Starting phenix.real_space_refine on Thu Jul 2 17:42:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ark_11885/07_2026/7ark_11885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ark_11885/07_2026/7ark_11885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ark_11885/07_2026/7ark_11885.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ark_11885/07_2026/7ark_11885.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ark_11885/07_2026/7ark_11885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ark_11885/07_2026/7ark_11885.map" model { file = "/net/cci-nas-00/data/ceres_data/7ark_11885/07_2026/7ark_11885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ark_11885/07_2026/7ark_11885.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6070 2.51 5 N 1686 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9570 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2922 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3125 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 14, 'TRANS': 390} Chain breaks: 1 Chain: "D" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1729 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.91, per 1000 atoms: 0.20 Number of scatterers: 9570 At special positions: 0 Unit cell: (126.75, 90.246, 138.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 6 15.00 Mg 2 11.99 O 1755 8.00 N 1686 7.00 C 6070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 392.8 milliseconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 9 sheets defined 34.0% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.620A pdb=" N ILE C 32 " --> pdb=" O TRP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 59 removed outlier: 3.695A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 56 " --> pdb=" O GLU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.979A pdb=" N TYR C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 200' Processing helix chain 'C' and resid 234 through 238 removed outlier: 4.165A pdb=" N GLN C 237 " --> pdb=" O SER C 234 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 238 " --> pdb=" O LEU C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 234 through 238' Processing helix chain 'C' and resid 255 through 272 removed outlier: 4.295A pdb=" N GLU C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.553A pdb=" N ALA C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.883A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 312 No H-bonds generated for 'chain 'C' and resid 310 through 312' Processing helix chain 'C' and resid 313 through 318 removed outlier: 4.008A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 338 removed outlier: 3.858A pdb=" N ILE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 379 removed outlier: 4.025A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'E' and resid 23 through 34 removed outlier: 3.676A pdb=" N VAL E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE E 32 " --> pdb=" O VAL E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 40 removed outlier: 4.020A pdb=" N VAL E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 59 removed outlier: 3.593A pdb=" N SER E 46 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 85 removed outlier: 3.512A pdb=" N LEU E 82 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.941A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.677A pdb=" N GLN E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 267 removed outlier: 3.519A pdb=" N ARG E 263 " --> pdb=" O GLY E 259 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP E 264 " --> pdb=" O TYR E 260 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 removed outlier: 3.640A pdb=" N TYR E 273 " --> pdb=" O ALA E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 284 Processing helix chain 'E' and resid 285 through 294 removed outlier: 3.677A pdb=" N THR E 290 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 317 removed outlier: 3.587A pdb=" N ARG E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 343 removed outlier: 3.750A pdb=" N TYR E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY E 323 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 339 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.655A pdb=" N THR E 386 " --> pdb=" O TYR E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 395 removed outlier: 3.822A pdb=" N LEU E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 401 removed outlier: 3.687A pdb=" N ARG E 401 " --> pdb=" O TYR E 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 55 removed outlier: 3.554A pdb=" N LEU D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.959A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 113 removed outlier: 3.704A pdb=" N LEU D 113 " --> pdb=" O MET D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 113' Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'D' and resid 121 through 134 removed outlier: 3.766A pdb=" N ALA D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET D 129 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 removed outlier: 3.563A pdb=" N ARG D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 186 removed outlier: 3.632A pdb=" N ASP D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN D 186 " --> pdb=" O ASP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 195 removed outlier: 3.721A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.517A pdb=" N ARG D 211 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 53 removed outlier: 3.539A pdb=" N LEU F 51 " --> pdb=" O GLY F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 85 removed outlier: 3.776A pdb=" N LYS F 81 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ALA F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU F 84 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 85 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 109 Processing helix chain 'F' and resid 109 through 115 removed outlier: 3.747A pdb=" N ILE F 114 " --> pdb=" O MET F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.886A pdb=" N ARG F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU F 127 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET F 129 " --> pdb=" O ARG F 125 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F 133 " --> pdb=" O MET F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 160 removed outlier: 3.583A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU F 160 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 189 removed outlier: 3.726A pdb=" N ASP F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN F 186 " --> pdb=" O ASP F 182 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY F 189 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.751A pdb=" N LYS F 210 " --> pdb=" O GLN F 207 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG F 211 " --> pdb=" O LEU F 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 94 through 96 removed outlier: 3.502A pdb=" N ALA C 94 " --> pdb=" O ARG C 223 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 96 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.718A pdb=" N ALA C 110 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N ASP C 100 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG C 163 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 164 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG C 182 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 166 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N SER C 168 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N ILE C 178 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 116 through 117 removed outlier: 6.804A pdb=" N VAL C 203 " --> pdb=" O ILE C 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 143 through 146 removed outlier: 3.588A pdb=" N ILE C 187 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU C 146 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR C 189 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 66 through 68 removed outlier: 3.532A pdb=" N GLY E 66 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU E 226 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS E 227 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA E 93 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E 98 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA E 204 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE E 206 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE E 203 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY E 151 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE E 148 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LEU E 193 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE E 150 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE E 170 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.819A pdb=" N PHE D 30 " --> pdb=" O CYS D 8 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS D 8 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 7 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 67 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP D 9 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP D 65 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 166 through 170 removed outlier: 6.289A pdb=" N VAL D 167 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL D 202 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ALA D 169 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET D 38 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR D 203 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE D 40 