Starting phenix.real_space_refine on Fri Mar 14 03:35:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ark_11885/03_2025/7ark_11885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ark_11885/03_2025/7ark_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ark_11885/03_2025/7ark_11885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ark_11885/03_2025/7ark_11885.map" model { file = "/net/cci-nas-00/data/ceres_data/7ark_11885/03_2025/7ark_11885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ark_11885/03_2025/7ark_11885.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.38, per 1000 atoms: 0.56 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: 2.09 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.97 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: 1.97 Time building geometry restraints manager: 2.50 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: 5515 21.75 - 43.49: 347 43.49 - 65.24: 32 65.24 - 86.98: 22 86.98 - 108.73: 3 Dihedral angle restraints: 5919 sinusoidal: 2389 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 5916 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 228 or resid 401 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: 0.440 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.740 Find NCS groups from input model: 0.180 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 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= 0.297 Angle : 0.850 16.989 13182 Z= 0.404 Chirality : 0.049 0.275 1536 Planarity : 0.005 0.048 1682 Dihedral : 14.620 108.725 3647 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP C 249 HIS 0.002 0.001 HIS E 376 PHE 0.011 0.001 PHE F 199 TYR 0.015 0.001 TYR E 248 ARG 0.002 0.000 ARG D 85 *********************** 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 : 1.001 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: 0.7529 (tp) REVERT: C 184 PHE cc_start: 0.7113 (m-80) cc_final: 0.6834 (m-80) REVERT: C 315 MET cc_start: 0.7886 (ppp) cc_final: 0.7584 (tmm) REVERT: E 237 LEU cc_start: 0.5024 (tt) cc_final: 0.3412 (mm) REVERT: E 285 PHE cc_start: 0.3833 (m-80) cc_final: 0.2992 (m-80) REVERT: D 37 MET cc_start: 0.6105 (mpp) cc_final: 0.5823 (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: 0.2489 time to fit residues: 100.4839 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 : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 0.0670 chunk 110 optimal weight: 0.7980 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN E 86 GLN E 146 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN F 107 ASN F 204 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.226606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.194234 restraints weight = 21508.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.197833 restraints weight = 14261.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.200365 restraints weight = 10388.650| |-----------------------------------------------------------------------------| r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9728 Z= 0.187 Angle : 0.599 9.053 13182 Z= 0.293 Chirality : 0.042 0.139 1536 Planarity : 0.005 0.047 1682 Dihedral : 8.961 112.990 1391 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.18), residues: 1229 helix: -3.76 (0.17), residues: 380 sheet: -1.55 (0.48), residues: 119 loop : -3.18 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 165 HIS 0.005 0.001 HIS F 96 PHE 0.012 0.001 PHE E 329 TYR 0.014 0.001 TYR C 128 ARG 0.006 0.001 ARG C 17 *********************** 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 256 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.933 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 28 TRP cc_start: 0.5348 (m-90) cc_final: 0.4888 (m-90) REVERT: C 88 ASP cc_start: 0.3461 (p0) cc_final: 0.3068 (p0) REVERT: C 164 VAL cc_start: 0.8859 (t) cc_final: 0.8531 (t) REVERT: C 184 PHE cc_start: 0.7101 (m-80) cc_final: 0.6618 (m-80) REVERT: C 291 MET cc_start: 0.6544 (ptp) cc_final: 0.6325 (ptp) REVERT: E 228 MET cc_start: 0.1681 (ptt) cc_final: 0.1184 (ptt) REVERT: E 276 MET cc_start: 0.5625 (mmp) cc_final: 0.5014 (mmp) REVERT: D 23 ASP cc_start: 0.6016 (m-30) cc_final: 0.5129 (m-30) REVERT: D 103 THR cc_start: 0.7295 (m) cc_final: 0.6860 (m) REVERT: D 195 GLN cc_start: 0.6385 (pm20) cc_final: 0.6092 (pm20) REVERT: F 38 MET cc_start: 0.7414 (ptp) cc_final: 0.7116 (ptp) REVERT: F 190 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7457 (tm-30) outliers start: 1 outliers final: 1 residues processed: 255 average time/residue: 0.2317 time to fit residues: 79.3992 Evaluate side-chains 203 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 84 optimal weight: 0.0670 chunk 68 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 ASN E 119 ASN E 198 GLN E 212 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN F 96 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.206922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.170208 restraints weight = 21839.