Starting phenix.real_space_refine on Sun Aug 24 16:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfz_37500/08_2025/8wfz_37500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfz_37500/08_2025/8wfz_37500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wfz_37500/08_2025/8wfz_37500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfz_37500/08_2025/8wfz_37500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wfz_37500/08_2025/8wfz_37500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfz_37500/08_2025/8wfz_37500.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 13811 2.51 5 N 3542 2.21 5 O 3813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21266 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5315 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 636} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5315 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 636} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5321 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 19, 'TRANS': 636} Chain: "D" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5315 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 636} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.16, per 1000 atoms: 0.24 Number of scatterers: 21266 At special positions: 0 Unit cell: (113.42, 104.94, 186.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3813 8.00 N 3542 7.00 C 13811 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: 1.98 Conformation dependent library (CDL) restraints added in 911.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 8 sheets defined 69.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 62 through 89 removed outlier: 3.574A pdb=" N VAL A 74 " --> pdb=" O MET A 70 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 94 through 115 Processing helix chain 'A' and resid 131 through 139 removed outlier: 4.215A pdb=" N ILE A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.835A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.672A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.594A pdb=" N VAL A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 226 removed outlier: 4.000A pdb=" N LEU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.259A pdb=" N GLY A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 233 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 removed outlier: 4.005A pdb=" N THR A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 313 removed outlier: 3.676A pdb=" N ILE A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 333 Processing helix chain 'A' and resid 336 through 364 removed outlier: 3.839A pdb=" N ARG A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLN A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 350 " --> pdb=" O HIS A 346 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 removed outlier: 3.655A pdb=" N LEU A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Proline residue: A 379 - end of helix Processing helix chain 'A' and resid 391 through 401 removed outlier: 4.148A pdb=" N ILE A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 396 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 462 Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 492 through 510 removed outlier: 4.037A pdb=" N GLU A 508 " --> pdb=" O MET A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 516 through 542 removed outlier: 3.566A pdb=" N GLU A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 529 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 576 through 586 removed outlier: 3.743A pdb=" N THR A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 609 through 620 removed outlier: 3.645A pdb=" N ILE A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 651 Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.944A pdb=" N VAL A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.796A pdb=" N GLU A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.795A pdb=" N ILE A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 removed outlier: 3.588A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 94 through 116 Processing helix chain 'B' and resid 131 through 142 removed outlier: 4.244A pdb=" N SER B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 removed outlier: 3.932A pdb=" N MET B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP B 147 " --> pdb=" O HIS B 143 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.786A pdb=" N ILE B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 removed outlier: 3.971A pdb=" N ARG B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'B' and resid 195 through 226 removed outlier: 4.054A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.510A pdb=" N LEU B 239 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 removed outlier: 3.593A pdb=" N ARG B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 312 removed outlier: 4.118A pdb=" N PHE B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 333 removed outlier: 3.748A pdb=" N ARG B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 363 removed outlier: 3.842A pdb=" N ARG B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 376 Processing helix chain 'B' and resid 376 through 384 removed outlier: 4.180A pdb=" N TYR B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 384 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.743A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 462 Processing helix chain 'B' and resid 482 through 492 Processing helix chain 'B' and resid 492 through 510 Processing helix chain 'B' and resid 516 through 541 removed outlier: 3.862A pdb=" N GLN B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 566 through 575 Processing helix chain 'B' and resid 576 through 586 removed outlier: 3.629A pdb=" N ILE B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 607 removed outlier: 3.528A pdb=" N ALA B 604 " --> pdb=" O PRO B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 640 through 650 Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 684 through 688 removed outlier: 3.779A pdb=" N ILE B 688 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.547A pdb=" N GLU B 700 " --> pdb=" O SER B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'C' and resid 62 through 89 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 94 through 116 removed outlier: 3.668A pdb=" N LEU C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 170 removed outlier: 3.733A pdb=" N ARG C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 195 through 226 removed outlier: 4.340A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 4.392A pdb=" N ASP C 243 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 removed outlier: 3.628A pdb=" N ARG C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 313 removed outlier: 4.101A pdb=" N ILE C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET C 289 " --> pdb=" O MET C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 