "OE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ASP 110": "OD1" <-> "OD2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O ASP 173": "OD1" <-> "OD2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 216": "OE1" <-> "OE2" Residue "O GLU 219": "OE1" <-> "OE2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "O ASP 250": "OD1" <-> "OD2" Residue "O ASP 253": "OD1" <-> "OD2" Residue "O PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 295": "OE1" <-> "OE2" Residue "O PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ASP 240": "OD1" <-> "OD2" Residue "P PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P ASP 282": "OD1" <-> "OD2" Residue "P ASP 302": "OD1" <-> "OD2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q GLU 90": "OE1" <-> "OE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "R ASP 19": "OD1" <-> "OD2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "T TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T GLU 49": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ASP 32": "OD1" <-> "OD2" Residue "V ASP 63": "OD1" <-> "OD2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 100": "OE1" <-> "OE2" Residue "W ARG 30": "NH1" <-> "NH2" Residue "W GLU 42": "OE1" <-> "OE2" Residue "W ASP 61": "OD1" <-> "OD2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 117": "OD1" <-> "OD2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ASP 112": "OD1" <-> "OD2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 148": "OE1" <-> "OE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "Y TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 84": "OD1" <-> "OD2" Residue "Y ASP 85": "OD1" <-> "OD2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Y TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 137": "OE1" <-> "OE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z GLU 123": "OE1" <-> "OE2" Residue "a GLU 35": "OE1" <-> "OE2" Residue "a TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 16": "OD1" <-> "OD2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 86": "NH1" <-> "NH2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 36": "OE1" <-> "OE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 52": "OE1" <-> "OE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "f ASP 9": "OD1" <-> "OD2" Residue "f TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "g ASP 29": "OD1" <-> "OD2" Residue "g GLU 39": "OE1" <-> "OE2" Residue "g ASP 48": "OD1" <-> "OD2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "h PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h ASP 81": "OD1" <-> "OD2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h GLU 99": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h GLU 131": "OE1" <-> "OE2" Residue "i GLU 6": "OE1" <-> "OE2" Residue "i GLU 7": "OE1" <-> "OE2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i ASP 124": "OD1" <-> "OD2" Residue "j GLU 8": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j ASP 61": "OD1" <-> "OD2" Residue "j GLU 62": "OE1" <-> "OE2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "k TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k GLU 29": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ASP 42": "OD1" <-> "OD2" Residue "k PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 84": "OE1" <-> "OE2" Residue "k TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 88": "OE1" <-> "OE2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l GLU 57": "OE1" <-> "OE2" Residue "l GLU 120": "OE1" <-> "OE2" Residue "l TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 141": "OE1" <-> "OE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l GLU 149": "OE1" <-> "OE2" Residue "l TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "m TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 18": "OD1" <-> "OD2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 109": "OD1" <-> "OD2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n ARG 37": "NH1" <-> "NH2" Residue "n GLU 49": "OE1" <-> "OE2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 65": "OE1" <-> "OE2" Residue "n GLU 69": "OE1" <-> "OE2" Residue "n GLU 91": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n ASP 105": "OD1" <-> "OD2" Residue "n TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 130": "OE1" <-> "OE2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n ASP 161": "OD1" <-> "OD2" Residue "n GLU 175": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ASP 11": "OD1" <-> "OD2" Residue "o ASP 17": "OD1" <-> "OD2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 37": "OE1" <-> "OE2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ASP 47": "OD1" <-> "OD2" Residue "o PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o GLU 102": "OE1" <-> "OE2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "p ASP 5": "OD1" <-> "OD2" Residue "p ASP 7": "OD1" <-> "OD2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 37": "OD1" <-> "OD2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 66": "OE1" <-> "OE2" Residue "p ASP 72": "OD1" <-> "OD2" Residue "p GLU 75": "OE1" <-> "OE2" Residue "p GLU 78": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 127": "OE1" <-> "OE2" Residue "p GLU 129": "OE1" <-> "OE2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 2": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q ASP 32": "OD1" <-> "OD2" Residue "q GLU 41": "OE1" <-> "OE2" Residue "q GLU 67": "OE1" <-> "OE2" Residue "q ASP 76": "OD1" <-> "OD2" Residue "q ASP 78": "OD1" <-> "OD2" Residue "q GLU 85": "OE1" <-> "OE2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q ASP 95": "OD1" <-> "OD2" Residue "q GLU 136": "OE1" <-> "OE2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 61": "OE1" <-> "OE2" Residue "r GLU 109": "OE1" <-> "OE2" Residue "s GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68045 Number of models: 1 Model: "" Number of chains: 115 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 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: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1230 Classifications: {'peptide': 154} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 143} Chain: "C" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 16, 'TRANS': 189} Chain: "D" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3327 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 24, 'TRANS': 387} Chain breaks: 2 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: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1650 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 190} Chain: "F" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3301 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 407} Chain: "G" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5279 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "H" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2428 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 285} Chain breaks: 1 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: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1337 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 3, 'TRANS': 170} 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: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 739 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} 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: 4765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4765 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 576} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3654 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2733 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2589 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "P" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2323 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 16, 'TRANS': 275} Chain breaks: 3 Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 730 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 681 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "V" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 911 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "W" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 971 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1402 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Y" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1030 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1152 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "a" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 561 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "b" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 11, 'TRANS': 70} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 405 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "d" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 934 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 9, 'TRANS': 102} Chain: "e" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 799 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "f" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 444 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "g" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 813 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "h" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1154 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "i" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 884 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 580 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain: "k" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "l" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1304 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "m" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 948 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain breaks: 1 Chain: "n" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1487 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 15, 'TRANS': 155} Chain: "o" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1043 Classifications: {'peptide': 121} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 113} Chain: "p" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1435 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain: "q" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1201 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "r" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 767 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 11, 'TRANS': 82} 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: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 353 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'LMT': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'3PE': 1, 'I49': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "K" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 157 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'3PE': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'3PE': 1, 'I49': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 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: 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: "Y" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 137 Unusual residues: {'3PE': 1, 'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "b" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "d" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'3PE': 1, 'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "e" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "h" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 137 Unusual residues: {'CDL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 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: "l" 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: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "D" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 155 Classifications: {'water': 155} Link IDs: {None: 154} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "F" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "G" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 208 Classifications: {'water': 208} Link IDs: {None: 207} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "I" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "M" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "O" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "R" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} 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: "U" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "V" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "W" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "X" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "a" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "b" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "d" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "e" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "g" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "h" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "l" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "m" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} 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: "o" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "p" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} 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 1535 SG CYS B 119 96.236 94.026 207.385 1.00 21.56 S ATOM 1765 SG CYS B 149 94.009 91.737 212.055 1.00 21.06 S ATOM 1031 SG CYS B 54 90.568 90.451 206.678 1.00 24.55 S ATOM 1037 SG CYS B 55 90.379 96.317 209.330 1.00 24.48 S ATOM 7869 SG CYS E 103 113.293 45.616 263.351 1.00 40.84 S ATOM 7903 SG CYS E 108 111.562 43.067 265.353 1.00 41.24 S ATOM 8183 SG CYS E 144 115.269 42.159 259.944 1.00 38.84 S ATOM 8206 SG CYS E 148 113.831 39.541 260.920 1.00 42.49 S ATOM 11415 SG CYS F 362 118.163 51.895 239.559 1.00 25.11 S ATOM 11435 SG CYS F 365 115.344 51.370 244.467 1.00 26.17 S ATOM 11759 SG CYS F 405 119.852 46.863 243.595 1.00 28.17 S ATOM 11396 SG CYS F 359 121.864 52.641 244.993 1.00 28.21 S ATOM 12847 SG CYS G 114 115.002 70.345 230.094 1.00 22.00 S ATOM 12786 SG CYS G 105 109.212 72.977 231.872 1.00 20.78 S ATOM 12807 SG CYS G 108 114.921 75.304 233.921 1.00 21.77 S ATOM 13179 SG CYS G 156 123.353 64.168 235.004 1.00 23.74 S ATOM 13156 SG CYS G 153 120.606 66.521 240.606 1.00 23.10 S ATOM 13203 SG CYS G 159 126.851 67.308 239.069 1.00 25.65 S ATOM 13533 SG CYS G 203 122.298 70.133 235.323 1.00 23.87 S ATOM 12292 SG CYS G 41 123.538 57.337 232.856 1.00 23.41 S ATOM 12378 SG CYS G 52 119.713 57.896 231.876 1.00 23.34 S ATOM 12403 SG CYS G 55 121.054 53.369 228.502 1.00 24.65 S ATOM 12504 SG CYS G 69 124.272 53.922 229.623 1.00 25.51 S ATOM 20682 SG CYS I 119 96.916 85.818 218.169 1.00 19.33 S ATOM 20656 SG CYS I 116 97.449 92.379 218.885 1.00 19.47 S ATOM 20703 SG CYS I 122 98.578 88.028 223.621 1.00 19.57 S ATOM 20430 SG CYS I 87 102.668 88.488 218.422 1.00 19.27 S ATOM 20732 SG CYS I 126 101.077 84.788 231.082 1.00 21.21 S ATOM 20361 SG CYS I 77 106.154 88.903 232.011 1.00 22.29 S ATOM 20403 SG CYS I 83 104.431 87.170 226.098 1.00 20.26 S ATOM 20380 SG CYS I 80 106.563 82.548 229.656 1.00 21.39 S ATOM 40757 SG CYS R 59 102.907 80.432 246.338 1.00 28.18 S ATOM 40935 SG CYS R 84 105.902 81.051 244.140 1.00 28.44 S ATOM 40957 SG CYS R 87 103.650 83.731 244.965 1.00 27.28 S Time building chain proxies: 26.17, per 1000 atoms: 0.38 Number of scatterers: 68045 At special positions: 0 Unit cell: (184.943, 201.025, 295.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 11 Type Number sf(0) I 2 52.95 Zn 1 29.99 Fe 28 26.01 K 1 19.00 Cl 2 17.00 S 465 16.00 P 35 15.00 Mg 1 11.99 O 13524 8.00 N 10995 7.00 C 42991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.04 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " 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: 21.08 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 148 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb=" SF4 B 201 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 149 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " 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 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 87 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 119 " pdb=" SF4 I 203 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 83 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15166 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 353 helices and 29 sheets defined 54.4% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.82 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.402A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.488A 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 27 through 43 Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.966A pdb=" N GLU B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 105 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.515A pdb=" N ARG B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 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 Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.937A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 3.857A 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: 3.698A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.712A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 3.516A pdb=" N LEU D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Proline residue: D 101 - end of helix removed outlier: 3.910A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 96 through 105' Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 removed outlier: 3.781A pdb=" N ILE D 161 " --> pdb=" O HIS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.778A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.775A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.729A 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: 4.504A 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 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.584A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.877A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.673A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.415A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.663A pdb=" N ASN E 58 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.573A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 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 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 62 Processing helix chain 'F' and resid 75 through 81 removed outlier: 3.618A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 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 243 Processing helix chain 'F' and resid 276 through 284 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: 4.387A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.574A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 436 Proline residue: F 414 - end of helix removed outlier: 3.581A 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: 3.965A 