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA D 39 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET D 218 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL D 41 " --> pdb=" O MET D 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 6 through 9 removed outlier: 3.914A pdb=" N ASP F 9 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP F 65 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.582A pdb=" N LEU F 168 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 167 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 200 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL F 202 " --> pdb=" O ALA F 169 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 474 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: 1.40 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3192 1.35 - 1.46: 1978 1.46 - 1.58: 4456 1.58 - 1.70: 6 1.70 - 1.82: 96 Bond restraints: 9728 Sorted by residual: bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C LEU E 129 " pdb=" N PRO E 130 " ideal model delta sigma weight residual 1.334 1.382 -0.049 8.40e-03 1.42e+04 3.38e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 9723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 13033 3.40 - 6.80: 124 6.80 - 10.19: 22 10.19 - 13.59: 1 13.59 - 16.99: 2 Bond angle restraints: 13182 Sorted by residual: angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 109.96 16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 111.05 15.90 3.00e+00 1.11e-01 2.81e+01 angle pdb=" C PRO F 61 " pdb=" N THR F 62 " pdb=" CA THR F 62 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 angle pdb=" C LEU E 158 " pdb=" N LYS E 159 " pdb=" CA LYS E 159 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C ILE E 302 " pdb=" N ALA E 303 " pdb=" CA ALA E 303 " ideal model delta sigma weight residual 120.38 125.74 -5.36 1.37e+00 5.33e-01 1.53e+01 ... (remaining 13177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 5486 21.75 - 43.49: 342 43.49 - 65.24: 24 65.24 - 86.98: 8 86.98 - 108.73: 3 Dihedral angle restraints: 5863 sinusoidal: 2333 harmonic: 3530 Sorted by residual: dihedral pdb=" O1B ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PB ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sinusoidal sigma weight residual 35.15 -73.58 108.73 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O1A ANP D 401 " pdb=" O3A ANP D 401 " pdb=" PA ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sinusoidal sigma weight residual 83.11 -168.48 -108.41 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" CA GLY D 47 " pdb=" C GLY D 47 " pdb=" N LYS D 48 " pdb=" CA LYS D 48 " ideal model delta harmonic sigma weight residual 180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1216 0.055 - 0.110: 268 0.110 - 0.165: 45 0.165 - 0.220: 5 0.220 - 0.275: 2 Chirality restraints: 1536 Sorted by residual: chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA THR F 62 " pdb=" N THR F 62 " pdb=" C THR F 62 " pdb=" CB THR F 62 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1533 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 382 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO C 383 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 383 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 383 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 397 " -0.031 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO E 398 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 398 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 398 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 206 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO E 207 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 207 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 207 " -0.025 5.00e-02 4.00e+02 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 476 2.73 - 3.27: 8374 3.27 - 3.82: 14687 3.82 - 4.36: 17119 4.36 - 4.90: 28338 Nonbonded interactions: 68994 Sorted by model distance: nonbonded pdb=" O1G ANP D 401 " pdb="MG MG D 402 " model vdw 2.191 2.170 nonbonded pdb=" OD1 ASP F 170 " pdb="MG MG F 402 " model vdw 2.205 2.170 nonbonded pdb=" NE2 GLN D 94 " pdb="MG MG D 402 " model vdw 2.258 2.250 nonbonded pdb=" O ILE C 96 " pdb=" OG1 THR C 220 " model vdw 2.326 3.040 nonbonded pdb=" OE2 GLU D 36 " pdb=" OG SER D 213 " model vdw 2.327 3.040 ... (remaining 68989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and ((resid 3 and (name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or resid 4 through 402)) selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.300 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 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 : 0.004 0.145 9728 Z= 0.228 Angle : 0.850 16.989 13182 Z= 0.404 Chirality : 0.049 0.275 1536 Planarity : 0.005 0.048 1682 Dihedral : 13.617 108.725 3591 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.10 % Allowed : 9.70 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.58 (0.16), residues: 1229 helix: -5.05 (0.08), residues: 333 sheet: -2.38 (0.44), residues: 119 loop : -3.49 (0.16), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 85 TYR 0.015 0.001 TYR E 248 PHE 0.011 0.001 PHE F 199 TRP 0.009 0.001 TRP C 249 HIS 0.002 0.001 HIS E 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.23 ( 9728) covalent geometry : angle 0.85048 / 0.40 (13182) hydrogen bonds : bond 0.34684 / 22.58 ( 166) hydrogen bonds : angle 11.84143 / 8.15 ( 474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.8346 (tp) cc_final: 0.7530 (tp) REVERT: C 184 PHE cc_start: 0.7112 (m-80) cc_final: 0.6834 (m-80) REVERT: C 315 MET cc_start: 0.7887 (ppp) cc_final: 0.7583 (tmm) REVERT: E 237 LEU cc_start: 0.5024 (tt) cc_final: 0.3413 (mm) REVERT: E 285 PHE cc_start: 0.3833 (m-80) cc_final: 0.2993 (m-80) REVERT: D 37 MET cc_start: 0.6105 (mpp) cc_final: 0.5824 (mpp) REVERT: F 24 VAL cc_start: 0.7397 (m) cc_final: 0.7066 (p) REVERT: F 25 LEU cc_start: 0.6648 (tp) cc_final: 0.6359 (tt) REVERT: F 99 LEU cc_start: 0.6611 (mp) cc_final: 0.5718 (mt) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.1104 time to fit residues: 45.3609 Evaluate side-chains 212 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN E 146 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 ASN D 7 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN F 96 HIS F 107 ASN F 204 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.222853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.189957 restraints weight = 21825.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.193229 restraints weight = 14838.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.195533 restraints weight = 11008.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.197201 restraints weight = 8795.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.197754 restraints weight = 7435.576| |-----------------------------------------------------------------------------| r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9728 Z= 0.140 Angle : 0.613 9.548 13182 Z= 0.304 Chirality : 0.042 0.136 1536 Planarity : 0.005 0.048 1682 Dihedral : 5.796 113.657 1335 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.20 % Allowed : 5.97 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.64 (0.18), residues: 1229 helix: -3.69 (0.17), residues: 380 sheet: -1.53 (0.48), residues: 119 loop : -3.14 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 219 TYR 0.017 0.002 TYR C 128 PHE 0.015 0.002 PHE F 95 TRP 0.018 0.001 TRP E 165 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9728) covalent geometry : angle 0.61327 / 0.30 (13182) hydrogen bonds : bond 0.03540 / 2.27 ( 166) hydrogen bonds : angle 5.93771 / 4.10 ( 474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 250 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5363 (m-90) cc_final: 0.5023 (m-90) REVERT: C 29 LEU cc_start: 0.8601 (tp) cc_final: 0.7899 (mm) REVERT: C 88 ASP cc_start: 0.3255 (p0) cc_final: 0.2846 (p0) REVERT: C 164 VAL cc_start: 0.8863 (t) cc_final: 0.8543 (t) REVERT: C 184 PHE cc_start: 0.7165 (m-80) cc_final: 0.6641 (m-80) REVERT: C 253 LYS cc_start: 0.6952 (mmmt) cc_final: 0.6241 (pttm) REVERT: C 289 MET cc_start: 0.7929 (mmp) cc_final: 0.7437 (mmp) REVERT: E 276 MET cc_start: 0.6016 (mmp) cc_final: 0.5259 (mmp) REVERT: E 285 PHE cc_start: 0.4888 (m-80) cc_final: 0.3260 (m-80) REVERT: D 171 GLU cc_start: 0.8052 (tp30) cc_final: 0.7084 (tp30) REVERT: D 190 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7611 (mt-10) REVERT: D 195 GLN cc_start: 0.6367 (pm20) cc_final: 0.6076 (pm20) REVERT: F 38 MET cc_start: 0.7556 (ptp) cc_final: 0.7247 (ptp) outliers start: 2 outliers final: 0 residues processed: 252 average time/residue: 0.1096 time to fit residues: 37.6586 Evaluate side-chains 198 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 67 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 266 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN F 94 GLN F 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.220163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.186891 restraints weight = 21435.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.190141 restraints weight = 14532.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.192463 restraints weight = 10759.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.194013 restraints weight = 8599.