Processing helix chain 'C' and resid 336 through 360 removed outlier: 3.982A pdb=" N ASP C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR C 355 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR C 356 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 383 removed outlier: 3.999A pdb=" N LYS C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Proline residue: C 379 - end of helix Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'C' and resid 455 through 462 Processing helix chain 'C' and resid 481 through 492 Processing helix chain 'C' and resid 492 through 510 removed outlier: 3.697A pdb=" N GLU C 508 " --> pdb=" O MET C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 542 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 566 through 575 removed outlier: 3.833A pdb=" N LEU C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 587 removed outlier: 3.505A pdb=" N GLY C 587 " --> pdb=" O LEU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 608 Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.662A pdb=" N ILE C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 639 Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.703A pdb=" N LEU C 644 " --> pdb=" O ASP C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 672 removed outlier: 4.089A pdb=" N VAL C 667 " --> pdb=" O THR C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 683 Processing helix chain 'C' and resid 696 through 705 removed outlier: 3.598A pdb=" N GLU C 700 " --> pdb=" O SER C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'D' and resid 62 through 88 removed outlier: 3.783A pdb=" N PHE D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 117 removed outlier: 3.963A pdb=" N LEU D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 152 removed outlier: 3.603A pdb=" N ILE D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS D 141 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N MET D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY D 150 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 161 Processing helix chain 'D' and resid 164 through 171 removed outlier: 3.531A pdb=" N ARG D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 191 removed outlier: 4.017A pdb=" N VAL D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 226 removed outlier: 3.553A pdb=" N TYR D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 removed outlier: 3.627A pdb=" N LEU D 239 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 312 removed outlier: 3.538A pdb=" N PHE D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 334 Processing helix chain 'D' and resid 336 through 362 removed outlier: 4.079A pdb=" N SER D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL D 359 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 384 removed outlier: 3.847A pdb=" N LYS D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Proline residue: D 379 - end of helix removed outlier: 3.878A pdb=" N VAL D 384 " --> pdb=" O TYR D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 400 Processing helix chain 'D' and resid 455 through 461 Processing helix chain 'D' and resid 482 through 492 Processing helix chain 'D' and resid 492 through 507 Processing helix chain 'D' and resid 510 through 541 removed outlier: 5.047A pdb=" N SER D 518 " --> pdb=" O LYS D 514 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 520 " --> pdb=" O LEU D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 566 through 575 Processing helix chain 'D' and resid 576 through 587 Processing helix chain 'D' and resid 599 through 608 removed outlier: 3.696A pdb=" N GLU D 603 " --> pdb=" O THR D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 620 removed outlier: 3.581A pdb=" N ILE D 613 " --> pdb=" O GLN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 639 removed outlier: 3.806A pdb=" N CYS D 633 " --> pdb=" O GLY D 629 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 650 Processing helix chain 'D' and resid 663 through 672 Processing helix chain 'D' and resid 673 through 684 Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 706 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 403 through 406 removed outlier: 6.485A pdb=" N HIS A 476 " --> pdb=" O CYS A 427 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 424 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 443 through 448 removed outlier: 6.185A pdb=" N SER A 444 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 435 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 446 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 403 through 407 removed outlier: 3.572A pdb=" N HIS B 403 " --> pdb=" O ARG B 479 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS B 476 " --> pdb=" O CYS B 427 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR B 452 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 446 through 448 removed outlier: 3.710A pdb=" N THR B 446 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 403 through 406 removed outlier: 6.565A pdb=" N HIS C 476 " --> pdb=" O CYS C 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 412 through 414 removed outlier: 7.735A pdb=" N VAL C 412 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL C 471 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 414 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR C 446 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL C 435 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER C 444 " --> pdb=" O VAL C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 405 through 407 removed outlier: 6.320A pdb=" N HIS D 476 " --> pdb=" O CYS D 427 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 452 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 412 through 414 removed outlier: 5.994A pdb=" N VAL D 412 " --> pdb=" O VAL D 471 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 471 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR D 414 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 469 " --> pdb=" O THR D 414 " (cutoff:3.500A) 1271 hydrogen bonds defined for protein. 