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.173270 restraints weight = 15004.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.175475 restraints weight = 11374.761| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9728 Z= 0.312 Angle : 0.767 9.214 13182 Z= 0.382 Chirality : 0.045 0.146 1536 Planarity : 0.005 0.053 1682 Dihedral : 9.353 143.765 1391 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.10 % Allowed : 7.44 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.20), residues: 1229 helix: -3.11 (0.20), residues: 385 sheet: -1.30 (0.51), residues: 110 loop : -2.87 (0.19), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 351 HIS 0.013 0.002 HIS D 96 PHE 0.026 0.003 PHE F 95 TYR 0.025 0.002 TYR F 93 ARG 0.028 0.001 ARG C 163 *********************** 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 244 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 1.602 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: 0.5719 (m-90) cc_final: 0.5138 (m-90) REVERT: C 88 ASP cc_start: 0.3672 (p0) cc_final: 0.3262 (p0) REVERT: C 164 VAL cc_start: 0.8956 (t) cc_final: 0.8583 (p) REVERT: C 184 PHE cc_start: 0.7477 (m-80) cc_final: 0.6477 (m-80) REVERT: C 264 LYS cc_start: 0.7762 (tttt) cc_final: 0.7395 (ttmm) REVERT: C 289 MET cc_start: 0.8611 (mmp) cc_final: 0.8261 (mmp) REVERT: C 291 MET cc_start: 0.6785 (ptp) cc_final: 0.6583 (ptp) REVERT: C 344 MET cc_start: 0.1948 (ppp) cc_final: 0.0283 (ptp) REVERT: E 125 ARG cc_start: 0.5553 (tpt90) cc_final: 0.4852 (tpm170) REVERT: E 228 MET cc_start: 0.2221 (ptt) cc_final: 0.1354 (ptt) REVERT: E 298 LYS cc_start: 0.3540 (tppt) cc_final: 0.3117 (tppt) REVERT: D 101 ASP cc_start: 0.7591 (p0) cc_final: 0.6957 (p0) REVERT: D 145 GLU cc_start: 0.6922 (pt0) cc_final: 0.6616 (pt0) REVERT: D 171 GLU cc_start: 0.8151 (tp30) cc_final: 0.7464 (tp30) REVERT: D 195 GLN cc_start: 0.6710 (pm20) cc_final: 0.6470 (pm20) REVERT: F 190 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7586 (tm-30) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 0.2471 time to fit residues: 81.3435 Evaluate side-chains 201 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 109 ASN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.207729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.172755 restraints weight = 21863.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.175521 restraints weight = 15410.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.177535 restraints weight = 11911.638| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9728 Z= 0.195 Angle : 0.620 6.451 13182 Z= 0.303 Chirality : 0.043 0.141 1536 Planarity : 0.004 0.041 1682 Dihedral : 9.058 146.435 1391 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.20), residues: 1229 helix: -2.52 (0.22), residues: 384 sheet: -1.36 (0.49), residues: 113 loop : -2.62 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 351 HIS 0.008 0.001 HIS F 96 PHE 0.024 0.002 PHE E 285 TYR 0.010 0.001 TYR F 93 ARG 0.006 0.001 ARG D 142 *********************** 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 241 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.002 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: 0.6092 (m-90) cc_final: 0.5434 (m-90) REVERT: C 39 MET cc_start: 0.6668 (ttp) cc_final: 0.6002 (ttp) REVERT: C 88 ASP cc_start: 0.3727 (p0) cc_final: 0.3304 (p0) REVERT: C 184 PHE cc_start: 0.7434 (m-80) cc_final: 0.6720 (m-80) REVERT: C 264 LYS cc_start: 0.7691 (tttt) cc_final: 0.7116 (ttmm) REVERT: C 366 ILE cc_start: 0.7761 (tt) cc_final: 0.7305 (mt) REVERT: E 169 MET cc_start: 0.2811 (tmm) cc_final: 0.1042 (mpp) REVERT: E 298 LYS cc_start: 0.2763 (tppt) cc_final: 0.2307 (tppt) REVERT: E 319 PHE cc_start: 0.7003 (m-10) cc_final: 0.6736 (m-10) REVERT: E 337 ILE cc_start: 0.8916 (pt) cc_final: 0.8398 (mp) REVERT: D 53 HIS cc_start: 0.8568 (m90) cc_final: 0.8206 (m90) REVERT: D 68 PHE cc_start: 0.7005 (t80) cc_final: 0.6735 (t80) REVERT: D 145 GLU cc_start: 0.6873 (pt0) cc_final: 0.6276 (pt0) REVERT: F 190 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7784 (tm-30) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2736 time to fit residues: 90.5453 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 : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 0.0470 chunk 77 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 60 optimal weight: 0.0970 chunk 110 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 0.0030 chunk 41 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 overall best weight: 0.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN E 266 GLN F 94 GLN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.212748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.178991 restraints weight = 21080.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.182298 restraints weight = 14169.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.184544 restraints weight = 10467.093| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9728 Z= 0.143 Angle : 0.581 6.237 13182 Z= 0.277 Chirality : 0.042 0.124 1536 Planarity : 0.004 0.035 1682 Dihedral : 8.696 143.181 1391 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.21), residues: 1229 helix: -2.10 (0.25), residues: 377 sheet: -1.27 (0.49), residues: 113 loop : -2.46 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 377 HIS 0.003 0.001 HIS D 96 PHE 0.020 0.001 PHE D 185 TYR 0.009 0.001 TYR F 93 ARG 0.013 0.000 ARG F 153 *********************** 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 252 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.928 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: 0.5985 (m-90) cc_final: 0.5420 (m-90) REVERT: C 88 ASP cc_start: 0.3938 (p0) cc_final: 0.3536 (p0) REVERT: C 164 VAL cc_start: 0.8674 (t) cc_final: 0.8228 (t) REVERT: C 184 PHE cc_start: 0.7200 (m-80) cc_final: 0.6581 (m-80) REVERT: C 264 LYS cc_start: 0.7436 (tttt) cc_final: 0.7140 (ttmm) REVERT: C 363 LEU cc_start: 0.7748 (mp) cc_final: 0.7483 (mt) REVERT: C 366 ILE cc_start: 0.7705 (tt) cc_final: 0.7039 (mm) REVERT: E 169 MET cc_start: 0.2633 (tmm) cc_final: 0.0991 (mpp) REVERT: E 228 MET cc_start: 0.2660 (ptt) cc_final: 0.2361 (ptp) REVERT: E 298 LYS cc_start: 0.2194 (tppt) cc_final: 0.1785 (tppt) REVERT: E 337 ILE cc_start: 0.8759 (pt) cc_final: 0.8186 (mp) REVERT: D 53 HIS cc_start: 0.8428 (m90) cc_final: 0.8121 (m90) REVERT: D 145 GLU cc_start: 0.6777 (pt0) cc_final: 0.6312 (pt0) REVERT: F 190 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7844 (tm-30) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2669 time to fit residues: 90.4957 Evaluate side-chains 200 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 94 optimal weight: 0.3980 chunk 15 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 109 ASN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.204162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.169190 restraints weight = 21652.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.172117 restraints weight = 15095.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.174055 restraints weight = 11526.802| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9728 Z= 0.206 Angle : 0.641 6.885 13182 Z= 0.314 Chirality : 0.043 0.148 1536 Planarity : 0.004 0.075 1682 Dihedral : 9.086 148.645 1391 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.21), residues: 1229 helix: -2.15 (0.24), residues: 392 sheet: -1.26 (0.48), residues: 115 loop : -2.35 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 321 HIS 0.008 0.001 HIS D 96 PHE 0.025 0.002 PHE E 285 TYR 0.009 0.001 TYR C 199 ARG 0.010 0.001 ARG D 125 *********************** 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 238 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.021 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: 0.5966 (m-90) cc_final: 0.5464 (m-90) REVERT: C 39 MET cc_start: 0.6812 (ttt) cc_final: 0.6185 (ttt) REVERT: C 88 ASP cc_start: 0.4116 (p0) cc_final: 0.3687 (p0) REVERT: C 164 VAL cc_start: 0.8869 (t) cc_final: 