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 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: 3.714A pdb=" N ILE G 202 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 265 through 275 removed outlier: 5.239A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 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: 3.612A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 438 through 445 removed outlier: 3.522A pdb=" N LEU G 443 " --> pdb=" O SER G 440 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN G 444 " --> pdb=" O GLN G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 455 through 458 No H-bonds generated for 'chain 'G' and resid 455 through 458' Processing helix chain 'G' and resid 461 through 479 removed outlier: 4.531A pdb=" N ALA G 464 " --> pdb=" O ASN G 461 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE G 477 " --> pdb=" O ALA G 474 " (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 596 through 606 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 Processing helix chain 'G' and resid 642 through 650 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 691 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix removed outlier: 3.823A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.180A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.564A pdb=" N LEU H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.068A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 4.021A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 274 removed outlier: 3.505A pdb=" N LEU H 271 " --> pdb=" O THR H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 41 Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 151 through 175 removed outlier: 5.570A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.522A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 removed outlier: 3.523A pdb=" N PHE J 57 " --> pdb=" O GLY J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 75 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 124 through 127 Processing helix chain 'J' and resid 138 through 147 removed outlier: 3.759A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 173 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.625A pdb=" N ASN K 7 " --> pdb=" O MET K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 55 through 85 removed outlier: 3.781A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.605A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.827A 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 'L' and resid 3 through 23 removed outlier: 3.848A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 29 through 57 removed outlier: 3.723A pdb=" N TYR L 32 " --> pdb=" O PRO L 29 " (cutoff:3.500A) Proline residue: L 33 - end of helix Proline residue: L 50 - end of helix removed outlier: 3.510A pdb=" N SER L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.815A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 removed outlier: 3.558A pdb=" N MET L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 removed outlier: 3.558A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.250A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.192A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 249 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.271A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.702A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.524A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.126A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.850A 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 367 through 380 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.532A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE L 396 " --> pdb=" O ASP L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.607A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 3.506A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 3.597A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 545 Proline residue: L 530 - end of helix removed outlier: 3.695A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG L 535 " --> pdb=" O ILE L 532 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.587A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER L 545 " --> pdb=" O LEU L 542 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 561 removed outlier: 3.848A pdb=" N TRP L 557 " --> pdb=" O LEU L 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 563 through 578 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.261A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 4.183A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL M 25 " --> pdb=" O MET M 22 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE M 34 " --> pdb=" O SER M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.617A 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 removed outlier: 3.526A pdb=" N THR M 111 " --> pdb=" O ILE M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.560A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.543A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.735A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.863A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.850A 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: 4.212A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.618A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.977A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.806A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.634A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.515A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.531A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 454 removed outlier: 3.529A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 3.919A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) Proline residue: M 451 - end of helix removed outlier: 5.131A pdb=" N ILE M 454 " --> pdb=" O ASN M 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 22 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 121 removed outlier: 4.107A 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: 4.402A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.641A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.853A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 removed outlier: 3.531A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.633A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.669A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.533A pdb=" N VAL N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.619A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 14 through 16 No H-bonds generated for 'chain 'O' and resid 14 through 16' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.560A pdb=" N THR O 62 " --> pdb=" O TYR O 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 58 through 62' Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 through 140 Processing helix chain 'O' and resid 146 through 162 removed outlier: 3.531A pdb=" N VAL O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 removed outlier: 3.667A pdb=" N GLN O 184 " --> pdb=" O GLN O 180 " (cutoff:3.500A) 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: 3.703A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 229 removed outlier: 3.509A pdb=" N GLN O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 225 through 229' Processing helix chain 'O' and resid 231 through 240 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 removed outlier: 4.003A pdb=" N SER O 274 " --> pdb=" O ASN O 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 271 through 274' Processing helix chain 'O' and resid 286 through 298 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: 3.982A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 3.507A pdb=" N MET P 57 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Proline residue: P 61 - end of helix Processing helix chain 'P' and resid 78 through 85 Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 183 Processing helix chain 'P' and resid 207 through 219 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 248 Processing helix chain 'P' and resid 281 through 288 Processing helix chain 'P' and resid 300 through 303 Processing helix chain 'P' and resid 310 through 321 removed outlier: 5.172A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 31 removed outlier: 4.066A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 52 No H-bonds generated for 'chain 'Q' and resid 50 through 52' Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 45 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: 4.803A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL S 41 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU S 42 " --> pdb=" O ARG S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 8 through 21 Processing helix chain 'T' and resid 44A through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.279A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44A through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.559A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.192A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 59 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.837A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 70 removed outlier: 4.198A pdb=" N ASN W 70 " --> pdb=" O MET W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 94 Processing helix chain 'W' and resid 100 through 106 removed outlier: 4.567A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 Processing helix chain 'X' and resid 9 through 11 No H-bonds