3723 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: 3.86 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4175 1.33 - 1.45: 5364 1.45 - 1.57: 12064 1.57 - 1.69: 0 1.69 - 1.82: 156 Bond restraints: 21759 Sorted by residual: bond pdb=" N PRO C 697 " pdb=" CD PRO C 697 " ideal model delta sigma weight residual 1.473 1.415 0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" C SER C 696 " pdb=" N PRO C 697 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.28e-02 6.10e+03 1.72e+01 bond pdb=" N LYS B 515 " pdb=" CA LYS B 515 " ideal model delta sigma weight residual 1.453 1.498 -0.045 1.22e-02 6.72e+03 1.34e+01 bond pdb=" N GLU B 189 " pdb=" CA GLU B 189 " ideal model delta sigma weight residual 1.454 1.499 -0.045 1.31e-02 5.83e+03 1.19e+01 bond pdb=" N LEU A 339 " pdb=" CA LEU A 339 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.17e-02 7.31e+03 1.05e+01 ... (remaining 21754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 28485 2.33 - 4.65: 794 4.65 - 6.98: 129 6.98 - 9.30: 23 9.30 - 11.63: 2 Bond angle restraints: 29433 Sorted by residual: angle pdb=" N GLU A 393 " pdb=" CA GLU A 393 " pdb=" C GLU A 393 " ideal model delta sigma weight residual 111.07 101.10 9.97 1.07e+00 8.73e-01 8.69e+01 angle pdb=" N GLN D 186 " pdb=" CA GLN D 186 " pdb=" C GLN D 186 " ideal model delta sigma weight residual 111.28 102.69 8.59 1.09e+00 8.42e-01 6.21e+01 angle pdb=" N VAL B 359 " pdb=" CA VAL B 359 " pdb=" C VAL B 359 " ideal model delta sigma weight residual 110.62 117.89 -7.27 1.02e+00 9.61e-01 5.07e+01 angle pdb=" N GLU D 95 " pdb=" CA GLU D 95 " pdb=" C GLU D 95 " ideal model delta sigma weight residual 111.82 103.68 8.14 1.16e+00 7.43e-01 4.92e+01 angle pdb=" N LEU C 326 " pdb=" CA LEU C 326 " pdb=" C LEU C 326 " ideal model delta sigma weight residual 111.28 103.73 7.55 1.09e+00 8.42e-01 4.80e+01 ... (remaining 29428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 11586 17.75 - 35.50: 1085 35.50 - 53.24: 171 53.24 - 70.99: 27 70.99 - 88.74: 22 Dihedral angle restraints: 12891 sinusoidal: 5227 harmonic: 7664 Sorted by residual: dihedral pdb=" C ASP B 511 " pdb=" N ASP B 511 " pdb=" CA ASP B 511 " pdb=" CB ASP B 511 " ideal model delta harmonic sigma weight residual -122.60 -136.45 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" N ASP B 511 " pdb=" C ASP B 511 " pdb=" CA ASP B 511 " pdb=" CB ASP B 511 " ideal model delta harmonic sigma weight residual 122.80 135.04 -12.24 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C VAL B 359 " pdb=" N VAL B 359 " pdb=" CA VAL B 359 " pdb=" CB VAL B 359 " ideal model delta harmonic sigma weight residual -122.00 -134.15 12.15 0 2.50e+00 1.60e-01 2.36e+01 ... (remaining 12888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2988 0.088 - 0.176: 242 0.176 - 0.264: 37 0.264 - 0.352: 16 0.352 - 0.440: 5 Chirality restraints: 3288 Sorted by residual: chirality pdb=" CA ASP B 511 " pdb=" N ASP B 511 " pdb=" C ASP B 511 " pdb=" CB ASP B 511 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA ASP B 691 " pdb=" N ASP B 691 " pdb=" C ASP B 691 " pdb=" CB ASP B 691 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA THR D 436 " pdb=" N THR D 436 " pdb=" C THR D 436 " pdb=" CB THR D 436 " both_signs ideal model delta sigma weight residual False 2.53 2.95 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3285 not shown) Planarity restraints: 3705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 190 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C LYS B 190 " 0.067 2.00e-02 2.50e+03 pdb=" O LYS B 190 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP B 191 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 337 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ARG A 337 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG A 337 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 338 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 252 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C ILE D 252 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE D 252 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP D 253 " 0.017 2.00e-02 2.50e+03 ... (remaining 3702 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 285 2.63 - 3.20: 21796 3.20 - 3.77: 35672 3.77 - 4.33: 46983 4.33 - 4.90: 72463 Nonbonded interactions: 177199 Sorted by model distance: nonbonded pdb=" O ASN B 558 " pdb=" OD1 ASN B 558 " model vdw 2.063 3.040 nonbonded pdb=" O TYR B 221 " pdb=" OG1 THR B 224 " model vdw 2.195 3.040 nonbonded pdb=" O TYR A 196 " pdb=" OG1 THR A 199 " model vdw 2.199 3.040 nonbonded pdb=" NH1 ARG A 369 " pdb=" O ILE A 400 " model vdw 2.199 3.120 nonbonded pdb=" OE1 GLU A 528 " pdb=" NZ LYS A 559 " model vdw 2.208 3.120 ... (remaining 177194 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 'A' selection = chain 'B' selection = (chain 'C' and (resid 58 through 352 or (resid 353 through 354 and (name N or na \ me CA or name C or name O or name CB )) or resid 355 through 713)) selection = chain 'D' } 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: 2.190 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.300 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 : 0.006 0.066 21759 Z= 0.325 Angle : 0.893 11.626 29433 Z= 0.570 Chirality : 0.058 0.440 3288 Planarity : 0.005 0.069 3705 Dihedral : 13.955 88.738 7971 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.56 % Allowed : 0.95 % Favored : 98.48 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.16), residues: 2616 helix: 1.31 (0.12), residues: 1691 sheet: 1.09 (0.49), residues: 110 loop : -0.46 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 401 TYR 0.034 0.002 TYR D 139 PHE 0.039 0.002 PHE C 319 TRP 0.028 0.002 TRP B 68 HIS 0.011 0.002 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00550 (21759) covalent geometry : angle 0.89321 (29433) hydrogen bonds : bond 0.16292 ( 1271) hydrogen bonds : angle 6.38074 ( 3723) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 347 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8104 (t-100) cc_final: 0.7869 (t-100) REVERT: A 81 LEU cc_start: 0.8655 (tp) cc_final: 0.8176 (tp) REVERT: A 148 PHE cc_start: 0.8902 (p90) cc_final: 0.8425 (p90) REVERT: A 335 LEU cc_start: 0.9094 (mt) cc_final: 0.8806 (tt) REVERT: A 342 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: B 197 LEU cc_start: 0.9016 (mt) cc_final: 0.8699 (mt) REVERT: B 208 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6953 (mm-30) REVERT: B 296 MET cc_start: 0.8649 (mtp) cc_final: 0.8218 (mtt) REVERT: B 298 LEU cc_start: 0.8963 (tp) cc_final: 0.8652 (tp) REVERT: B 321 ASP cc_start: 0.9320 (m-30) cc_final: 0.9062 (m-30) REVERT: B 330 MET cc_start: 0.8501 (ttt) cc_final: 0.8291 (ttt) REVERT: B 688 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6346 (mp) REVERT: C 81 LEU cc_start: 0.8814 (tt) cc_final: 0.8438 (tp) REVERT: C 307 THR cc_start: 0.9452 (m) cc_final: 0.9172 (p) REVERT: C 321 ASP cc_start: 0.9457 (t70) cc_final: 0.9151 (m-30) REVERT: C 327 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9020 (mm) REVERT: C 330 MET cc_start: 0.9528 (tmm) cc_final: 0.8655 (ppp) REVERT: C 351 TYR cc_start: 0.8820 (t80) cc_final: 0.8467 (t80) REVERT: C 355 TYR cc_start: 0.8864 (p90) cc_final: 0.8576 (p90) REVERT: C 506 GLU cc_start: 0.9223 (tp30) cc_final: 0.8970 (tp30) REVERT: C 661 HIS cc_start: 0.7920 (t70) cc_final: 0.7495 (t-90) REVERT: D 146 MET cc_start: 0.8931 (mmt) cc_final: 0.8571 (mpp) REVERT: D 264 PHE cc_start: 0.8085 (t80) cc_final: 0.7725 (t80) outliers start: 13 outliers final: 1 residues processed: 358 average time/residue: 0.1605 time to fit residues: 89.6609 Evaluate side-chains 228 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 224 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.0050 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 258 optimal weight: 30.0000 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN B 416 GLN C 523 HIS ** D 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.094003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.064595 restraints weight = 83403.