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.195219 restraints weight = 7293.686| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9728 Z= 0.104 Angle : 0.554 7.140 13182 Z= 0.271 Chirality : 0.041 0.126 1536 Planarity : 0.004 0.035 1682 Dihedral : 5.716 115.683 1335 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.20), residues: 1229 helix: -2.67 (0.23), residues: 379 sheet: -1.20 (0.51), residues: 115 loop : -2.84 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 163 TYR 0.010 0.001 TYR F 93 PHE 0.032 0.002 PHE C 257 TRP 0.018 0.001 TRP E 377 HIS 0.006 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 9728) covalent geometry : angle 0.55420 / 0.27 (13182) hydrogen bonds : bond 0.02823 / 1.72 ( 166) hydrogen bonds : angle 5.26153 / 3.58 ( 474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5502 (m-90) cc_final: 0.5073 (m-90) REVERT: C 88 ASP cc_start: 0.2851 (p0) cc_final: 0.2466 (p0) REVERT: C 184 PHE cc_start: 0.7129 (m-80) cc_final: 0.6629 (m-80) REVERT: C 253 LYS cc_start: 0.6678 (mmmt) cc_final: 0.6131 (pttm) REVERT: C 264 LYS cc_start: 0.7294 (tttt) cc_final: 0.6468 (ttpp) REVERT: C 289 MET cc_start: 0.8109 (mmp) cc_final: 0.7610 (mmp) REVERT: C 344 MET cc_start: 0.1765 (ppp) cc_final: -0.0068 (ptp) REVERT: E 272 MET cc_start: 0.6070 (mmt) cc_final: 0.5437 (mmp) REVERT: E 276 MET cc_start: 0.6608 (mmp) cc_final: 0.5661 (mmp) REVERT: E 298 LYS cc_start: 0.2623 (mmmt) cc_final: 0.2024 (mmmt) REVERT: D 68 PHE cc_start: 0.6492 (t80) cc_final: 0.6264 (t80) REVERT: D 103 THR cc_start: 0.7755 (m) cc_final: 0.7081 (m) REVERT: D 171 GLU cc_start: 0.7981 (tp30) cc_final: 0.7217 (tp30) REVERT: F 81 LYS cc_start: 0.8653 (pttt) cc_final: 0.8453 (pttt) REVERT: F 190 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7288 (tm-30) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1027 time to fit residues: 34.3986 Evaluate side-chains 201 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 62 optimal weight: 0.0370 overall best weight: 1.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN E 212 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN F 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.210328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.176701 restraints weight = 21702.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.179642 restraints weight = 14784.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.181644 restraints weight = 11089.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.183134 restraints weight = 8978.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.183869 restraints weight = 7707.981| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9728 Z= 0.139 Angle : 0.617 7.246 13182 Z= 0.301 Chirality : 0.043 0.142 1536 Planarity : 0.004 0.039 1682 Dihedral : 6.163 125.386 1335 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.21), residues: 1229 helix: -2.18 (0.25), residues: 377 sheet: -1.05 (0.52), residues: 110 loop : -2.55 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 18 TYR 0.018 0.002 TYR F 93 PHE 0.023 0.002 PHE C 257 TRP 0.015 0.001 TRP E 321 HIS 0.009 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9728) covalent geometry : angle 0.61734 / 0.30 (13182) hydrogen bonds : bond 0.02924 / 1.77 ( 166) hydrogen bonds : angle 5.01684 / 3.46 ( 474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5467 (m-90) cc_final: 0.5067 (m-90) REVERT: C 88 ASP cc_start: 0.3066 (p0) cc_final: 0.2650 (p0) REVERT: C 164 VAL cc_start: 0.8815 (t) cc_final: 0.8332 (t) REVERT: C 184 PHE cc_start: 0.7422 (m-80) cc_final: 0.6716 (m-80) REVERT: C 289 MET cc_start: 0.8543 (mmp) cc_final: 0.8041 (mmp) REVERT: E 228 MET cc_start: 0.2007 (ptt) cc_final: 0.1661 (ptt) REVERT: E 298 LYS cc_start: 0.3277 (mmmt) cc_final: 0.2182 (mmmt) REVERT: E 337 ILE cc_start: 0.8944 (pt) cc_final: 0.8408 (mp) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.0989 time to fit residues: 32.7564 Evaluate side-chains 187 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 0.0060 chunk 117 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN F 69 ASN F 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.208508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.172120 restraints weight = 21910.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.175128 restraints weight = 14928.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.177447 restraints weight = 11326.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.178929 restraints weight = 9181.