generated for 'chain 'X' and resid 9 through 11' Processing helix chain 'X' and resid 21 through 34 removed outlier: 4.878A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 73 removed outlier: 4.125A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN X 64 " --> pdb=" O LEU X 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU X 68 " --> pdb=" O CYS X 65 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG X 71 " --> pdb=" O GLU X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 100 through 114 Processing helix chain 'Y' and resid 3 through 10 Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 80 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 32 through 97 Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 121 through 125 Processing helix chain 'Z' and resid 130 through 143 removed outlier: 5.909A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 4 No H-bonds generated for 'chain 'a' and resid 2 through 4' Processing helix chain 'a' and resid 6 through 31 Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 3 through 14 removed outlier: 3.530A pdb=" N ASN b 10 " --> pdb=" O ALA b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.954A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 97 removed outlier: 3.576A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 42 Processing helix chain 'e' and resid 48 through 54 removed outlier: 4.138A pdb=" N LYS e 53 " --> pdb=" O ILE e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 85 Processing helix chain 'f' and resid 11 through 33 removed outlier: 5.098A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.620A pdb=" N LYS f 29 " --> pdb=" O LEU f 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 65 Processing helix chain 'g' and resid 69 through 78 Processing helix chain 'g' and resid 83 through 102 removed outlier: 3.569A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP g 88 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA g 89 " --> pdb=" O GLN g 86 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU g 101 " --> pdb=" O LYS g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 117 No H-bonds generated for 'chain 'g' and resid 115 through 117' Processing helix chain 'h' and resid 16 through 46 removed outlier: 4.108A 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 removed outlier: 3.747A pdb=" N TYR h 66 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 66' Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 117 Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 25 Processing helix chain 'i' and resid 60 through 73 Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 48 removed outlier: 6.928A pdb=" N ASP j 45 " --> pdb=" O TRP j 41 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA j 46 " --> pdb=" O HIS j 42 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL j 47 " --> pdb=" O ASP j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 18 through 20 No H-bonds generated for 'chain 'k' and resid 18 through 20' Processing helix chain 'k' and resid 27 through 38 removed outlier: 3.737A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 47 No H-bonds generated for 'chain 'k' and resid 45 through 47' Processing helix chain 'k' and resid 49 through 52 Processing helix chain 'k' and resid 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 62 through 66 Processing helix chain 'k' and resid 70 through 89 Processing helix chain 'l' and resid 6 through 8 No H-bonds generated for 'chain 'l' and resid 6 through 8' Processing helix chain 'l' and resid 17 through 26 Processing helix chain 'l' and resid 55 through 57 No H-bonds generated for 'chain 'l' and resid 55 through 57' Processing helix chain 'l' and resid 81 through 84 No H-bonds generated for 'chain 'l' and resid 81 through 84' Processing helix chain 'l' and resid 98 through 121 Processing helix chain 'l' and resid 134 through 138 Processing helix chain 'm' and resid 15 through 17 No H-bonds generated for 'chain 'm' and resid 15 through 17' Processing helix chain 'm' and resid 19 through 22 No H-bonds generated for 'chain 'm' and resid 19 through 22' Processing helix chain 'm' and resid 27 through 50 removed outlier: 3.640A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 95 through 116 Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 50 removed outlier: 3.982A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 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 142 removed outlier: 3.706A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.759A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.334A 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 9 Processing helix chain 'o' and resid 12 through 14 No H-bonds generated for 'chain 'o' and resid 12 through 14' 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 120 removed outlier: 3.655A pdb=" N ARG o 117 " --> pdb=" O ARG o 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 57 Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 3.524A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY p 117 " --> pdb=" O GLN p 113 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.323A 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 16 removed outlier: 3.749A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 30 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.206A 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 58 through 61 No H-bonds generated for 'chain 'r' and resid 58 through 61' Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 50 through 61 removed outlier: 4.627A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE s 61 " --> pdb=" O ASP s 57 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.271A pdb=" N VAL B 85 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N PHE B 50 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 87 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE B 144 " --> pdb=" O SER B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.705A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR C 110 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 49 removed outlier: 6.375A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.745A 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: 6.521A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.116A 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: 7.002A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.690A 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: 6.195A 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: 3.507A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= N, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.459A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.128A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= R, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.984A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.840A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.082A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.580A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) 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: 3.502A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.448A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2890 hydrogen bonds defined for protein. 7836 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: 21.03 Time building geometry restraints manager: 23.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27448 1.40 - 1.63: 39819 1.63 - 1.86: 824 1.86 - 2.09: 0 2.09 - 2.31: 82 Bond restraints: 68173 Sorted by residual: bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.520 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.397 -0.167 2.00e-02 2.50e+03 6.93e+01 bond pdb=" C SAC i 1 " pdb=" O SAC i 1 " ideal model delta sigma weight residual 1.231 1.363 -0.132 2.00e-02 2.50e+03 4.39e+01 bond pdb=" CB7 CDL Y 403 " pdb=" OB8 CDL Y 403 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.94e+01 bond pdb=" CB7 CDL X1701 " pdb=" OB8 CDL X1701 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.91e+01 ... (remaining 68168 not shown) Histogram of bond angle deviations from ideal: 72.58 - 84.88: 76 84.88 - 97.19: 3 97.19 - 109.49: 7353 109.49 - 121.80: 71732 121.80 - 134.10: 13081 Bond angle restraints: 92245 Sorted by residual: angle pdb=" O SAC i 1 " pdb=" C SAC i 1 " pdb=" N GLY i 2 " ideal model delta sigma weight residual 123.00 96.36 26.64 1.60e+00 3.91e-01 2.77e+02 angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 121.29 -9.96 1.32e+00 5.72e-01 5.67e+01 angle pdb=" C51 CDL d1202 " pdb=" CB5 CDL d1202 " pdb=" OB6 CDL d1202 " ideal model delta sigma weight residual 111.33 120.91 -9.58 1.32e+00 5.72e-01 5.25e+01 angle pdb=" C11 CDL L 702 " pdb=" CA5 CDL L 702 " pdb=" OA6 CDL L 702 " ideal model delta sigma weight residual 111.33 120.56 -9.23 1.32e+00 5.72e-01 4.88e+01 angle pdb=" C11 CDL d1202 " pdb=" CA5 CDL d1202 " pdb=" OA6 CDL d1202 " ideal model delta sigma weight residual 111.33 120.53 -9.20 1.32e+00 5.72e-01 4.84e+01 ... (remaining 92240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 40374 35.08 - 70.16: 1032 70.16 - 105.24: 180 105.24 - 140.32: 44 140.32 - 175.40: 7 Dihedral angle restraints: 41637 sinusoidal: 18123 harmonic: 23514 Sorted by residual: dihedral pdb=" CA ASN G 259 " pdb=" C ASN G 259 " pdb=" N GLU G 260 " pdb=" CA GLU G 260 " ideal model delta harmonic sigma weight residual 180.00 -133.30 -46.70 0 5.00e+00 4.00e-02 8.72e+01 dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 82.19 175.40 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP O 401 " pdb=" O3A GTP O 401 " pdb=" PA GTP O 401 " pdb=" PB GTP O 401 " ideal model delta sinusoidal sigma weight residual 274.12 102.47 171.66 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.277: 10081 4.277 - 8.554: 0 8.554 - 12.831: 0 12.831 - 17.108: 0 17.108 - 21.385: 16 Chirality restraints: 10097 Sorted by residual: chirality pdb="FE2 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.83 21.39 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.82 -21.37 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.78 -21.33 2.00e-01 2.50e+01 1.14e+04 ... (remaining 10094 not shown) Planarity restraints: 11488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 I49 N 903 " 0.467 2.00e-02 2.50e+03 5.63e-01 6.34e+03 pdb=" C14 I49 N 903 " -0.269 2.00e-02 2.50e+03 pdb=" C15 I49 N 903 " -0.023 2.00e-02 2.50e+03 pdb=" N01 I49 N 903 " -0.034 2.00e-02 2.50e+03 pdb=" N02 I49 N 903 " -0.739 2.00e-02 2.50e+03 pdb=" N03 I49 N 903 " -0.126 2.00e-02 2.50e+03 pdb=" N04 I49 N 903 " -0.481 2.00e-02 2.50e+03 pdb=" N05 I49 N 903 " 1.