Starting phenix.real_space_refine on Fri Oct 23 19:32:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25mk_80204/10_2026/25mk_80204.cif Found real_map, /net/cci-nas-00/data/ceres_data/25mk_80204/10_2026/25mk_80204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/25mk_80204/10_2026/25mk_80204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25mk_80204/10_2026/25mk_80204.map" model { file = "/net/cci-nas-00/data/ceres_data/25mk_80204/10_2026/25mk_80204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25mk_80204/10_2026/25mk_80204.cif" } resolution = 3.04 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= -0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 60 5.16 5 C 6944 2.51 5 N 1700 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10586 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5265 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "B" Number of atoms: 5265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5265 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.30, per 1000 atoms: 0.22 Number of scatterers: 10586 At special positions: 0 Unit cell: (79.351, 122.831, 108.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 60 16.00 P 4 15.00 O 1876 8.00 N 1700 7.00 C 6944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 370.4 milliseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 5 sheets defined 53.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.778A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 59 through 64' Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.553A pdb=" N THR A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 76 " --> pdb=" O ILE A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.863A pdb=" N PHE A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 removed outlier: 3.541A pdb=" N VAL A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.596A pdb=" N TYR A 133 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS A 141 " --> pdb=" O CYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.661A pdb=" N ASN A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 211 removed outlier: 3.534A pdb=" N PHE A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.787A pdb=" N VAL A 210 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.599A pdb=" N ILE A 217 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 218 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.712A pdb=" N ILE A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.598A pdb=" N ILE A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.627A pdb=" N LEU A 278 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 280 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 281 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 282 " --> pdb=" O LYS A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 282' Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.628A pdb=" N LEU A 301 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 302 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL A 304 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 306 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.544A pdb=" N ALA A 313 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 314 " --> pdb=" O THR A 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 314' Processing helix chain 'A' and resid 322 through 334 removed outlier: 3.590A pdb=" N VAL A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.504A pdb=" N VAL A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.820A pdb=" N ASN A 355 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 356 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER A 357 " --> pdb=" O TYR A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.670A pdb=" N SER A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 389 removed outlier: 3.582A pdb=" N VAL A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.831A pdb=" N VAL A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.544A pdb=" N ASN A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 431 " --> pdb=" O TYR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.633A pdb=" N HIS A 448 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.654A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 500 removed outlier: 3.887A pdb=" N ILE A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.961A pdb=" N GLY A 505 " --> pdb=" O PHE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.699A pdb=" N ILE A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 538 removed outlier: 3.634A pdb=" N TRP A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 527 " --> pdb=" O TRP A 523 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 removed outlier: 3.676A pdb=" N GLN A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.758A pdb=" N SER A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 581 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 605 Processing helix chain 'A' and resid 634 through 648 removed outlier: 3.636A pdb=" N GLU A 639 " --> pdb=" O PRO A 635 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 644 " --> pdb=" O ARG A 640 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 647 " --> pdb=" O VAL A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.636A pdb=" N ILE A 750 " --> pdb=" O PHE A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 removed outlier: 3.663A pdb=" N ASN A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 removed outlier: 3.627A pdb=" N LEU A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.820A