0.8416 (p) REVERT: C 184 PHE cc_start: 0.7292 (m-80) cc_final: 0.6224 (m-80) REVERT: C 289 MET cc_start: 0.8696 (mmp) cc_final: 0.8286 (mmp) REVERT: C 292 GLU cc_start: 0.7545 (pt0) cc_final: 0.7126 (pt0) REVERT: C 363 LEU cc_start: 0.7949 (mp) cc_final: 0.7694 (mt) REVERT: C 366 ILE cc_start: 0.7854 (tt) cc_final: 0.7222 (mm) REVERT: E 228 MET cc_start: 0.3300 (ptt) cc_final: 0.2929 (ptp) REVERT: E 298 LYS cc_start: 0.2876 (tppt) cc_final: 0.2361 (tppt) REVERT: E 319 PHE cc_start: 0.7174 (m-10) cc_final: 0.6949 (m-10) REVERT: E 337 ILE cc_start: 0.8898 (pt) cc_final: 0.8380 (mp) REVERT: E 400 ARG cc_start: 0.6782 (tpm170) cc_final: 0.6179 (tpt-90) REVERT: D 53 HIS cc_start: 0.8470 (m90) cc_final: 0.8179 (m90) REVERT: D 68 PHE cc_start: 0.7026 (t80) cc_final: 0.6733 (t80) REVERT: D 103 THR cc_start: 0.7870 (m) cc_final: 0.7662 (m) REVERT: D 122 ILE cc_start: 0.7801 (mm) cc_final: 0.7212 (mm) REVERT: F 190 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7965 (tm-30) REVERT: F 206 LEU cc_start: 0.7705 (mt) cc_final: 0.7493 (mt) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2075 time to fit residues: 68.3700 Evaluate side-chains 204 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 106 optimal weight: 0.1980 chunk 55 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 65 HIS E 109 ASN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.198624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.162026 restraints weight = 21974.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.164825 restraints weight = 15592.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.166778 restraints weight = 12051.851| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.7040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9728 Z= 0.257 Angle : 0.714 7.615 13182 Z= 0.348 Chirality : 0.046 0.149 1536 Planarity : 0.005 0.083 1682 Dihedral : 9.498 155.435 1391 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.21), residues: 1229 helix: -2.25 (0.23), residues: 418 sheet: -1.35 (0.50), residues: 97 loop : -2.33 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 321 HIS 0.008 0.002 HIS D 96 PHE 0.029 0.002 PHE E 285 TYR 0.020 0.002 TYR D 15 ARG 0.006 0.001 ARG E 18 *********************** 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 254 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.6122 (m-90) cc_final: 0.5723 (m-90) REVERT: C 39 MET cc_start: 0.6751 (ttt) cc_final: 0.6304 (ttt) REVERT: C 88 ASP cc_start: 0.4177 (p0) cc_final: 0.3856 (p0) REVERT: C 114 MET cc_start: 0.4242 (ppp) cc_final: 0.4021 (ppp) REVERT: C 164 VAL cc_start: 0.8909 (t) cc_final: 0.8488 (p) REVERT: C 184 PHE cc_start: 0.7385 (m-80) cc_final: 0.6270 (m-80) REVERT: C 289 MET cc_start: 0.8786 (mmp) cc_final: 0.8307 (mmp) REVERT: C 292 GLU cc_start: 0.7575 (pt0) cc_final: 0.7131 (pt0) REVERT: C 363 LEU cc_start: 0.8113 (mp) cc_final: 0.7798 (mt) REVERT: C 366 ILE cc_start: 0.7925 (tt) cc_final: 0.7346 (mm) REVERT: E 22 MET cc_start: 0.4494 (tpp) cc_final: 0.2466 (tmm) REVERT: E 48 MET cc_start: 0.6849 (ttm) cc_final: 0.6510 (ttm) REVERT: E 228 MET cc_start: 0.3667 (ptt) cc_final: 0.2889 (ptt) REVERT: E 267 MET cc_start: 0.7026 (ttt) cc_final: 0.6811 (ttp) REVERT: E 298 LYS cc_start: 0.3233 (tppt) cc_final: 0.2757 (tppt) REVERT: E 337 ILE cc_start: 0.8952 (pt) cc_final: 0.8556 (mp) REVERT: D 53 HIS cc_start: 0.8354 (m90) cc_final: 0.7961 (m170) REVERT: D 103 THR cc_start: 0.8032 (m) cc_final: 0.7780 (m) REVERT: D 195 GLN cc_start: 0.6857 (pm20) cc_final: 0.6449 (pm20) REVERT: D 205 ASP cc_start: 0.5822 (p0) cc_final: 0.5315 (p0) REVERT: F 190 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8079 (tm-30) REVERT: F 206 LEU cc_start: 0.8019 (mt) cc_final: 0.7727 (mt) REVERT: F 218 MET cc_start: 0.7382 (ppp) cc_final: 0.7156 (ppp) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2239 time to fit residues: 77.4186 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 : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 62 optimal weight: 0.7980 chunk 101 optimal weight: 0.0870 chunk 106 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN E 57 ASN E 266 GLN E 376 HIS D 141 HIS F 53 HIS F 97 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.203301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.168926 restraints weight = 21689.