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 I49 H 602 " 0.282 2.00e-02 2.50e+03 5.47e-01 5.98e+03 pdb=" C14 I49 H 602 " 0.085 2.00e-02 2.50e+03 pdb=" C15 I49 H 602 " 0.075 2.00e-02 2.50e+03 pdb=" N01 I49 H 602 " -0.175 2.00e-02 2.50e+03 pdb=" N02 I49 H 602 " 0.803 2.00e-02 2.50e+03 pdb=" N03 I49 H 602 " -0.298 2.00e-02 2.50e+03 pdb=" N04 I49 H 602 " -1.173 2.00e-02 2.50e+03 pdb=" N05 I49 H 602 " 0.400 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SAC i 1 " 0.124 2.00e-02 2.50e+03 2.08e-01 4.31e+02 pdb=" C SAC i 1 " -0.359 2.00e-02 2.50e+03 pdb=" O SAC i 1 " 0.113 2.00e-02 2.50e+03 pdb=" N GLY i 2 " 0.123 2.00e-02 2.50e+03 ... (remaining 11485 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.55: 709 2.55 - 3.20: 65459 3.20 - 3.85: 146126 3.85 - 4.49: 210723 4.49 - 5.14: 318521 Nonbonded interactions: 741538 Sorted by model distance: nonbonded pdb=" OH TYR O 83 " pdb=" O3' GTP O 401 " model vdw 1.908 2.440 nonbonded pdb=" OD2 ASP L 163 " pdb=" O HOH L 801 " model vdw 1.941 2.440 nonbonded pdb=" O HOH G 937 " pdb=" O HOH G1076 " model vdw 1.942 2.440 nonbonded pdb=" O HOH C 399 " pdb=" O HOH V 216 " model vdw 1.952 2.440 nonbonded pdb=" O HOH L 833 " pdb=" O HOH L 846 " model vdw 1.958 2.440 ... (remaining 741533 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 7 through 82 or resid 101)) } 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: 10.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 56.630 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 154.910 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 236.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 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 : 0.007 0.170 68173 Z= 0.481 Angle : 0.811 26.643 92245 Z= 0.381 Chirality : 0.848 21.385 10097 Planarity : 0.009 0.563 11488 Dihedral : 17.010 175.400 26453 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 0.01 % Allowed : 0.14 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.69 (0.09), residues: 7944 helix: 0.73 (0.08), residues: 4323 sheet: 0.12 (0.26), residues: 387 loop : 0.33 (0.11), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 121 HIS 0.016 0.001 HIS p 143 PHE 0.047 0.002 PHE K 53 TYR 0.083 0.002 TYR B 125 ARG 0.015 0.001 ARG G 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1068 time to evaluate : 6.002 Fit side-chains REVERT: A 23 TRP cc_start: 0.6309 (m-10) cc_final: 0.6052 (m-10) REVERT: G 192 MET cc_start: 0.8213 (mmm) cc_final: 0.7667 (mmm) REVERT: M 335 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8403 (mt-10) REVERT: V 70 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7835 (ttp80) REVERT: Y 69 PHE cc_start: 0.8640 (t80) cc_final: 0.8244 (t80) REVERT: Y 85 ASP cc_start: 0.8318 (t70) cc_final: 0.7671 (t70) REVERT: Y 88 ASN cc_start: 0.8183 (m-40) cc_final: 0.7864 (m-40) REVERT: c 34 GLN cc_start: 0.8391 (tp40) cc_final: 0.8069 (tp-100) REVERT: i 26 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8305 (mt-10) outliers start: 1 outliers final: 0 residues processed: 1069 average time/residue: 1.8180 time to fit residues: 2428.7055 Evaluate side-chains 970 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 970 time to evaluate : 5.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 664 optimal weight: 0.7980 chunk 596 optimal weight: 4.9990 chunk 330 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 402 optimal weight: 0.6980 chunk 318 optimal weight: 0.8980 chunk 616 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 375 optimal weight: 3.9990 chunk 459 optimal weight: 3.9990 chunk 714 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 82 GLN D 114 ASN G 237 ASN G 444 GLN G 654 GLN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN O 287 HIS P 180 ASN V 72 GLN W 99 GLN X 15 GLN X 63 ASN Y 7 GLN Y 128 GLN Z 85 GLN a 68 ASN c 5 GLN g 86 GLN k 90 GLN m 32 GLN n 140 GLN q 135 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.257 68173 Z= 0.478 Angle : 1.321 50.308 92245 Z= 0.844 Chirality : 0.262 6.619 10097 Planarity : 0.005 0.072 11488 Dihedral : 14.184 174.697 10525 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.32 % Favored : 98.67 % Rotamer: Outliers : 0.97 % Allowed : 5.06 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.33 (0.09), residues: 7944 helix: 1.44 (0.08), residues: 4312 sheet: 0.10 (0.26), residues: 365 loop : 0.39 (0.11), residues: 3267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 144 HIS 0.008 0.001 HIS G 101 PHE 0.025 0.002 PHE M 122 TYR 0.042 0.002 TYR B 125 ARG 0.009 0.000 ARG o 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1006 time to evaluate : 5.971 Fit side-chains REVERT: A 19 ILE cc_start: 0.8365 (pt) cc_final: 0.8038 (mm) REVERT: A 23 TRP cc_start: 0.6325 (m-10) cc_final: 0.5966 (m-10) REVERT: B 176 TRP cc_start: 0.8528 (t-100) cc_final: 0.7922 (t60) REVERT: G 192 MET cc_start: 0.8215 (mmm) cc_final: 0.7741 (mmm) REVERT: I 122 CYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7948 (p) REVERT: M 114 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: S 74 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8057 (ptmm) REVERT: T 72 CYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8019 (p) REVERT: T 75 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: U 37 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7528 (mmm) REVERT: V 70 ARG cc_start: 0.8072 (mtp180) cc_final: 0.7822 (ttp80) REVERT: W 100 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7997 (ttp-110) REVERT: Y 69 PHE cc_start: 0.8646 (t80) cc_final: 0.8268 (t80) REVERT: b 78 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: d 25 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8168 (mtpp) REVERT: e 69 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: l 77 MET cc_start: 0.8881 (mtp) cc_final: 0.8557 (mtp) REVERT: o 118 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5630 (mp0) outliers start: 68 outliers final: 20 residues processed: 1030 average time/residue: 1.8133 time to fit residues: 2343.1656 Evaluate side-chains 1010 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 980 time to evaluate : 5.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain I residue 122 CYS Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain j residue 57 SER Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain r residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 397 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 594 optimal weight: 8.9990 chunk 486 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 715 optimal weight: 0.7980 chunk 773 optimal weight: 10.0000 chunk 637 optimal weight: 6.9990 chunk 710 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 574 optimal weight: 20.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 82 GLN B 106 GLN G 237 ASN G 444 GLN G 654 GLN H 317 GLN M 88 ASN V 72 GLN W 45 ASN X 15 GLN Y 7 GLN Z 85 GLN c 5 GLN g 86 GLN m 32 GLN ** m 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 140 GLN q 135 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 68173 Z= 0.476 Angle : 1.309 50.486 92245 Z= 0.841 Chirality : 0.259 6.590 10097 Planarity : 0.004 0.065 11488 Dihedral : 12.366 173.432 10525 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.80 % Favored : 98.19 % Rotamer: Outliers : 1.08 % Allowed : 6.84 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.51 (0.09), residues: 7944 helix: 1.64 (0.08), residues: 4320 sheet: 0.05 (0.26), residues: 368 loop : 0.39 (0.11), residues: 3256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.008 0.001 HIS D 150 PHE 0.023 0.002 PHE M 122 TYR 0.026 0.002 TYR B 125 ARG 0.008 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1015 time to evaluate : 5.901 Fit side-chains REVERT: B 176 TRP cc_start: 0.8531 (t-100) cc_final: 0.7922 (t60) REVERT: D 10 TRP cc_start: 0.9013 (t-100) cc_final: 0.8810 (t-100) REVERT: F 339 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7470 (mtp-110) REVERT: G 192 MET cc_start: 0.8183 (mmm) cc_final: 0.7761 (mmm) REVERT: G 693 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6641 (mt-10) REVERT: H 234 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7927 (mmp) REVERT: I 122 CYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8010 (p) REVERT: J 100 GLU cc_start: 0.7717 (tp30) cc_final: 0.6997 (tp30) REVERT: L 544 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7695 (ttt) REVERT: M 114 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: M 378 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: O 81 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8018 (ttmm) REVERT: T 75 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: U 37 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7505 (mmm) REVERT: V 70 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7829 (ttp80) REVERT: d 25 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8205 (mtpp) REVERT: d 111 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7990 (mt-10) outliers start: 76 outliers final: 25 residues processed: 1046 average time/residue: 1.7956 time to fit residues: 2356.6904 Evaluate side-chains 1027 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 991 time to evaluate : 5.