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065694 restraints weight = 63917.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.066182 restraints weight = 53580.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.066704 restraints weight = 48796.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.066886 restraints weight = 45762.812| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21759 Z= 0.140 Angle : 0.642 9.717 29433 Z= 0.338 Chirality : 0.041 0.174 3288 Planarity : 0.004 0.048 3705 Dihedral : 4.503 20.245 2888 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.26 % Allowed : 5.58 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.16), residues: 2616 helix: 1.16 (0.12), residues: 1724 sheet: 1.41 (0.53), residues: 100 loop : -0.65 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 369 TYR 0.029 0.002 TYR B 351 PHE 0.032 0.002 PHE A 148 TRP 0.019 0.001 TRP D 235 HIS 0.007 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00281 (21759) covalent geometry : angle 0.64189 (29433) hydrogen bonds : bond 0.05294 ( 1271) hydrogen bonds : angle 4.94487 ( 3723) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 315 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8841 (t-100) cc_final: 0.8321 (t-100) REVERT: A 81 LEU cc_start: 0.9176 (tp) cc_final: 0.8766 (tp) REVERT: A 101 ASP cc_start: 0.9514 (t0) cc_final: 0.9235 (t0) REVERT: A 148 PHE cc_start: 0.9175 (p90) cc_final: 0.8799 (p90) REVERT: A 154 TRP cc_start: 0.8597 (m100) cc_final: 0.8358 (m100) REVERT: A 264 PHE cc_start: 0.8920 (t80) cc_final: 0.8267 (t80) REVERT: A 679 MET cc_start: 0.3611 (tmm) cc_final: 0.3252 (tmm) REVERT: B 208 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8791 (mm-30) REVERT: B 287 PHE cc_start: 0.9052 (t80) cc_final: 0.8843 (t80) REVERT: B 298 LEU cc_start: 0.9627 (tp) cc_final: 0.9250 (tp) REVERT: B 582 PHE cc_start: 0.9154 (m-10) cc_final: 0.8879 (m-10) REVERT: B 652 MET cc_start: 0.6908 (ppp) cc_final: 0.6270 (ppp) REVERT: C 281 ASN cc_start: 0.8034 (t0) cc_final: 0.7766 (t0) REVERT: C 296 MET cc_start: 0.9184 (tmm) cc_final: 0.8936 (tmm) REVERT: C 307 THR cc_start: 0.9701 (m) cc_final: 0.9453 (p) REVERT: C 321 ASP cc_start: 0.9562 (t70) cc_final: 0.9230 (m-30) REVERT: C 330 MET cc_start: 0.9464 (tmm) cc_final: 0.8912 (ppp) REVERT: C 351 TYR cc_start: 0.8897 (t80) cc_final: 0.8470 (t80) REVERT: C 355 TYR cc_start: 0.9194 (p90) cc_final: 0.8985 (p90) REVERT: C 407 PHE cc_start: 0.8583 (m-10) cc_final: 0.8345 (m-80) REVERT: C 477 LEU cc_start: 0.9268 (mp) cc_final: 0.8929 (mp) REVERT: C 506 GLU cc_start: 0.9237 (tp30) cc_final: 0.8960 (tp30) REVERT: C 661 HIS cc_start: 0.7893 (t70) cc_final: 0.7572 (t-90) REVERT: D 85 MET cc_start: 0.9060 (mmp) cc_final: 0.8635 (mmp) REVERT: D 86 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: D 146 MET cc_start: 0.8977 (mmt) cc_final: 0.8479 (mpp) REVERT: D 199 THR cc_start: 0.9004 (m) cc_final: 0.8692 (p) REVERT: D 205 LEU cc_start: 0.9586 (tt) cc_final: 0.9351 (pp) REVERT: D 258 TYR cc_start: 0.9528 (t80) cc_final: 0.9238 (t80) REVERT: D 264 PHE cc_start: 0.9458 (t80) cc_final: 0.8876 (t80) REVERT: D 285 MET cc_start: 0.9350 (tpp) cc_final: 0.9068 (tpp) REVERT: D 291 TYR cc_start: 0.9006 (t80) cc_final: 0.8717 (t80) REVERT: D 330 MET cc_start: 0.9567 (tpt) cc_final: 0.9207 (tpt) REVERT: D 360 MET cc_start: 0.9426 (ptp) cc_final: 0.8980 (ppp) outliers start: 6 outliers final: 1 residues processed: 320 average time/residue: 0.1450 time to fit residues: 73.8740 Evaluate side-chains 237 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 235 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 107 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 227 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 591 ASN B 483 GLN ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 541 GLN C 630 ASN D 105 GLN ** D 422 HIS ** 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 = 0.3974 r_free = 0.3974 target = 0.095012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.078306 restraints weight = 162660.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.079970 restraints weight = 75837.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.080929 restraints weight = 44015.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.081524 restraints weight = 30640.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.081813 restraints weight = 24417.735| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21759 Z= 0.135 Angle : 0.597 8.531 29433 Z= 0.316 Chirality : 0.040 0.236 3288 Planarity : 0.004 0.050 3705 Dihedral : 4.471 18.904 2888 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.16), residues: 2616 helix: 1.17 (0.12), residues: 1726 sheet: 1.18 (0.52), residues: 98 loop : -0.64 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 369 TYR 0.028 0.002 TYR C 246 PHE 0.027 0.001 PHE A 319 TRP 0.016 0.001 TRP B 68 HIS 0.004 0.001 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00285 (21759) covalent geometry : angle 0.59666 (29433) hydrogen bonds : bond 0.04644 ( 1271) hydrogen bonds : angle 4.77235 ( 3723) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8759 (t-100) cc_final: 0.8183 (t-100) REVERT: A 81 LEU cc_start: 0.9195 (tp) cc_final: 0.8742 (tp) REVERT: A 85 MET cc_start: 0.9220 (ptp) cc_final: 0.8966 (ptt) REVERT: A 101 ASP cc_start: 0.9458 (t0) cc_final: 0.9168 (t0) REVERT: A 114 LEU cc_start: 0.9120 (mm) cc_final: 0.8876 (mm) REVERT: A 148 PHE cc_start: 0.9106 (p90) cc_final: 0.8784 (p90) REVERT: A 154 TRP cc_start: 0.8558 (m100) cc_final: 0.8216 (m100) REVERT: A 183 GLU cc_start: 0.9177 (mp0) cc_final: 0.8805 (mp0) REVERT: A 264 PHE cc_start: 0.9359 (t80) cc_final: 0.8823 (t80) REVERT: A 285 MET cc_start: 0.9597 (mmm) cc_final: 0.9387 (mmm) REVERT: A 321 ASP cc_start: 0.9609 (m-30) cc_final: 0.9206 (m-30) REVERT: A 406 TYR cc_start: 0.9075 (m-80) cc_final: 0.8767 (m-80) REVERT: B 78 TYR cc_start: 0.9429 (t80) cc_final: 0.9199 (t80) REVERT: B 146 MET cc_start: 0.9105 (mpp) cc_final: 0.8893 (mpp) REVERT: B 208 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8747 (mm-30) REVERT: B 298 LEU cc_start: 0.9731 (tp) cc_final: 0.9212 (tp) REVERT: B 330 MET cc_start: 0.8671 (ttt) cc_final: 0.8355 (ttt) REVERT: B 676 MET cc_start: 0.8212 (mtt) cc_final: 0.7699 (mtt) REVERT: C 281 ASN cc_start: 0.8290 (t0) cc_final: 0.8018 (t0) REVERT: C 294 PHE cc_start: 0.9238 (t80) cc_final: 0.8974 (t80) REVERT: C 296 MET cc_start: 0.9294 (tmm) cc_final: 0.9040 (tmm) REVERT: C 307 THR cc_start: 0.9628 (m) cc_final: 0.9361 (p) REVERT: C 321 ASP cc_start: 0.9476 (t70) cc_final: 0.9168 (m-30) REVERT: C 330 MET cc_start: 0.9472 (tmm) cc_final: 