pdb=" N PHE B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.830A pdb=" N TYR B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 129 through 141 removed outlier: 3.614A pdb=" N TYR B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 141 " --> pdb=" O CYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 179 removed outlier: 3.676A pdb=" N ASN B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 211 removed outlier: 3.560A pdb=" N THR B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B 197 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 206 - end of helix removed outlier: 3.833A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 removed outlier: 3.598A pdb=" N ILE B 217 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 218 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.752A pdb=" N ILE B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 282 removed outlier: 3.625A pdb=" N LEU B 278 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 280 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU B 281 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 282 " --> pdb=" O LYS B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 275 through 282' Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.604A pdb=" N TYR B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 292 " --> pdb=" O TYR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.611A pdb=" N LEU B 301 " --> pdb=" O TRP B 298 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 302 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.660A pdb=" N THR B 309 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.539A pdb=" N ALA B 313 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 314 " --> pdb=" O THR B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 314' Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.621A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 349 removed outlier: 3.513A pdb=" N VAL B 339 " --> pdb=" O TYR B 335 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 340 " --> pdb=" O PRO B 336 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 349 " --> pdb=" O GLN B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.816A pdb=" N ASN B 355 " --> pdb=" O HIS B 352 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER B 357 " --> pdb=" O TYR B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 357' Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.703A pdb=" N SER B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 389 removed outlier: 3.643A pdb=" N VAL B 374 " --> pdb=" O TRP B 370 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 377 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 386 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 399 removed outlier: 3.711A pdb=" N ILE B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 399' Processing helix chain 'B' and resid 425 through 430 removed outlier: 3.660A pdb=" N MET B 430 " --> pdb=" O ASN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 468 removed outlier: 3.645A pdb=" N VAL B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 462 " --> pdb=" O MET B 458 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 468 " --> pdb=" O MET B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'B' and resid 480 through 500 removed outlier: 3.616A pdb=" N LEU B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 496 " --> pdb=" O MET B 492 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 498 " --> pdb=" O TYR B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 505 removed outlier: 3.979A pdb=" N GLY B 505 " --> pdb=" O PHE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 512 removed outlier: 3.738A pdb=" N ILE B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 535 removed outlier: 3.656A pdb=" N TRP B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 527 " --> pdb=" O TRP B 523 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS B 530 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 547 removed outlier: 3.603A pdb=" N GLN B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 605 Processing helix chain 'B' and resid 637 through 652 removed outlier: 3.955A pdb=" N VAL B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 644 " --> pdb=" O ARG B 640 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 645 " --> pdb=" O HIS B 641 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.634A pdb=" N ILE B 750 " --> pdb=" O PHE B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 762 removed outlier: 3.540A pdb=" N LEU B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 761 " --> pdb=" O PHE B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 774 No H-bonds generated for 'chain 'B' and resid 772 through 774' Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA2, first strand: chain 'A' and resid 554 through 556 removed outlier: 6.226A pdb=" N ASN A 554 " --> pdb=" O VAL A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 607 through 611 removed outlier: 3.623A pdb=" N LEU A 590 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY A 560 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE A 591 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE A 562 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE A 593 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 559 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU A 731 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 561 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLY A 733 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N TYR A 563 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N THR A 735 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N LEU A 777 " --> pdb=" O MET A 728 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 730 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL A 779 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET A 732 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N MET A 781 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 734 " --> pdb=" O MET A 781 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N TYR A 783 " --> pdb=" O LYS A 734 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A 736 " --> pdb=" O TYR A 783 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 785 " --> pdb=" O GLU A 736 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR A 738 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU A 776 " --> pdb=" O GLY B 780 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU B 776 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N LEU B 777 " --> pdb=" O MET B 728 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR B 730 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL B 779 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET B 732 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N MET B 781 " --> pdb=" O MET B 732 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS B 734 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR B 783 " --> pdb=" O LYS B 734 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU B 736 " --> pdb=" O TYR B 783 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 785 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N THR B 738 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 559 " --> pdb=" O VAL B 729 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU B 731 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 561 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N GLY B 733 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N TYR B 563 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N THR B 735 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU B 590 " --> pdb=" O CYS B 622 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL B 624 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER B 592 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N TYR B 626 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS B 594 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 410 through 411 Processing sheet with id=AA5, first strand: chain 'B' and resid 554 through 556 removed outlier: 6.149A pdb=" N ASN B 554 " --> pdb=" O VAL B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 263 hydrogen bonds defined for protein. 726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1598 1.29 - 1.42: 2939 1.42 - 1.55: 6182 1.55 - 1.68: 11 1.68 - 1.81: 104 Bond restraints: 10834 Sorted by residual: bond pdb=" C LEU A 777 " pdb=" O LEU A 777 " ideal model delta sigma weight residual 1.235 1.159 0.076 1.26e-02 6.30e+03 3.60e+01 bond pdb=" C LEU B 777 " pdb=" O LEU B 777 " ideal model delta sigma weight residual 1.235 1.160 0.074 1.26e-02 6.30e+03 3.49e+01 bond pdb=" C GLU A 778 " pdb=" O GLU A 778 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.21e-02 6.83e+03 1.75e+01 bond pdb=" C GLU B 778 " pdb=" O GLU B 778 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.21e-02 6.83e+03 1.68e+01 bond pdb=" C LYS B 734 " pdb=" O LYS B 734 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.13e-02 7.83e+03 1.53e+01 ... (remaining 10829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 14416 3.06 - 6.12: 281 6.12 - 9.18: 10 9.18 - 12.24: 4 12.24 - 15.30: 5 Bond angle restraints: 14716 Sorted by residual: angle pdb=" N ARG B 527 " pdb=" CA ARG B 527 " pdb=" C ARG B 527 " ideal model delta sigma weight residual 114.56 102.31 12.25 1.27e+00 6.20e-01 9.30e+01 angle pdb=" C ASN A 565 " pdb=" CA ASN A 565 " pdb=" CB ASN A 565 " ideal model delta sigma weight residual 110.17 94.87 15.30 1.69e+00 3.50e-01 8.20e+01 angle pdb=" C LYS A 734 " pdb=" CA LYS A 734 " pdb=" CB LYS A 734 " ideal model delta sigma weight residual 110.62 97.19 13.43 1.51e+00 4.39e-01 7.92e+01 angle pdb=" C LYS B 734 " pdb=" CA LYS B 734 " pdb=" CB LYS B 734 " ideal model delta sigma weight residual 110.62 97.29 13.33 1.51e+00 4.39e-01 7.80e+01 angle pdb=" N MET B 519 " pdb=" CA MET B 519 " pdb=" C MET B 519 " ideal model delta sigma weight residual 114.75 104.28 10.47 1.26e+00 6.30e-01 6.91e+01 ... (remaining 14711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 5800 27.06 - 54.13: 484 54.13 - 81.19: 44 81.19 - 108.25: 6 108.25 - 135.32: 2 Dihedral angle restraints: 6336 sinusoidal: 2460 harmonic: 3876 Sorted by residual: dihedral pdb=" CD ARG B 527 " pdb=" NE ARG B 527 " pdb=" CZ ARG B 527 " pdb=" NH1 ARG B 527 " ideal model delta sinusoidal sigma weight residual 0.00 79.77 -79.77 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" C ASN B 565 " pdb=" N ASN B 565 " pdb=" CA ASN B 565 " pdb=" CB ASN B 565 " ideal model delta harmonic sigma weight residual -122.60 -105.01 -17.59 0 2.50e+00 1.60e-01 4.95e+01 dihedral pdb=" C LYS B 734 " pdb=" N LYS B 734 " pdb=" CA LYS B 734 " pdb=" CB LYS B 734 " ideal model delta harmonic sigma weight residual -122.60 -106.20 -16.40 0 2.50e+00 1.60e-01 4.31e+01 ... (remaining 6333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1572 0.081 - 0.162: 141 0.162 - 0.243: 6 0.243 - 0.324: 6 0.324 - 0.404: 1 