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain I residue 122 CYS Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 121 MET Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain j residue 57 SER Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain r residue 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 707 optimal weight: 6.9990 chunk 538 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 341 optimal weight: 0.5980 chunk 480 optimal weight: 0.0670 chunk 718 optimal weight: 0.9990 chunk 760 optimal weight: 0.6980 chunk 375 optimal weight: 0.9980 chunk 680 optimal weight: 0.0270 chunk 205 optimal weight: 5.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 82 GLN F 431 GLN G 237 ASN G 444 GLN G 654 GLN H 5 ASN H 317 GLN L 603 ASN M 88 ASN V 72 GLN W 45 ASN W 99 GLN X 15 GLN Y 7 GLN Z 85 GLN c 5 GLN g 86 GLN j 6 HIS m 32 GLN m 116 GLN n 140 GLN q 135 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 68173 Z= 0.444 Angle : 1.284 50.676 92245 Z= 0.832 Chirality : 0.254 6.395 10097 Planarity : 0.004 0.058 11488 Dihedral : 11.323 171.396 10525 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.97 % Allowed : 7.93 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.73 (0.09), residues: 7944 helix: 1.87 (0.08), residues: 4301 sheet: 0.15 (0.26), residues: 364 loop : 0.42 (0.11), residues: 3279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 85 HIS 0.005 0.001 HIS N 112 PHE 0.022 0.001 PHE J 20 TYR 0.024 0.001 TYR L 422 ARG 0.010 0.000 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1032 time to evaluate : 5.951 Fit side-chains REVERT: B 176 TRP cc_start: 0.8518 (t-100) cc_final: 0.7936 (t60) REVERT: B 178 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7681 (mtt90) REVERT: G 192 MET cc_start: 0.8136 (mmm) cc_final: 0.7717 (mmm) REVERT: G 693 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: H 234 MET cc_start: 0.8184 (mmp) cc_final: 0.7833 (mmt) REVERT: L 544 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7632 (ttt) REVERT: M 114 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: O 81 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7984 (ttmm) REVERT: R 92 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7869 (ttm110) REVERT: T 37 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6881 (mtt) REVERT: U 83 LYS cc_start: 0.8692 (mptt) cc_final: 0.8286 (mppt) REVERT: V 70 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7804 (ttp80) REVERT: W 27 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7276 (mt-10) REVERT: Z 93 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6343 (tt0) REVERT: h 77 ARG cc_start: 0.8396 (ttt180) cc_final: 0.8126 (ttm110) REVERT: i 121 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.7010 (mm-30) REVERT: q 21 ARG cc_start: 0.7408 (ttm-80) cc_final: 0.7134 (ttm170) REVERT: q 145 LYS cc_start: 0.5967 (OUTLIER) cc_final: 0.5255 (ttpt) outliers start: 68 outliers final: 21 residues processed: 1062 average time/residue: 1.8151 time to fit residues: 2424.0759 Evaluate side-chains 1022 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 994 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 74 CYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 121 MET Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain q residue 145 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 633 optimal weight: 0.9990 chunk 431 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 566 optimal weight: 1.9990 chunk 313 optimal weight: 7.9990 chunk 649 optimal weight: 1.9990 chunk 525 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 388 optimal weight: 0.7980 chunk 682 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN G 237 ASN G 444 GLN G 654 GLN H 317 GLN L 605 HIS M 88 ASN W 45 ASN X 15 GLN Y 7 GLN Y 128 GLN Z 85 GLN c 5 GLN g 86 GLN l 126 GLN m 32 GLN m 116 GLN n 140 GLN q 135 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 68173 Z= 0.459 Angle : 1.293 50.555 92245 Z= 0.835 Chirality : 0.257 6.522 10097 Planarity : 0.004 0.057 11488 Dihedral : 11.078 172.542 10525 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.21 % Allowed : 8.29 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 7944 helix: 1.88 (0.08), residues: 4319 sheet: 0.13 (0.26), residues: 367 loop : 0.45 (0.11), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.021 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.007 0.000 ARG r 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 997 time to evaluate : 6.166 Fit side-chains REVERT: B 176 TRP cc_start: 0.8524 (t-100) cc_final: 0.7906 (t60) REVERT: B 178 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7698 (mtt90) REVERT: F 339 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7552 (mtp-110) REVERT: G 192 MET cc_start: 0.8153 (mmm) cc_final: 0.7748 (mmm) REVERT: G 693 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6668 (mt-10) REVERT: H 234 MET cc_start: 0.8159 (mmp) cc_final: 0.7809 (mmt) REVERT: L 544 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7622 (ttt) REVERT: M 114 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: N 269 GLU cc_start: 0.8235 (tp30) cc_final: 0.8027 (tp30) REVERT: O 81 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8015 (ttmm) REVERT: O 178 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: Q 58 GLU cc_start: 0.7729 (pt0) cc_final: 0.7495 (pt0) REVERT: T 37 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6858 (mtt) REVERT: T 57 GLU cc_start: 0.7183 (tp30) cc_final: 0.6877 (tm-30) REVERT: U 12 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8573 (tmmm) REVERT: U 37 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7450 (mmm) REVERT: U 83 LYS cc_start: 0.8715 (mptt) cc_final: 0.8219 (mppt) REVERT: V 65 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7381 (mttp) REVERT: V 70 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7809 (ttp80) REVERT: W 27 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7326 (mt-10) REVERT: d 25 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8214 (mtpp) REVERT: h 77 ARG cc_start: 0.8412 (ttt180) cc_final: 0.8131 (ttm110) REVERT: i 121 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7104 (mm-30) REVERT: m 21 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7109 (mm-30) REVERT: p 38 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8564 (tm) REVERT: q 21 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.7138 (ttm170) REVERT: s 74 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7774 (mtp180) outliers start: 85 outliers final: 32 residues processed: 1037 average time/residue: 1.8075 time to fit residues: 2349.5835 Evaluate side-chains 1030 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 983 time to evaluate : 5.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 598 SER Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain O residue 178 GLU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 65 LYS Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 74 CYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 121 MET Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain j residue 57 SER Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain s residue 74 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 255 optimal weight: 20.0000 chunk 685 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 446 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 761 optimal weight: 9.9990 chunk 632 optimal weight: 9.9990 chunk 352 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 251 optimal weight: 7.9990 chunk 399 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN G 237 ASN G 444 GLN G 654 GLN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 605 HIS M 88 ASN V 72 GLN W 45 ASN X 15 GLN Y 7 GLN Z 85 GLN g 86 GLN m 32 GLN ** m 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 116 GLN n 140 GLN p 130 GLN q 135 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 68173 Z= 0.577 Angle : 1.344 50.480 92245 Z= 0.855 Chirality : 0.263 6.750 10097 Planarity : 0.005 0.059 11488 Dihedral : 11.633 175.306 10525 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.70 % Favored : 98.29 % Rotamer: Outliers : 1.24 % Allowed : 8.67 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.09), residues: 7944 helix: 1.59 (0.08), residues: 4314 sheet: 0.04 (0.26), residues: 369 loop : 0.33 (0.11), residues: 3261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 557 HIS 0.010 0.001 HIS D 150 PHE 0.025 0.002 PHE q 55 TYR 0.029 0.002 TYR O 94 ARG 0.008 0.001 ARG G 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 976 time to evaluate : 5.964 Fit side-chains REVERT: B 176 TRP cc_start: 0.8518 (t-100) cc_final: 0.7882 (t60) REVERT: G 192 MET cc_start: 0.8200 (mmm) cc_final: 0.7743 (mmm) REVERT: G 693 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6624 (mt-10) REVERT: I 122 CYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7974 (p) REVERT: L 544 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7774 (ttt) REVERT: L 581 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8069 (mtpt) REVERT: M 114 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: O 81 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8055 (ttmm) REVERT: O 178 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: T 37 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7038 (mtt) REVERT: T 57 GLU cc_start: 0.7187 (tp30) cc_final: 0.6867 (tm-30) REVERT: U 12 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8680 (tmmm) REVERT: U 37 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7531 (mmm) REVERT: V 65 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7529 (mtpp) REVERT: V 70 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7782 (mtm-85) REVERT: g 85 MET cc_start: 0.8516 (ptm) cc_final: 0.8221 (ptp) REVERT: l 15 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7872 (mmpt) REVERT: m 21 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7180 (mm-30) REVERT: p 38 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8584 (tm) REVERT: s 74 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7798 (mtp180) outliers start: 87 outliers final: 40 residues processed: 1022 average time/residue: 1.8257 time to fit residues: 2340.6713 Evaluate side-chains 1021 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 966 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain I residue 122 CYS Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain L residue 598 SER Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain O residue 178 GLU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 65 LYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 74 CYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 121 MET Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain j residue 57 SER Chi-restraints excluded: chain l residue 15 LYS Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 74 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 734 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 433 optimal weight: 0.7980 chunk 556 optimal weight: 0.9990 chunk 430 optimal weight: 4.9990 chunk 640 optimal weight: 3.9990 chunk 425 optimal weight: 0.9980 chunk 758 optimal weight: 5.9990 chunk 474 optimal weight: 0.9990 chunk 462 optimal weight: 5.9990 chunk 350 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 82 GLN G 237 ASN G 444 GLN G 654 GLN H 317 GLN L 605 HIS M 88 ASN V 72 GLN W 45 ASN X 15 GLN Y 7 GLN Z 85 GLN c 5 GLN g 86 GLN m 32 GLN m 116 GLN n 140 GLN q 135 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 68173 Z= 0.451 Angle : 1.289 50.590 92245 Z= 0.834 Chirality : 0.255 6.446 10097 Planarity : 0.004 0.055 11488 Dihedral : 10.961 172.368 10525 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.92 % Allowed : 9.48 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.09), residues: 7944 helix: 1.83 (0.08), residues: 4302 sheet: 0.04 (0.26), residues: 368 loop : 0.40 (0.11), residues: 3274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP L 557 HIS 0.005 0.001 HIS G 101 PHE 0.022 0.001 PHE M 122 TYR 0.022 0.001 TYR L 422 ARG 0.011 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 994 time to evaluate : 6.100 Fit side-chains REVERT: A 109 LYS cc_start: 0.8547 (mmpt) cc_final: 0.8317 (mmtm) REVERT: B 176 TRP cc_start: 0.8521 (t-100) cc_final: 0.7935 (t60) REVERT: B 178 ARG cc_start: 0.7993 (mtt-85) cc_final: 0.7630 (mtt90) REVERT: G 192 MET cc_start: 0.8150 (mmm) cc_final: 0.7731 (mmm) REVERT: G 693 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6673 (mt-10) REVERT: H 225 MET cc_start: 0.7589 (mmm) cc_final: 0.7274 (mmm) REVERT: I 78 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8592 (pp) REVERT: L 544 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7796 (ttt) REVERT: L 558 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6942 (mt) REVERT: M 114 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: O 81 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8009 (ttmm) REVERT: Q 58 GLU cc_start: 0.7704 (pt0) cc_final: 0.7469 (pt0) REVERT: T 37 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6884 (mtt) REVERT: T 57 GLU cc_start: 0.7157 (tp30) cc_final: 0.6844 (tm-30) REVERT: U 37 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7456 (mmm) REVERT: V 70 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7806 (ttp80) REVERT: W 27 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7325 (mt-10) REVERT: W 99 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: h 77 ARG cc_start: 0.8422 (ttt180) cc_final: 0.8161 (ttm110) REVERT: l 15 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7806 (mmpt) REVERT: m 21 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7079 (mm-30) REVERT: m 29 ARG cc_start: 0.7685 (mmt180) cc_final: 0.7423 (mmt90) REVERT: p 38 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8600 (tm) REVERT: q 21 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.7122 (ttm170) REVERT: s 74 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7761 (mtp180) outliers start: 65 outliers final: 25 residues processed: 1026 average time/residue: 1.8158 time to fit residues: 2343.6705 Evaluate side-chains 1017 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 979 time to evaluate : 5.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 598 SER Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain W residue 99 GLN Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 74 CYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 121 MET Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain l residue 15 LYS Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain s residue 74 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 469 optimal weight: 0.8980 chunk 302 optimal weight: 6.9990 chunk 453 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 482 optimal weight: 0.9980 chunk 516 optimal weight: 3.9990 chunk 375 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 596 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 82 GLN G 237 ASN G 444 GLN G 654 GLN H 317 GLN L 605 HIS M 88 ASN P 184 ASN W 45 ASN X 15 GLN Y 7 GLN Z 85 GLN c 5 GLN g 86 GLN m 32 GLN m 116 GLN n 140 GLN o 109 GLN o 116 GLN p 130 GLN q 13 GLN q 135 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 68173 Z= 0.451 Angle : 1.288 50.568 92245 Z= 0.833 Chirality : 0.255 6.445 10097 Planarity : 0.004 0.056 11488 Dihedral : 10.576 171.898 10525 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.91 % Allowed : 9.74 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.79 (0.09), residues: 7944 helix: 1.90 (0.08), residues: 4307 sheet: 0.14 (0.26), residues: 367 loop : 0.48 (0.11), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 557 HIS 0.005 0.001 HIS G 101 PHE 0.021 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.008 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 988 time to evaluate : 7.396 Fit side-chains REVERT: B 176 TRP cc_start: 0.8519 (t-100) cc_final: 0.7931 (t60) REVERT: B 178 ARG cc_start: 0.8015 (mtt-85) cc_final: 0.7672 (mtt90) REVERT: G 192 MET cc_start: 0.8127 (mmm) cc_final: 0.7755 (mmm) REVERT: G 693 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6712 (mt-10) REVERT: I 78 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.8496 (pp) REVERT: K 59 MET cc_start: 0.9082 (tmt) cc_final: 0.8443 (tmt) REVERT: L 544 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7635 (ttt) REVERT: L 558 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6896 (mt) REVERT: M 114 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: N 269 GLU cc_start: 0.8249 (tp30) cc_final: 0.8035 (tp30) REVERT: O 81 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8006 (ttmm) REVERT: O 178 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: Q 58 GLU cc_start: 0.7683 (pt0) cc_final: 0.7451 (pt0) REVERT: T 37 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6845 (mtt) REVERT: T 57 GLU cc_start: 0.7145 (tp30) cc_final: 0.6898 (tm-30) REVERT: U 12 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8477 (tmmm) REVERT: U 37 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7455 (mmm) REVERT: V 70 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7800 (ttp80) REVERT: W 27 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7318 (mt-10) REVERT: W 99 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: Y 57 ARG cc_start: 0.7291 (ttm110) cc_final: 0.6840 (mtm110) REVERT: b 42 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8346 (OUTLIER) REVERT: h 77 ARG cc_start: 0.8411 (ttt180) cc_final: 0.8158 (ttm110) REVERT: i 92 LYS cc_start: 0.8704 (mttt) cc_final: 0.8495 (mttt) REVERT: l 15 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7792 (mmpt) REVERT: m 21 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: m 29 ARG cc_start: 0.7700 (mmt180) cc_final: 0.7437 (mmt90) REVERT: p 38 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8595 (tm) REVERT: s 74 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7752 (mtp180) outliers start: 64 outliers final: 31 residues processed: 1023 average time/residue: 1.8297 time to fit residues: 2344.2256 Evaluate side-chains 1020 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 974 time to evaluate : 5.