0.8881 (ppp) REVERT: C 355 TYR cc_start: 0.9098 (p90) cc_final: 0.8797 (p90) REVERT: C 407 PHE cc_start: 0.8625 (m-10) cc_final: 0.8250 (m-80) REVERT: C 477 LEU cc_start: 0.9303 (mp) cc_final: 0.8938 (mp) REVERT: C 506 GLU cc_start: 0.9173 (tp30) cc_final: 0.8908 (tp30) REVERT: C 661 HIS cc_start: 0.7928 (t70) cc_final: 0.7643 (t-90) REVERT: D 146 MET cc_start: 0.9046 (mmt) cc_final: 0.8483 (mpp) REVERT: D 199 THR cc_start: 0.8958 (m) cc_final: 0.8681 (p) REVERT: D 264 PHE cc_start: 0.9473 (t80) cc_final: 0.9055 (t80) REVERT: D 284 GLU cc_start: 0.9039 (mp0) cc_final: 0.8834 (mp0) REVERT: D 285 MET cc_start: 0.9229 (tpp) cc_final: 0.8974 (tpt) REVERT: D 291 TYR cc_start: 0.9157 (t80) cc_final: 0.8694 (t80) REVERT: D 296 MET cc_start: 0.9534 (ttp) cc_final: 0.9309 (ttp) REVERT: D 305 ASN cc_start: 0.9585 (m-40) cc_final: 0.9124 (m110) REVERT: D 330 MET cc_start: 0.9249 (tpt) cc_final: 0.8852 (tpt) REVERT: D 360 MET cc_start: 0.9251 (ptp) cc_final: 0.8816 (ppp) outliers start: 2 outliers final: 0 residues processed: 309 average time/residue: 0.1431 time to fit residues: 70.9487 Evaluate side-chains 233 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 38 optimal weight: 0.0370 chunk 36 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 190 optimal weight: 30.0000 chunk 75 optimal weight: 7.9990 chunk 235 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS B 305 ASN B 422 HIS ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.076966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.052708 restraints weight = 140599.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054402 restraints weight = 77209.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.055451 restraints weight = 50904.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056139 restraints weight = 37959.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.056518 restraints weight = 30977.634| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21759 Z= 0.213 Angle : 0.641 8.541 29433 Z= 0.344 Chirality : 0.040 0.170 3288 Planarity : 0.004 0.047 3705 Dihedral : 4.606 18.501 2888 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.16), residues: 2616 helix: 1.09 (0.12), residues: 1728 sheet: 0.91 (0.52), residues: 98 loop : -0.74 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 497 TYR 0.032 0.002 TYR A 233 PHE 0.033 0.002 PHE A 319 TRP 0.019 0.001 TRP B 68 HIS 0.010 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00442 (21759) covalent geometry : angle 0.64052 (29433) hydrogen bonds : bond 0.04615 ( 1271) hydrogen bonds : angle 4.91210 ( 3723) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.9086 (tp) cc_final: 0.8565 (tp) REVERT: A 85 MET cc_start: 0.9243 (ptp) cc_final: 0.8927 (ptt) REVERT: A 101 ASP cc_start: 0.9542 (t0) cc_final: 0.9274 (t0) REVERT: A 111 ASP cc_start: 0.9432 (t70) cc_final: 0.8923 (m-30) REVERT: A 148 PHE cc_start: 0.9245 (p90) cc_final: 0.8868 (p90) REVERT: A 406 TYR cc_start: 0.9194 (m-80) cc_final: 0.8881 (m-80) REVERT: B 78 TYR cc_start: 0.9435 (t80) cc_final: 0.9218 (t80) REVERT: B 146 MET cc_start: 0.9191 (mpp) cc_final: 0.8970 (mpp) REVERT: B 241 LEU cc_start: 0.9302 (tp) cc_final: 0.8966 (tt) REVERT: B 647 LEU cc_start: 0.9513 (tp) cc_final: 0.9242 (tp) REVERT: B 676 MET cc_start: 0.8382 (mtt) cc_final: 0.7881 (mtt) REVERT: C 294 PHE cc_start: 0.9409 (t80) cc_final: 0.9162 (t80) REVERT: C 296 MET cc_start: 0.9480 (tmm) cc_final: 0.9192 (tmm) REVERT: C 307 THR cc_start: 0.9701 (m) cc_final: 0.9451 (p) REVERT: C 321 ASP cc_start: 0.9569 (t70) cc_final: 0.9276 (m-30) REVERT: C 330 MET cc_start: 0.9524 (tmm) cc_final: 0.8986 (ppp) REVERT: C 351 TYR cc_start: 0.9107 (t80) cc_final: 0.8793 (t80) REVERT: C 407 PHE cc_start: 0.8865 (m-10) cc_final: 0.8258 (m-80) REVERT: C 506 GLU cc_start: 0.9284 (tp30) cc_final: 0.8994 (tp30) REVERT: C 585 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.9159 (pp30) REVERT: C 661 HIS cc_start: 0.7940 (t70) cc_final: 0.7668 (t-90) REVERT: D 146 MET cc_start: 0.9017 (mmt) cc_final: 0.8450 (mpp) REVERT: D 264 PHE cc_start: 0.9493 (t80) cc_final: 0.9090 (t80) REVERT: D 268 THR cc_start: 0.9594 (m) cc_final: 0.9037 (m) REVERT: D 285 MET cc_start: 0.9264 (tpp) cc_final: 0.8900 (tpt) REVERT: D 291 TYR cc_start: 0.9296 (t80) cc_final: 0.8776 (t80) REVERT: D 296 MET cc_start: 0.9513 (ttp) cc_final: 0.9282 (ttp) REVERT: D 305 ASN cc_start: 0.9529 (m-40) cc_final: 0.9019 (m110) REVERT: D 330 MET cc_start: 0.9307 (tpt) cc_final: 0.8844 (tpt) REVERT: D 360 MET cc_start: 0.9302 (ptp) cc_final: 0.9023 (ppp) REVERT: D 363 ASP cc_start: 0.8925 (m-30) cc_final: 0.8607 (m-30) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.1471 time to fit residues: 65.7151 Evaluate side-chains 211 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 56 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 185 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 184 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.092490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.075781 restraints weight = 163487.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.077377 restraints weight = 77360.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.078303 restraints weight = 45025.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.078808 restraints weight = 31046.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.079170 restraints weight = 24971.334| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21759 Z= 0.135 Angle : 0.600 7.938 29433 Z= 0.315 Chirality : 0.039 0.154 3288 Planarity : 0.004 0.050 3705 Dihedral : 4.537 22.691 2888 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.16), residues: 2616 helix: 1.13 (0.12), residues: 1736 sheet: 0.91 (0.51), residues: 98 loop : -0.78 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 565 TYR 0.028 0.002 TYR A 355 PHE 0.027 0.001 PHE A 319 TRP 0.014 0.001 TRP B 68 HIS 0.005 0.001 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00285 (21759) covalent geometry : angle 0.60007 (29433) hydrogen bonds : bond 0.04386 ( 1271) hydrogen bonds : angle 4.69034 ( 3723) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8805 (t-100) cc_final: 0.8245 (t-100) REVERT: A 81 LEU cc_start: 0.9176 (tp) cc_final: 0.8716 (tp) REVERT: A 85 MET cc_start: 0.9242 (ptp) cc_final: 0.8982 (ptt) REVERT: A 101 ASP cc_start: 0.9488 (t0) cc_final: 0.9203 (t0) REVERT: A 148 PHE cc_start: 0.9110 (p90) cc_final: 0.8759 (p90) REVERT: A 154 TRP cc_start: 0.8778 (m100) cc_final: 0.8160 (m100) REVERT: A 183 GLU cc_start: 0.9233 (mp0) cc_final: 0.8854 (mp0) REVERT: A 264 PHE cc_start: 0.9438 (t80) cc_final: 0.8881 (t80) REVERT: A 296 MET cc_start: 0.9492 (tpp) cc_final: 0.9123 (tpp) REVERT: A 652 MET cc_start: 0.6675 (mtt) cc_final: 0.5543 (mpp) REVERT: B 78 TYR cc_start: 0.9452 (t80) cc_final: 0.9200 (t80) REVERT: B 111 ASP cc_start: 0.9368 (t70) cc_final: 0.9156 (t70) REVERT: B 146 MET cc_start: 0.9136 (mpp) cc_final: 0.8887 (mpp) REVERT: B 676 MET cc_start: 0.8292 (mtt) cc_final: 0.7763 (mtt) REVERT: C 294 PHE cc_start: 0.9288 (t80) cc_final: 0.9085 (t80) REVERT: C 296 MET cc_start: 0.9552 (tmm) cc_final: 0.9220 (tmm) REVERT: C 307 THR cc_start: 0.9656 (m) cc_final: 0.9404 (p) REVERT: C 321 ASP cc_start: 0.9529 (t70) cc_final: 0.9226 (m-30) REVERT: C 330 MET cc_start: 0.9498 (tmm) cc_final: 0.8944 (ppp) REVERT: C 351 TYR cc_start: 0.9057 (t80) cc_final: 0.8780 (t80) REVERT: C 407 PHE cc_start: 0.8744 (m-10) cc_final: 0.8160 (m-80) REVERT: C 506 GLU cc_start: 0.9203 (tp30) cc_final: 0.8908 (tp30) REVERT: C 661 HIS cc_start: 0.7959 (t70) cc_final: 0.7661 (t-90) REVERT: D 146 MET cc_start: 0.8909 (mmt) cc_final: 0.8385 (mpp) REVERT: D 264 PHE cc_start: 0.9528 (t80) cc_final: 0.9150 (t80) REVERT: D 268 THR cc_start: 0.9560 (m) cc_final: 0.9074 (m) REVERT: D 285 MET cc_start: 0.9241 (tpp) cc_final: 0.9037 (tpt) REVERT: D 291 TYR cc_start: 0.9085 (t80) cc_final: 0.8691 (t80) REVERT: D 305 ASN cc_start: 0.9713 (m-40) cc_final: 0.9069 (m110) REVERT: D 330 MET cc_start: 0.9283 (tpt) cc_final: 0.8831 (tpt) REVERT: D 360 MET cc_start: 0.9224 (ptp) cc_final: 0.8818 (ppp) outliers start: 1 outliers final: 1 residues processed: 283 average time/residue: 0.1379 time to fit residues: 62.2630 Evaluate side-chains 215 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN D 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.078077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.053860 restraints weight = 138371.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055538 restraints weight = 76354.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056622 restraints weight = 50409.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057314 restraints weight = 37435.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057703 restraints weight = 30600.641| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21759 Z= 0.140 Angle : 0.597 7.990 29433 Z= 0.315 Chirality : 0.039 0.149 3288 Planarity : 0.004 0.053 3705 Dihedral : 4.513 22.277 2888 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.16), residues: 2616 helix: 1.11 (0.12), residues: 1735 sheet: 0.83 (0.50), residues: 98 loop : -0.77 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 692 TYR 0.026 0.002 TYR D 355 PHE 0.037 0.001 PHE B 582 TRP 0.015 0.001 TRP B 68 HIS 0.005 0.001 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00297 (21759) covalent geometry : angle 0.59723 (29433) hydrogen bonds : bond 0.04276 ( 1271) hydrogen bonds : angle 4.65582 ( 3723) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8802 (t-100) cc_final: 0.8321 (t-100) REVERT: A 81 LEU cc_start: 0.9143 (tp) cc_final: 0.8649 (tp) REVERT: A 101 ASP cc_start: 0.9534 (t0) cc_final: 0.9279 (t0) REVERT: A 114 LEU cc_start: 0.9205 (tt) cc_final: 0.9000 (tt) REVERT: A 148 PHE cc_start: 0.9140 (p90) cc_final: 0.8767 (p90) REVERT: A 154 TRP cc_start: 0.8872 (m100) cc_final: 0.8643 (m100) REVERT: A 269 MET cc_start: 0.9230 (tmm) cc_final: 0.8933 (tmm) REVERT: A 296 MET cc_start: 0.9455 (tpp) cc_final: 0.9074 (tpp) REVERT: A 652 MET cc_start: 0.7557 (mtt) cc_final: 0.6481 (mpp) REVERT: B 78 TYR cc_start: 0.9437 (t80) cc_final: 0.9166 (t80) REVERT: B 111 ASP cc_start: 0.9415 (t70) cc_final: 0.9200 (t70) REVERT: B 146 MET cc_start: 0.9193 (mpp) cc_final: 0.8941 (mpp) REVERT: B 676 MET cc_start: 0.8322 (mtt) cc_final: 0.7775 (mtt) REVERT: C 285 MET cc_start: 0.9023 (tpp) cc_final: 0.8611 (tpp) REVERT: C 294 PHE cc_start: 0.9342 (t80) cc_final: 0.9124 (t80) REVERT: C 296 MET cc_start: 0.9572 (tmm) cc_final: 0.9287 (tmm) REVERT: C 307 THR cc_start: 0.9689 (m) cc_final: 0.9444 (p) REVERT: C 321 ASP cc_start: 0.9578 (t70) cc_final: 0.9237 (m-30) REVERT: C 351 TYR cc_start: 0.9073 (t80) cc_final: 0.8827 (t80) REVERT: C 407 PHE cc_start: 0.8846 (m-10) cc_final: 0.8268 (m-80) REVERT: C 506 GLU cc_start: 0.9284 (tp30) cc_final: 0.9030 (tp30) REVERT: C 661 HIS cc_start: 0.7912 (t70) cc_final: 0.7635 (t-90) REVERT: D 146 MET cc_start: 0.8910 (mmt) cc_final: 0.8395 (mpp) REVERT: D 264 PHE cc_start: 0.9534 (t80) cc_final: 0.9111 (t80) REVERT: D 268 THR cc_start: 0.9537 (m) cc_final: 0.9065 (m) REVERT: D 291 TYR cc_start: 0.9121 (t80) cc_final: 0.8708 (t80) REVERT: D 296 MET cc_start: 0.9559 (ttp) cc_final: 0.9286 (ttp) REVERT: D 305 ASN cc_start: 0.9522 (m-40) cc_final: 0.8992 (m110) REVERT: D 330 MET cc_start: 0.9338 (tpt) cc_final: 0.8843 (tpt) REVERT: D 360 MET cc_start: 0.9245 (ptp) cc_final: 0.8843 (ppp) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1305 time to fit residues: 58.2078 Evaluate side-chains 212 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 202 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 201 optimal weight: 7.9990 chunk 255 optimal weight: 20.0000 chunk 59 optimal weight: 0.0050 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS A 591 ASN B 164 HIS ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.075767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051260 restraints weight = 140762.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.053045 restraints weight = 74594.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.054161 restraints weight = 48203.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054863 restraints weight = 35339.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.055290 restraints weight = 28564.256| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21759 Z= 0.148 Angle : 0.609 8.154 29433 Z= 0.322 Chirality : 0.039 0.160 3288 Planarity : 0.004 0.050 3705 Dihedral : 4.543 21.864 2888 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.16), residues: 2616 helix: 1.13 (0.12), residues: 1730 sheet: 0.76 (0.48), residues: 104 loop : -0.79 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 497 TYR 0.034 0.002 TYR A 355 PHE 0.023 0.001 PHE A 319 TRP 0.015 0.001 TRP B 68 HIS 0.007 0.001 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00314 (21759) covalent geometry : angle 0.60892 (29433) hydrogen bonds : bond 0.04216 ( 1271) hydrogen bonds : angle 4.69359 ( 3723) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8779 (t-100) cc_final: 0.8331 (t-100) REVERT: A 81 LEU cc_start: 0.9150 (tp) cc_final: 0.8696 (tp) REVERT: A 85 MET cc_start: 0.9157 (ptp) cc_final: 0.8900 (ptt) REVERT: A 101 ASP cc_start: 0.9528 (t0) cc_final: 0.9267 (t0) REVERT: A 148 PHE cc_start: 0.9184 (p90) cc_final: 0.8809 (p90) REVERT: A 183 GLU cc_start: 0.9331 (mp0) cc_final: 0.9004 (mp0) REVERT: A 407 PHE cc_start: 0.8266 (m-80) cc_final: 0.8016 (m-80) REVERT: A 652 MET cc_start: 0.7309 (mtt) cc_final: 0.6214 (mpp) REVERT: B 78 TYR cc_start: 0.9439 (t80) cc_final: 0.9139 (t80) REVERT: B 111 ASP cc_start: 0.9400 (t70) cc_final: 0.9185 (t70) REVERT: B 146 MET cc_start: 0.9189 (mpp) cc_final: 0.8937 (mpp) REVERT: B 676 MET cc_start: 0.8300 (mtt) cc_final: 0.7742 (mtt) REVERT: C 285 MET cc_start: 0.8991 (tpp) cc_final: 0.8630 (tpp) REVERT: C 294 PHE cc_start: 