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.179782 restraints weight = 7920.106| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9728 Z= 0.126 Angle : 0.602 7.032 13182 Z= 0.291 Chirality : 0.043 0.142 1536 Planarity : 0.004 0.036 1682 Dihedral : 6.261 127.383 1335 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.22), residues: 1229 helix: -2.08 (0.24), residues: 389 sheet: -1.17 (0.51), residues: 110 loop : -2.45 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 151 TYR 0.011 0.001 TYR F 93 PHE 0.043 0.002 PHE E 285 TRP 0.009 0.001 TRP E 321 HIS 0.007 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9728) covalent geometry : angle 0.60238 / 0.29 (13182) hydrogen bonds : bond 0.02726 / 1.74 ( 166) hydrogen bonds : angle 4.95645 / 3.40 ( 474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.3565 (p0) cc_final: 0.3159 (p0) REVERT: C 164 VAL cc_start: 0.8878 (t) cc_final: 0.8417 (p) REVERT: C 184 PHE cc_start: 0.7449 (m-80) cc_final: 0.6366 (m-80) REVERT: E 99 ASN cc_start: 0.7976 (p0) cc_final: 0.7765 (p0) REVERT: E 217 MET cc_start: 0.5756 (mtp) cc_final: 0.5484 (mpp) REVERT: E 228 MET cc_start: 0.2110 (ptt) cc_final: 0.1894 (ptp) REVERT: E 298 LYS cc_start: 0.2777 (mmmt) cc_final: 0.1871 (mmmt) REVERT: E 337 ILE cc_start: 0.8943 (pt) cc_final: 0.8473 (mp) REVERT: D 195 GLN cc_start: 0.6615 (pm20) cc_final: 0.6306 (pm20) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0953 time to fit residues: 31.1469 Evaluate side-chains 190 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 90 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.0010 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 56 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN E 266 GLN D 215 GLN F 53 HIS F 69 ASN F 94 GLN F 215 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.211513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.177651 restraints weight = 21738.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.180470 restraints weight = 15414.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.182437 restraints weight = 11895.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.183715 restraints weight = 9813.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.184692 restraints weight = 8549.533| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9728 Z= 0.091 Angle : 0.571 7.373 13182 Z= 0.272 Chirality : 0.042 0.131 1536 Planarity : 0.004 0.072 1682 Dihedral : 6.117 125.101 1335 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.22), residues: 1229 helix: -1.81 (0.26), residues: 382 sheet: -1.15 (0.51), residues: 110 loop : -2.33 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 142 TYR 0.010 0.001 TYR F 93 PHE 0.022 0.001 PHE D 185 TRP 0.029 0.001 TRP C 28 HIS 0.003 0.000 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 ( 9728) covalent geometry : angle 0.57145 / 0.27 (13182) hydrogen bonds : bond 0.02271 / 1.48 ( 166) hydrogen bonds : angle 4.71497 / 3.23 ( 474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.3835 (p0) cc_final: 0.3404 (p0) REVERT: C 164 VAL cc_start: 0.8774 (t) cc_final: 0.8382 (p) REVERT: C 184 PHE cc_start: 0.7466 (m-80) cc_final: 0.6349 (m-80) REVERT: C 253 LYS cc_start: 0.7160 (mmmt) cc_final: 0.6769 (tppt) REVERT: C 366 ILE cc_start: 0.7736 (tt) cc_final: 0.7129 (mm) REVERT: E 298 LYS cc_start: 0.2448 (mmmt) cc_final: 0.1739 (mmmt) REVERT: E 337 ILE cc_start: 0.8954 (pt) cc_final: 0.8489 (mp) REVERT: D 195 GLN cc_start: 0.6646 (pm20) cc_final: 0.6400 (pm20) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0977 time to fit residues: 31.7673 Evaluate side-chains 193 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 22 optimal weight: 0.0980 chunk 19 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS F 53 HIS F 69 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.204016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.169078 restraints weight = 21880.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.171877 restraints weight = 15252.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.173843 restraints weight = 11616.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.175188 restraints weight = 9562.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.176041 restraints weight = 8370.502| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9728 Z= 0.143 Angle : 0.662 7.889 13182 Z= 0.320 Chirality : 0.044 0.145 1536 Planarity : 0.004 0.062 1682 Dihedral : 6.479 130.707 1335 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.10 % Allowed : 2.84 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.22), residues: 1229 helix: -2.01 (0.24), residues: 403 sheet: -1.34 (0.52), residues: 108 loop : -2.26 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 151 TYR 0.010 0.001 TYR D 15 PHE 0.021 0.002 PHE E 285 TRP 0.032 0.002 TRP C 28 HIS 0.007 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9728) covalent geometry : angle 0.66186 / 0.32 (13182) hydrogen bonds : bond 0.02891 / 1.79 ( 166) hydrogen bonds : angle 4.88556 / 3.36 ( 474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5530 (m-90) cc_final: 0.5254 (m-90) REVERT: C 88 ASP cc_start: 0.3987 (p0) cc_final: 0.3553 (p0) REVERT: C 289 MET cc_start: 0.8736 (mmp) cc_final: 0.8293 (mmp) REVERT: C 292 GLU cc_start: 0.7511 (pt0) cc_final: 0.7042 (pt0) REVERT: C 363 LEU cc_start: 0.7880 (mp) cc_final: 0.7624 (mt) REVERT: C 366 ILE cc_start: 0.7852 (tt) cc_final: 0.7203 (mm) REVERT: E 298 LYS cc_start: 0.3206 (mmmt) cc_final: 0.2183 (mmmt) REVERT: E 337 ILE cc_start: 0.8908 (pt) cc_final: 0.8483 (mp) REVERT: E 382 TYR cc_start: 0.6859 (t80) cc_final: 0.6615 (t80) REVERT: D 68 PHE cc_start: 0.7204 (t80) cc_final: 0.6893 (t80) REVERT: D 217 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6834 (tm-30) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.0974 time to fit residues: 33.4705 Evaluate side-chains 205 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 13 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 97 optimal weight: 0.0470 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN E 198 GLN E 201 HIS E 266 GLN D 53 HIS D 163 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.208086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.173862 restraints weight = 21779.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.176708 restraints weight = 15197.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.178777 restraints weight = 11619.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.179856 restraints weight = 9513.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.181029 restraints weight = 8350.537| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9728 Z= 0.098 Angle : 0.616 8.321 13182 Z= 0.291 Chirality : 0.042 0.133 1536 Planarity : 0.004 0.055 1682 Dihedral : 6.269 125.834 1335 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.22), residues: 1229 helix: -1.70 (0.25), residues: 413 sheet: -1.28 (0.50), residues: 112 loop : -2.17 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.007 0.001 TYR D 15 PHE 0.019 0.001 PHE C 257 TRP 0.022 0.001 TRP C 28 HIS 0.008 0.001 HIS D 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 9728) covalent geometry : angle 0.61590 / 0.29 (13182) hydrogen bonds : bond 0.02278 / 1.49 ( 166) hydrogen bonds : angle 4.70011 / 3.24 ( 474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5457 (m-90) cc_final: 0.5182 (m-90) REVERT: C 88 ASP cc_start: 0.3687 (p0) cc_final: 0.3266 (p0) REVERT: C 264 LYS cc_start: 0.7730 (tttt) cc_final: 0.7286 (ttmm) REVERT: C 289 MET cc_start: 0.8692 (mmp) cc_final: 0.8491 (mmp) REVERT: C 292 GLU cc_start: 0.7272 (pt0) cc_final: 0.7060 (pt0) REVERT: C 363 LEU cc_start: 0.7722 (mp) cc_final: 0.7520 (mt) REVERT: C 366 ILE cc_start: 0.7831 (tt) cc_final: 0.7182 (mm) REVERT: E 298 LYS cc_start: 0.2726 (mmmt) cc_final: 0.1782 (mmmt) REVERT: E 319 PHE cc_start: 0.6956 (m-10) cc_final: 0.6494 (m-10) REVERT: E 337 ILE cc_start: 0.8818 (pt) cc_final: 0.8401 (mp) REVERT: E 382 TYR cc_start: 0.6817 (t80) cc_final: 0.6552 (t80) REVERT: D 122 ILE cc_start: 0.7818 (mm) cc_final: 0.7199 (pt) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.0975 time to fit residues: 32.5370 Evaluate side-chains 203 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 30.0000 chunk 71 optimal weight: 1.9990 chunk 120 optimal weight: 0.0010 chunk 72 optimal weight: 0.0050 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 238 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.206255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.170700 restraints weight = 21794.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.173603 restraints weight = 15245.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.175543 restraints weight = 11680.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.177068 restraints weight = 9641.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.178042 restraints weight = 8354.782| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9728 Z= 0.105 Angle : 0.629 7.886 13182 Z= 0.296 Chirality : 0.043 0.130 1536 Planarity : 0.004 0.053 1682 Dihedral : 6.300 125.719 1335 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.22), residues: 1229 helix: -1.56 (0.25), residues: 406 sheet: -1.16 (0.51), residues: 112 loop : -2.09 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 142 TYR 0.009 0.001 TYR D 15 PHE 0.019 0.002 PHE E 285 TRP 0.020 0.001 TRP C 28 HIS 0.005 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.10 ( 9728) covalent geometry : angle 0.62852 / 0.30 (13182) hydrogen bonds : bond 0.02339 / 1.51 ( 166) hydrogen bonds : angle 4.63722 / 3.18 ( 474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5533 (m-90) cc_final: 0.5254 (m-90) REVERT: C 88 ASP cc_start: 0.3817 (p0) cc_final: 0.3399 (p0) REVERT: C 264 LYS cc_start: 0.7775 (tttt) cc_final: 0.7326 (ttmm) REVERT: C 289 MET cc_start: 0.8684 (mmp) cc_final: 0.8403 (mmp) REVERT: C 292 GLU cc_start: 0.7393 (pt0) cc_final: 0.7085 (pt0) REVERT: C 311 MET cc_start: 0.5135 (pmm) cc_final: 0.4342 (mmt) REVERT: C 363 LEU cc_start: 