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain O residue 178 GLU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain W residue 99 GLN Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 74 CYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 121 MET Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain l residue 15 LYS Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 74 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 690 optimal weight: 0.9990 chunk 726 optimal weight: 2.9990 chunk 663 optimal weight: 2.9990 chunk 706 optimal weight: 2.9990 chunk 425 optimal weight: 0.8980 chunk 307 optimal weight: 0.9990 chunk 555 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 638 optimal weight: 0.0670 chunk 668 optimal weight: 0.0980 chunk 704 optimal weight: 6.9990 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 82 GLN G 237 ASN G 444 GLN G 654 GLN H 317 GLN L 605 HIS M 88 ASN W 45 ASN X 15 GLN Y 7 GLN Z 85 GLN c 5 GLN f 13 HIS g 86 GLN m 32 GLN m 116 GLN n 140 GLN o 109 GLN q 135 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.249 68173 Z= 0.444 Angle : 1.282 50.642 92245 Z= 0.831 Chirality : 0.255 6.434 10097 Planarity : 0.004 0.054 11488 Dihedral : 10.228 171.493 10525 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.78 % Allowed : 10.02 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.88 (0.10), residues: 7944 helix: 1.98 (0.08), residues: 4310 sheet: 0.17 (0.25), residues: 385 loop : 0.52 (0.11), residues: 3249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP L 557 HIS 0.005 0.001 HIS N 112 PHE 0.020 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.008 0.000 ARG d 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 986 time to evaluate : 6.040 Fit side-chains REVERT: A 90 MET cc_start: 0.8616 (mmm) cc_final: 0.8366 (mmp) REVERT: B 176 TRP cc_start: 0.8513 (t-100) cc_final: 0.7913 (t60) REVERT: B 178 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7729 (mtt90) REVERT: G 192 MET cc_start: 0.8101 (mmm) cc_final: 0.7751 (mmm) REVERT: G 693 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6733 (mt-10) REVERT: H 234 MET cc_start: 0.8164 (mmp) cc_final: 0.7762 (mmt) REVERT: I 78 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8548 (pp) REVERT: K 43 MET cc_start: 0.8076 (ttp) cc_final: 0.7778 (ttp) REVERT: K 59 MET cc_start: 0.9065 (tmt) cc_final: 0.8786 (tmt) REVERT: L 544 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7605 (ttt) REVERT: L 558 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6840 (mt) REVERT: M 114 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: N 269 GLU cc_start: 0.8231 (tp30) cc_final: 0.8017 (tp30) REVERT: O 81 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7999 (ttmm) REVERT: O 178 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: Q 58 GLU cc_start: 0.7655 (pt0) cc_final: 0.7419 (pt0) REVERT: T 37 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6826 (mtt) REVERT: V 70 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7794 (ttp80) REVERT: W 27 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7217 (mt-10) REVERT: Y 57 ARG cc_start: 0.7241 (ttm110) cc_final: 0.6873 (mtm110) REVERT: Y 119 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7674 (mt) REVERT: Z 93 GLU cc_start: 0.6594 (tt0) cc_final: 0.6298 (tp30) REVERT: b 42 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8318 (mt) REVERT: g 85 MET cc_start: 0.8445 (ptm) cc_final: 0.8219 (ptp) REVERT: h 77 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8136 (ttm110) REVERT: i 92 LYS cc_start: 0.8708 (mttt) cc_final: 0.8504 (mttt) REVERT: l 15 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7774 (mmpt) REVERT: m 21 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: m 29 ARG cc_start: 0.7701 (mmt180) cc_final: 0.7437 (mmt90) REVERT: p 38 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8578 (tm) REVERT: q 21 ARG cc_start: 0.7556 (ttm110) cc_final: 0.7345 (ttm-80) REVERT: s 74 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7748 (mtp180) outliers start: 55 outliers final: 23 residues processed: 1012 average time/residue: 1.8130 time to fit residues: 2303.6486 Evaluate side-chains 1014 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 977 time to evaluate : 5.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain O residue 178 GLU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 74 CYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain l residue 15 LYS Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 24 ILE Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 74 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 464 optimal weight: 5.9990 chunk 747 optimal weight: 1.9990 chunk 456 optimal weight: 5.9990 chunk 354 optimal weight: 7.9990 chunk 519 optimal weight: 5.9990 chunk 784 optimal weight: 10.0000 chunk 721 optimal weight: 2.9990 chunk 624 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 482 optimal weight: 0.8980 chunk 382 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN G 237 ASN G 444 GLN G 654 GLN H 317 GLN K 97 GLN L 605 HIS M 88 ASN W 45 ASN X 15 GLN Y 7 GLN Z 85 GLN g 86 GLN m 32 GLN ** m 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 116 GLN n 140 GLN o 116 GLN p 130 GLN q 135 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 68173 Z= 0.468 Angle : 1.300 50.542 92245 Z= 0.838 Chirality : 0.257 6.569 10097 Planarity : 0.004 0.056 11488 Dihedral : 10.416 173.151 10525 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.74 % Allowed : 10.14 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.79 (0.09), residues: 7944 helix: 1.88 (0.08), residues: 4326 sheet: 0.15 (0.26), residues: 369 loop : 0.50 (0.11), residues: 3249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP r 9 HIS 0.006 0.001 HIS G 101 PHE 0.022 0.001 PHE N 292 TYR 0.021 0.001 TYR O 94 ARG 0.007 0.000 ARG J 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 976 time to evaluate : 6.123 Fit side-chains REVERT: B 176 TRP cc_start: 0.8528 (t-100) cc_final: 0.7918 (t60) REVERT: B 178 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7682 (mtt90) REVERT: G 192 MET cc_start: 0.8111 (mmm) cc_final: 0.7694 (mmm) REVERT: G 693 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: H 234 MET cc_start: 0.8177 (mmp) cc_final: 0.7767 (mmt) REVERT: I 78 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.8526 (pp) REVERT: L 544 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7700 (ttt) REVERT: M 114 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: O 81 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8020 (ttmm) REVERT: O 178 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: Q 58 GLU cc_start: 0.7691 (pt0) cc_final: 0.7463 (pt0) REVERT: S 92 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7684 (m110) REVERT: T 37 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6896 (mtt) REVERT: T 57 GLU cc_start: 0.7253 (tp30) cc_final: 0.7016 (tm-30) REVERT: U 12 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8482 (tmmm) REVERT: V 70 ARG cc_start: 0.8044 (mtp180) cc_final: 0.7799 (ttp80) REVERT: W 27 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7343 (mt-10) REVERT: W 99 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: Z 93 GLU cc_start: 0.6726 (tt0) cc_final: 0.6419 (tp30) REVERT: h 77 ARG cc_start: 0.8418 (ttt180) cc_final: 0.8159 (ttm110) REVERT: l 15 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7807 (mmpt) REVERT: m 21 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: m 29 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7468 (mmt90) REVERT: p 38 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8586 (tm) REVERT: s 74 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7756 (mtp180) outliers start: 52 outliers final: 26 residues processed: 1004 average time/residue: 1.8144 time to fit residues: 2283.0859 Evaluate side-chains 1013 residues out of total 7040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 973 time to evaluate : 5.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain O residue 178 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain S residue 92 ASN Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain W residue 99 GLN Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 74 CYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 121 MET Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain j residue 57 SER Chi-restraints excluded: chain l residue 15 LYS Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 74 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 495 optimal weight: 6.9990 chunk 665 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 575 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 625 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 642 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN G 237 ASN G 444 GLN G 654 GLN H 317 GLN L 605 HIS M 88 ASN W 45 ASN X 15 GLN Y 7 GLN Z 85 GLN g 86 GLN m 32 GLN m 116 GLN n 140 GLN o 116 GLN q 135 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.076596 restraints weight = 61664.802| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.09 r_work: 0.2807 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 68173 Z= 0.468 Angle : 1.299 50.542 92245 Z= 0.838 Chirality : 0.258 6.579 10097 Planarity : 0.004 0.056 11488 Dihedral : 10.458 173.487 10525 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.77 % Allowed : 10.25 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 7944 helix: 1.85 (0.08), residues: 4320 sheet: 0.12 (0.26), residues: 369 loop : 0.48 (0.11), residues: 3255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP r 9 HIS 0.006 0.001 HIS G 101 PHE 0.023 0.001 PHE N 292 TYR 0.020 0.001 TYR O 94 ARG 0.008 0.000 ARG J 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31984.57 seconds wall clock time: 553 minutes 56.10 seconds (33236.10 seconds total)