0.9334 (t80) cc_final: 0.9128 (t80) REVERT: C 296 MET cc_start: 0.9603 (tmm) cc_final: 0.9327 (tmm) REVERT: C 307 THR cc_start: 0.9678 (m) cc_final: 0.9434 (p) REVERT: C 321 ASP cc_start: 0.9580 (t70) cc_final: 0.9259 (m-30) REVERT: C 351 TYR cc_start: 0.9104 (t80) cc_final: 0.8769 (t80) REVERT: C 407 PHE cc_start: 0.8893 (m-10) cc_final: 0.8314 (m-80) REVERT: C 506 GLU cc_start: 0.9292 (tp30) cc_final: 0.9047 (tp30) REVERT: C 661 HIS cc_start: 0.7959 (t70) cc_final: 0.7659 (t-90) REVERT: D 146 MET cc_start: 0.8948 (mmt) cc_final: 0.8444 (mpp) REVERT: D 264 PHE cc_start: 0.9537 (t80) cc_final: 0.9087 (t80) REVERT: D 285 MET cc_start: 0.9297 (tpp) cc_final: 0.8962 (tpp) REVERT: D 291 TYR cc_start: 0.9112 (t80) cc_final: 0.8768 (t80) REVERT: D 296 MET cc_start: 0.9539 (ttp) cc_final: 0.9316 (ttp) REVERT: D 305 ASN cc_start: 0.9590 (m-40) cc_final: 0.8864 (m110) REVERT: D 330 MET cc_start: 0.9350 (tpt) cc_final: 0.8905 (tpt) REVERT: D 360 MET cc_start: 0.9248 (ptp) cc_final: 0.8912 (ppp) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1282 time to fit residues: 57.1011 Evaluate side-chains 216 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 53 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 13 optimal weight: 0.0470 chunk 75 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.076600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051897 restraints weight = 139463.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.053697 restraints weight = 73102.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.054794 restraints weight = 46771.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.055555 restraints weight = 34420.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.056019 restraints weight = 27850.484| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21759 Z= 0.125 Angle : 0.615 9.996 29433 Z= 0.318 Chirality : 0.040 0.166 3288 Planarity : 0.004 0.050 3705 Dihedral : 4.495 21.268 2888 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 2616 helix: 1.17 (0.12), residues: 1718 sheet: 0.66 (0.47), residues: 111 loop : -0.74 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 497 TYR 0.029 0.001 TYR D 355 PHE 0.020 0.001 PHE A 319 TRP 0.013 0.001 TRP B 68 HIS 0.005 0.001 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00267 (21759) covalent geometry : angle 0.61533 (29433) hydrogen bonds : bond 0.04142 ( 1271) hydrogen bonds : angle 4.61031 ( 3723) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8822 (t-100) cc_final: 0.8361 (t-100) REVERT: A 81 LEU cc_start: 0.9168 (tp) cc_final: 0.8791 (tp) REVERT: A 85 MET cc_start: 0.9180 (ptp) cc_final: 0.8903 (ptt) REVERT: A 101 ASP cc_start: 0.9564 (t0) cc_final: 0.9307 (t0) REVERT: A 148 PHE cc_start: 0.9168 (p90) cc_final: 0.8803 (p90) REVERT: A 154 TRP cc_start: 0.8733 (m100) cc_final: 0.8237 (m100) REVERT: A 183 GLU cc_start: 0.9299 (mp0) cc_final: 0.8916 (mp0) REVERT: A 340 ARG cc_start: 0.9160 (tpp-160) cc_final: 0.8510 (tpp80) REVERT: A 407 PHE cc_start: 0.8289 (m-80) cc_final: 0.8028 (m-80) REVERT: A 652 MET cc_start: 0.7409 (mtt) cc_final: 0.6387 (mpp) REVERT: B 78 TYR cc_start: 0.9483 (t80) cc_final: 0.9134 (t80) REVERT: B 111 ASP cc_start: 0.9444 (t70) cc_final: 0.9209 (t70) REVERT: B 146 MET cc_start: 0.9213 (mpp) cc_final: 0.8939 (mpp) REVERT: B 309 LEU cc_start: 0.9710 (tp) cc_final: 0.9489 (tp) REVERT: B 676 MET cc_start: 0.8306 (mtt) cc_final: 0.7741 (mtt) REVERT: C 294 PHE cc_start: 0.9307 (t80) cc_final: 0.9077 (t80) REVERT: C 296 MET cc_start: 0.9655 (tmm) cc_final: 0.9373 (tmm) REVERT: C 307 THR cc_start: 0.9670 (m) cc_final: 0.9430 (p) REVERT: C 321 ASP cc_start: 0.9584 (t70) cc_final: 0.9265 (m-30) REVERT: C 351 TYR cc_start: 0.9138 (t80) cc_final: 0.8846 (t80) REVERT: C 407 PHE cc_start: 0.8874 (m-10) cc_final: 0.8338 (m-80) REVERT: C 506 GLU cc_start: 0.9308 (tp30) cc_final: 0.9055 (tp30) REVERT: C 661 HIS cc_start: 0.7888 (t70) cc_final: 0.7611 (t-90) REVERT: D 146 MET cc_start: 0.8917 (mmt) cc_final: 0.8404 (mpp) REVERT: D 199 THR cc_start: 0.8971 (m) cc_final: 0.8746 (p) REVERT: D 264 PHE cc_start: 0.9548 (t80) cc_final: 0.9036 (t80) REVERT: D 268 THR cc_start: 0.9546 (m) cc_final: 0.9242 (m) REVERT: D 285 MET cc_start: 0.9231 (tpp) cc_final: 0.8875 (tpp) REVERT: D 291 TYR cc_start: 0.9057 (t80) cc_final: 0.8848 (t80) REVERT: D 296 MET cc_start: 0.9562 (ttp) cc_final: 0.9358 (ttp) REVERT: D 305 ASN cc_start: 0.9548 (m-40) cc_final: 0.8831 (m110) REVERT: D 330 MET cc_start: 0.9421 (tpt) cc_final: 0.8949 (tpt) REVERT: D 360 MET cc_start: 0.9258 (ptp) cc_final: 0.8930 (ppp) REVERT: D 363 ASP cc_start: 0.8747 (m-30) cc_final: 0.8436 (m-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1223 time to fit residues: 55.4470 Evaluate side-chains 220 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 252 optimal weight: 40.0000 chunk 21 optimal weight: 0.0980 chunk 175 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 84 optimal weight: 6.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** B 706 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 = 0.3730 r_free = 0.3730 target = 0.076956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.052469 restraints weight = 140664.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054232 restraints weight = 76116.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.055323 restraints weight = 49702.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.056013 restraints weight = 36801.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.056457 restraints weight = 29947.598| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21759 Z= 0.160 Angle : 0.639 10.289 29433 Z= 0.333 Chirality : 0.040 0.173 3288 Planarity : 0.004 0.097 3705 Dihedral : 4.541 21.142 2888 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.16), residues: 2616 helix: 1.11 (0.12), residues: 1726 sheet: 0.49 (0.47), residues: 113 loop : -0.79 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 552 TYR 0.031 0.002 TYR A 355 PHE 0.021 0.001 PHE A 319 TRP 0.010 0.001 TRP D 75 HIS 0.005 0.001 HIS C 569 Details of bonding type rmsd covalent geometry : bond 0.00340 (21759) covalent geometry : angle 0.63945 (29433) hydrogen bonds : bond 0.04193 ( 1271) hydrogen bonds : angle 4.72526 ( 3723) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8869 (t-100) cc_final: 0.8381 (t-100) REVERT: A 81 LEU cc_start: 0.9183 (tp) cc_final: 0.8740 (tp) REVERT: A 85 MET cc_start: 0.9192 (ptp) cc_final: 0.8928 (ptt) REVERT: A 101 ASP cc_start: 0.9604 (t0) cc_final: 0.9359 (t0) REVERT: A 114 LEU cc_start: 0.9202 (tt) cc_final: 0.8997 (tt) REVERT: A 148 PHE cc_start: 0.9210 (p90) cc_final: 0.8839 (p90) REVERT: A 183 GLU cc_start: 0.9270 (mp0) cc_final: 0.8961 (mp0) REVERT: A 340 ARG cc_start: 0.9203 (tpp-160) cc_final: 0.8542 (tpp80) REVERT: A 407 PHE cc_start: 0.8272 (m-80) cc_final: 0.7995 (m-80) REVERT: A 652 MET cc_start: 0.7967 (mtt) cc_final: 0.7108 (mpp) REVERT: B 78 TYR cc_start: 