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.171800 restraints weight = 14964.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.173900 restraints weight = 11376.586| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.7080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9728 Z= 0.166 Angle : 0.646 7.915 13182 Z= 0.306 Chirality : 0.043 0.136 1536 Planarity : 0.004 0.058 1682 Dihedral : 9.054 151.042 1391 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.22), residues: 1229 helix: -1.93 (0.24), residues: 421 sheet: -1.15 (0.49), residues: 107 loop : -2.12 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 321 HIS 0.006 0.001 HIS E 376 PHE 0.020 0.001 PHE E 285 TYR 0.007 0.001 TYR F 15 ARG 0.008 0.000 ARG E 15 *********************** 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 249 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.080 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: 0.5947 (m-90) cc_final: 0.5672 (m-90) REVERT: C 32 ILE cc_start: 0.9073 (mm) cc_final: 0.8862 (mm) REVERT: C 39 MET cc_start: 0.6643 (ttt) cc_final: 0.6191 (ttt) REVERT: C 88 ASP cc_start: 0.4180 (p0) cc_final: 0.3729 (p0) REVERT: C 164 VAL cc_start: 0.8836 (t) cc_final: 0.8370 (t) REVERT: C 184 PHE cc_start: 0.7430 (m-80) cc_final: 0.6542 (m-80) REVERT: C 264 LYS cc_start: 0.7744 (tttt) cc_final: 0.7373 (ttmm) REVERT: C 366 ILE cc_start: 0.7858 (tt) cc_final: 0.7234 (mm) REVERT: E 298 LYS cc_start: 0.2806 (tppt) cc_final: 0.2115 (tppt) REVERT: E 337 ILE cc_start: 0.8882 (pt) cc_final: 0.8466 (mp) REVERT: D 53 HIS cc_start: 0.8286 (m90) cc_final: 0.7956 (m-70) REVERT: D 127 LEU cc_start: 0.8706 (tp) cc_final: 0.8238 (tp) REVERT: D 205 ASP cc_start: 0.5721 (p0) cc_final: 0.5284 (p0) REVERT: F 14 ARG cc_start: 0.8769 (mmp-170) cc_final: 0.8540 (mmp-170) REVERT: F 38 MET cc_start: 0.8039 (ptp) cc_final: 0.7812 (tmm) REVERT: F 190 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7995 (tm-30) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2988 time to fit residues: 101.9266 Evaluate side-chains 206 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS F 69 ASN F 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.187696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.154202 restraints weight = 22554.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.154819 restraints weight = 16216.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.155355 restraints weight = 12744.605| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.8737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.153 9728 Z= 0.479 Angle : 1.014 14.590 13182 Z= 0.505 Chirality : 0.055 0.281 1536 Planarity : 0.007 0.073 1682 Dihedral : 10.835 169.158 1391 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.21), residues: 1229 helix: -2.53 (0.22), residues: 405 sheet: -1.41 (0.57), residues: 72 loop : -2.22 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP E 75 HIS 0.028 0.004 HIS D 96 PHE 0.051 0.005 PHE E 285 TYR 0.037 0.003 TYR F 93 ARG 0.024 0.001 ARG C 250 *********************** 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 239 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 2.748 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: 0.5951 (m-90) cc_final: 0.5562 (m-90) REVERT: C 39 MET cc_start: 0.7638 (ttt) cc_final: 0.7276 (ttt) REVERT: C 88 ASP cc_start: 0.3999 (p0) cc_final: 0.3562 (p0) REVERT: C 114 MET cc_start: 0.3978 (ppp) cc_final: 0.3709 (ppp) REVERT: C 289 MET cc_start: 0.8900 (mmp) cc_final: 0.8353 (mmp) REVERT: C 294 GLN cc_start: 0.7347 (mm-40) cc_final: 0.7025 (mm-40) REVERT: C 332 LEU cc_start: 0.8173 (tp) cc_final: 0.7622 (tp) REVERT: C 373 MET cc_start: 0.9275 (mmp) cc_final: 0.8607 (mmp) REVERT: E 22 MET cc_start: 0.3960 (tpp) cc_final: 0.2337 (tmm) REVERT: E 169 MET cc_start: 0.2603 (ppp) cc_final: 0.0451 (pmm) REVERT: D 53 HIS cc_start: 0.8285 (m90) cc_final: 0.7985 (m-70) REVERT: D 103 THR cc_start: 0.7892 (m) cc_final: 0.7674 (m) REVERT: D 141 HIS cc_start: 0.7151 (m-70) cc_final: 0.6939 (m170) REVERT: D 145 GLU cc_start: 0.6942 (pt0) cc_final: 0.6436 (pt0) REVERT: D 195 GLN cc_start: 0.7005 (pm20) cc_final: 0.6359 (mp10) REVERT: D 217 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6920 (tm-30) REVERT: F 190 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8051 (tm-30) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.4804 time to fit residues: 160.9769 Evaluate side-chains 202 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 117 optimal weight: 0.0050 chunk 41 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 116 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN C 341 ASN E 57 ASN E 86 GLN ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 141 HIS F 69 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.196277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.160988 restraints weight = 22077.