0.7811 (mp) cc_final: 0.7533 (mt) REVERT: C 366 ILE cc_start: 0.7819 (tt) cc_final: 0.7193 (mm) REVERT: E 298 LYS cc_start: 0.2404 (mmmt) cc_final: 0.1503 (mmmt) REVERT: E 319 PHE cc_start: 0.7012 (m-10) cc_final: 0.6544 (m-10) REVERT: E 337 ILE cc_start: 0.8830 (pt) cc_final: 0.8382 (mp) REVERT: D 53 HIS cc_start: 0.8111 (m90) cc_final: 0.7769 (m170) REVERT: D 217 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6974 (tm-30) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0826 time to fit residues: 27.2147 Evaluate side-chains 199 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 0.0020 chunk 63 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 HIS D 87 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.199564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.164594 restraints weight = 21873.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.166602 restraints weight = 15905.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.167562 restraints weight = 12504.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.168572 restraints weight = 10531.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.169081 restraints weight = 9392.836| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.7243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9728 Z= 0.145 Angle : 0.711 10.567 13182 Z= 0.339 Chirality : 0.045 0.155 1536 Planarity : 0.004 0.056 1682 Dihedral : 6.640 128.562 1335 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.22), residues: 1229 helix: -1.57 (0.25), residues: 411 sheet: -1.08 (0.53), residues: 103 loop : -2.13 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 142 TYR 0.014 0.002 TYR D 15 PHE 0.023 0.002 PHE D 95 TRP 0.020 0.002 TRP C 28 HIS 0.010 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 9728) covalent geometry : angle 0.71052 / 0.34 (13182) hydrogen bonds : bond 0.02909 / 1.84 ( 166) hydrogen bonds : angle 4.85500 / 3.35 ( 474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5669 (m-90) cc_final: 0.5276 (m-90) REVERT: C 39 MET cc_start: 0.7323 (ttp) cc_final: 0.6928 (ttp) REVERT: C 88 ASP cc_start: 0.3784 (p0) cc_final: 0.3452 (p0) REVERT: C 289 MET cc_start: 0.8635 (mmp) cc_final: 0.8105 (mmp) REVERT: C 292 GLU cc_start: 0.7543 (pt0) cc_final: 0.7064 (pt0) REVERT: C 311 MET cc_start: 0.5320 (pmm) cc_final: 0.4874 (mmt) REVERT: C 363 LEU cc_start: 0.8021 (mp) cc_final: 0.7814 (mt) REVERT: C 366 ILE cc_start: 0.7901 (tt) cc_final: 0.7269 (mm) REVERT: E 22 MET cc_start: 0.4326 (tpp) cc_final: 0.3060 (tmm) REVERT: E 169 MET cc_start: 0.2891 (ppp) cc_final: 0.0985 (pmm) REVERT: E 298 LYS cc_start: 0.3033 (mmmt) cc_final: 0.1932 (mmmt) REVERT: E 319 PHE cc_start: 0.7294 (m-10) cc_final: 0.6802 (m-10) REVERT: E 337 ILE cc_start: 0.8897 (pt) cc_final: 0.8522 (mp) REVERT: E 400 ARG cc_start: 0.6836 (tpm170) cc_final: 0.5809 (tpt-90) REVERT: D 53 HIS cc_start: 0.8344 (m90) cc_final: 0.7919 (m170) REVERT: D 127 LEU cc_start: 0.9089 (tp) cc_final: 0.8548 (tp) REVERT: D 205 ASP cc_start: 0.5625 (p0) cc_final: 0.5187 (p0) REVERT: D 217 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6836 (tm-30) REVERT: F 16 GLN cc_start: 0.7732 (pp30) cc_final: 0.7405 (pp30) REVERT: F 131 LYS cc_start: 0.8568 (tppt) cc_final: 0.8340 (tppt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.0863 time to fit residues: 29.0092 Evaluate side-chains 209 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS F 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.203550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.170808 restraints weight = 21709.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.172339 restraints weight = 15793.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.173323 restraints weight = 12801.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.175064 restraints weight = 10549.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.175058 restraints weight = 9259.333| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.7249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9728 Z= 0.109 Angle : 0.649 8.984 13182 Z= 0.306 Chirality : 0.043 0.145 1536 Planarity : 0.004 0.052 1682 Dihedral : 6.344 120.593 1335 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.23), residues: 1229 helix: -1.35 (0.25), residues: 407 sheet: -1.17 (0.50), residues: 114 loop : -2.01 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.031 0.001 TYR F 93 PHE 0.018 0.002 PHE C 257 TRP 0.019 0.001 TRP C 28 HIS 0.005 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9728) covalent geometry : angle 0.64875 / 0.31 (13182) hydrogen bonds : bond 0.02253 / 1.47 ( 166) hydrogen bonds : angle 4.61297 / 3.19 ( 474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.96 seconds wall clock time: 32 minutes 56.65 seconds (1976.65 seconds total)