0.9493 (t80) cc_final: 0.9142 (t80) REVERT: B 111 ASP cc_start: 0.9421 (t70) cc_final: 0.9204 (t70) REVERT: B 146 MET cc_start: 0.9306 (mpp) cc_final: 0.8956 (mpp) REVERT: B 676 MET cc_start: 0.8446 (mtt) cc_final: 0.7900 (mtt) REVERT: C 294 PHE cc_start: 0.9364 (t80) cc_final: 0.9140 (t80) REVERT: C 296 MET cc_start: 0.9704 (tmm) cc_final: 0.9383 (tmm) REVERT: C 307 THR cc_start: 0.9685 (m) cc_final: 0.9453 (p) REVERT: C 321 ASP cc_start: 0.9604 (t70) cc_final: 0.9245 (m-30) REVERT: C 351 TYR cc_start: 0.9167 (t80) cc_final: 0.8823 (t80) REVERT: C 407 PHE cc_start: 0.8893 (m-10) cc_final: 0.8587 (m-80) REVERT: C 477 LEU cc_start: 0.9387 (mp) cc_final: 0.9164 (tt) REVERT: C 506 GLU cc_start: 0.9311 (tp30) cc_final: 0.9059 (tp30) REVERT: C 661 HIS cc_start: 0.7929 (t70) cc_final: 0.7660 (t-90) REVERT: D 146 MET cc_start: 0.8919 (mmt) cc_final: 0.8428 (mpp) REVERT: D 264 PHE cc_start: 0.9558 (t80) cc_final: 0.9166 (t80) REVERT: D 268 THR cc_start: 0.9575 (m) cc_final: 0.9276 (m) REVERT: D 291 TYR cc_start: 0.9136 (t80) cc_final: 0.8814 (t80) REVERT: D 296 MET cc_start: 0.9578 (ttp) cc_final: 0.9373 (ttp) REVERT: D 305 ASN cc_start: 0.9577 (m-40) cc_final: 0.9054 (m-40) REVERT: D 330 MET cc_start: 0.9394 (tpt) cc_final: 0.8916 (tpt) REVERT: D 360 MET cc_start: 0.9269 (ptp) cc_final: 0.8951 (ppp) REVERT: D 363 ASP cc_start: 0.8794 (m-30) cc_final: 0.8537 (m-30) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1322 time to fit residues: 58.3132 Evaluate side-chains 205 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 220 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 148 optimal weight: 0.0030 chunk 88 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.077456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052406 restraints weight = 135047.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.054277 restraints weight = 71953.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.055472 restraints weight = 46444.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056257 restraints weight = 34030.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.056719 restraints weight = 27163.321| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21759 Z= 0.122 Angle : 0.653 11.855 29433 Z= 0.332 Chirality : 0.041 0.189 3288 Planarity : 0.004 0.052 3705 Dihedral : 4.494 20.533 2888 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.16), residues: 2616 helix: 1.12 (0.13), residues: 1718 sheet: 0.72 (0.48), residues: 116 loop : -0.79 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 552 TYR 0.037 0.002 TYR A 351 PHE 0.027 0.001 PHE A 319 TRP 0.020 0.001 TRP A 154 HIS 0.006 0.001 HIS C 569 Details of bonding type rmsd covalent geometry : bond 0.00251 (21759) covalent geometry : angle 0.65330 (29433) hydrogen bonds : bond 0.04110 ( 1271) hydrogen bonds : angle 4.57555 ( 3723) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8840 (t-100) cc_final: 0.8419 (t-100) REVERT: A 81 LEU cc_start: 0.9160 (tp) cc_final: 0.8775 (tp) REVERT: A 101 ASP cc_start: 0.9592 (t0) cc_final: 0.9333 (t0) REVERT: A 148 PHE cc_start: 0.9160 (p90) cc_final: 0.8785 (p90) REVERT: A 154 TRP cc_start: 0.8669 (m100) cc_final: 0.8146 (m100) REVERT: A 183 GLU cc_start: 0.9232 (mp0) cc_final: 0.8818 (mp0) REVERT: A 208 GLU cc_start: 0.9276 (tp30) cc_final: 0.8789 (tm-30) REVERT: A 269 MET cc_start: 0.9025 (tmm) cc_final: 0.8729 (tmm) REVERT: A 340 ARG cc_start: 0.9115 (tpp-160) cc_final: 0.8438 (tpp80) REVERT: A 407 PHE cc_start: 0.8090 (m-80) cc_final: 0.7851 (m-80) REVERT: A 652 MET cc_start: 0.7550 (mtt) cc_final: 0.6587 (mpp) REVERT: B 78 TYR cc_start: 0.9475 (t80) cc_final: 0.9082 (t80) REVERT: B 111 ASP cc_start: 0.9481 (t70) cc_final: 0.9260 (t70) REVERT: B 146 MET cc_start: 0.9119 (mpp) cc_final: 0.8871 (mpp) REVERT: B 196 TYR cc_start: 0.9299 (t80) cc_final: 0.9096 (t80) REVERT: B 269 MET cc_start: 0.9350 (tmm) cc_final: 0.9132 (tmm) REVERT: B 309 LEU cc_start: 0.9683 (tp) cc_final: 0.9402 (mt) REVERT: B 676 MET cc_start: 0.8240 (mtt) cc_final: 0.7659 (mtt) REVERT: C 183 GLU cc_start: 0.9272 (pp20) cc_final: 0.9029 (pp20) REVERT: C 188 LEU cc_start: 0.9391 (tp) cc_final: 0.9076 (pp) REVERT: C 291 TYR cc_start: 0.9042 (t80) cc_final: 0.8831 (t80) REVERT: C 294 PHE cc_start: 0.9242 (t80) cc_final: 0.9021 (t80) REVERT: C 296 MET cc_start: 0.9670 (tmm) cc_final: 0.9405 (tmm) REVERT: C 307 THR cc_start: 0.9653 (m) cc_final: 0.9403 (p) REVERT: C 321 ASP cc_start: 0.9565 (t70) cc_final: 0.9262 (m-30) REVERT: C 351 TYR cc_start: 0.9182 (t80) cc_final: 0.8969 (t80) REVERT: C 407 PHE cc_start: 0.8888 (m-10) cc_final: 0.8572 (m-80) REVERT: C 477 LEU cc_start: 0.9382 (mp) cc_final: 0.9146 (tt) REVERT: C 506 GLU cc_start: 0.9303 (tp30) cc_final: 0.9068 (tp30) REVERT: C 661 HIS cc_start: 0.7853 (t70) cc_final: 0.7556 (t-90) REVERT: D 146 MET cc_start: 0.8882 (mmt) cc_final: 0.8397 (mpp) REVERT: D 264 PHE cc_start: 0.9539 (t80) cc_final: 0.9058 (t80) REVERT: D 268 THR cc_start: 0.9517 (m) cc_final: 0.9087 (m) REVERT: D 291 TYR cc_start: 0.8998 (t80) cc_final: 0.8698 (t80) REVERT: D 296 MET cc_start: 0.9568 (ttp) cc_final: 0.9344 (ttp) REVERT: D 305 ASN cc_start: 0.9547 (m-40) cc_final: 0.8811 (m-40) REVERT: D 330 MET cc_start: 0.9400 (tpt) cc_final: 0.8916 (tpp) REVERT: D 360 MET cc_start: 0.9267 (ptp) cc_final: 0.8861 (ppp) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1304 time to fit residues: 61.1982 Evaluate side-chains 229 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 195 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 HIS ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 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 = 0.3734 r_free = 0.3734 target = 0.074886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.050297 restraints weight = 142149.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.052133 restraints weight = 74732.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053258 restraints weight = 47806.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.053968 restraints weight = 34897.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.054375 restraints weight = 28138.900| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21759 Z= 0.176 Angle : 0.645 9.435 29433 Z= 0.338 Chirality : 0.040 0.188 3288 Planarity : 0.004 0.048 3705 Dihedral : 4.487 20.862 2888 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.16), residues: 2616 helix: 1.14 (0.12), residues: 1716 sheet: 0.60 (0.47), residues: 111 loop : -0.74 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 497 TYR 0.033 0.002 TYR A 351 PHE 0.022 0.002 PHE A 206 TRP 0.015 0.001 TRP B 68 HIS 0.016 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00370 (21759) covalent geometry : angle 0.64490 (29433) hydrogen bonds : bond 0.04135 ( 1271) hydrogen bonds : angle 4.71405 ( 3723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.47 seconds wall clock time: 71 minutes 1.40 seconds (4261.40 seconds total)