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.163901 restraints weight = 14955.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.165893 restraints weight = 11220.621| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.8512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9728 Z= 0.207 Angle : 0.747 18.799 13182 Z= 0.357 Chirality : 0.045 0.192 1536 Planarity : 0.004 0.051 1682 Dihedral : 9.836 173.169 1391 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.10 % Allowed : 0.98 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.23), residues: 1229 helix: -1.93 (0.24), residues: 406 sheet: -0.94 (0.49), residues: 115 loop : -2.10 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 377 HIS 0.015 0.001 HIS D 96 PHE 0.022 0.002 PHE E 285 TYR 0.013 0.001 TYR F 93 ARG 0.007 0.001 ARG C 250 ********************** 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 260 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 1.110 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: 0.6051 (m-90) cc_final: 0.5628 (m-90) REVERT: C 39 MET cc_start: 0.6986 (ttt) cc_final: 0.6735 (ttt) REVERT: C 88 ASP cc_start: 0.4251 (p0) cc_final: 0.3812 (p0) REVERT: C 114 MET cc_start: 0.4490 (ppp) cc_final: 0.4159 (ppp) REVERT: C 289 MET cc_start: 0.8706 (mmp) cc_final: 0.8293 (mmp) REVERT: C 311 MET cc_start: 0.5462 (pmm) cc_final: 0.4944 (mmt) REVERT: C 312 MET cc_start: 0.8469 (mmt) cc_final: 0.8177 (mmp) REVERT: C 366 ILE cc_start: 0.7958 (tt) cc_final: 0.7399 (mm) REVERT: E 22 MET cc_start: 0.3621 (tpp) cc_final: 0.3089 (tmm) REVERT: E 169 MET cc_start: 0.2399 (ppp) cc_final: 0.0411 (pmm) REVERT: E 298 LYS cc_start: 0.3521 (tptt) cc_final: 0.3186 (tptt) REVERT: D 53 HIS cc_start: 0.8264 (m90) cc_final: 0.7973 (m-70) REVERT: D 95 PHE cc_start: 0.7679 (m-80) cc_final: 0.7420 (m-80) REVERT: D 205 ASP cc_start: 0.6501 (p0) cc_final: 0.6181 (p0) REVERT: D 217 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6666 (tm-30) REVERT: D 218 MET cc_start: 0.7703 (tmm) cc_final: 0.7422 (tmm) REVERT: F 38 MET cc_start: 0.8399 (ptp) cc_final: 0.8158 (ptp) REVERT: F 166 LEU cc_start: 0.7342 (mp) cc_final: 0.7026 (mp) REVERT: F 190 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8046 (tm-30) REVERT: F 212 MET cc_start: 0.8032 (tpp) cc_final: 0.7702 (tpp) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.2227 time to fit residues: 79.1524 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 : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 78 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 114 optimal weight: 0.0470 chunk 113 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 0.0050 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN E 57 ASN ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.199405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.166640 restraints weight = 22074.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.168468 restraints weight = 16526.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.171949 restraints weight = 11638.165| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.8369 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= 0.176 Angle : 0.700 10.070 13182 Z= 0.336 Chirality : 0.044 0.152 1536 Planarity : 0.005 0.054 1682 Dihedral : 9.532 169.671 1391 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.10 % Allowed : 0.49 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.22), residues: 1229 helix: -1.66 (0.25), residues: 408 sheet: -0.67 (0.50), residues: 115 loop : -2.13 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 377 HIS 0.009 0.001 HIS D 96 PHE 0.020 0.001 PHE E 285 TYR 0.015 0.001 TYR E 397 ARG 0.011 0.001 ARG D 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3868.68 seconds wall clock time: 70 minutes 27.14 seconds (4227.14 seconds total)