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA ASN B 565 " pdb=" N ASN B 565 " pdb=" C ASN B 565 " pdb=" CB ASN B 565 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA LYS B 734 " pdb=" N LYS B 734 " pdb=" C LYS B 734 " pdb=" CB LYS B 734 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA LYS A 734 " pdb=" N LYS A 734 " pdb=" C LYS A 734 " pdb=" CB LYS A 734 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 1723 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 527 " 1.073 9.50e-02 1.11e+02 4.81e-01 1.40e+02 pdb=" NE ARG B 527 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 527 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 527 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 527 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 527 " 0.287 9.50e-02 1.11e+02 1.29e-01 1.02e+01 pdb=" NE ARG A 527 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 527 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 527 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 527 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 734 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C LYS A 734 " -0.046 2.00e-02 2.50e+03 pdb=" O LYS A 734 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 735 " 0.016 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 3655 2.84 - 3.42: 9303 3.42 - 3.99: 17261 3.99 - 4.57: 25493 4.57 - 5.14: 39394 Nonbonded interactions: 95106 Sorted by model distance: nonbonded pdb=" NH2 ARG A 527 " pdb=" O2B ADP A 901 " model vdw 2.269 3.120 nonbonded pdb=" N ASN A 565 " pdb=" OD1 ASN A 565 " model vdw 2.353 3.120 nonbonded pdb=" O LYS A 734 " pdb=" CB LYS A 734 " model vdw 2.369 2.752 nonbonded pdb=" O LYS B 734 " pdb=" CB LYS B 734 " model vdw 2.370 2.752 nonbonded pdb=" CB GLU A 778 " pdb=" OE1 GLU A 778 " model vdw 2.398 2.752 ... (remaining 95101 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.930 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10834 Z= 0.271 Angle : 0.978 15.304 14716 Z= 0.648 Chirality : 0.051 0.404 1726 Planarity : 0.013 0.481 1786 Dihedral : 18.594 135.319 3856 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.90 % Favored : 92.02 % Rotamer: Outliers : 2.85 % Allowed : 30.45 % Favored : 66.70 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.31 (0.19), residues: 1316 helix: -4.27 (0.12), residues: 742 sheet: -0.28 (0.54), residues: 106 loop : -2.61 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 541 TYR 0.015 0.001 TYR A 158 PHE 0.013 0.001 PHE A 588 TRP 0.006 0.001 TRP A 370 HIS 0.004 0.001 HIS B 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.27 (10834) covalent geometry : angle 0.97811 / 0.65 (14716) hydrogen bonds : bond 0.34819 / 22.11 ( 263) hydrogen bonds : angle 9.79177 / 6.41 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7213 (mp) REVERT: A 167 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7703 (tp) REVERT: A 570 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7039 (mm) REVERT: A 718 GLU cc_start: 0.7713 (tt0) cc_final: 0.6975 (tp30) REVERT: A 719 LEU cc_start: 0.6059 (tp) cc_final: 0.5665 (mt) REVERT: B 119 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7237 (mp) REVERT: B 184 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.5967 (ttpt) REVERT: B 492 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6857 (mmm) REVERT: B 570 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7075 (mm) REVERT: B 651 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6514 (t-90) REVERT: B 718 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7212 (mm-30) outliers start: 33 outliers final: 20 residues processed: 147 average time/residue: 0.1178 time to fit residues: 23.6771 Evaluate side-chains 145 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 760 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.0470 overall best weight: 1.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN B 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107863 restraints weight = 12849.429| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.92 r_work: 0.3095 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10834 Z= 0.194 Angle : 0.700 7.737 14716 Z= 0.370 Chirality : 0.046 0.171 1726 Planarity : 0.006 0.052 1786 Dihedral : 9.748 132.668 1533 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.66 % Favored : 91.26 % Rotamer: Outliers : 7.01 % Allowed : 24.91 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.20), residues: 1316 helix: -3.69 (0.14), residues: 756 sheet: -0.28 (0.53), residues: 108 loop : -2.46 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 541 TYR 0.020 0.002 TYR A 158 PHE 0.022 0.002 PHE A 588 TRP 0.008 0.001 TRP A 258 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (10834) covalent geometry : angle 0.69963 / 0.37 (14716) hydrogen bonds : bond 0.07453 / 4.71 ( 263) hydrogen bonds : angle 5.27371 / 3.56 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 125 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 167 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7991 (tp) REVERT: A 491 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 570 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 718 GLU cc_start: 0.7904 (tt0) cc_final: 0.7322 (tp30) REVERT: B 119 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 366 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7690 (t0) REVERT: B 491 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: B 492 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7652 (mmm) REVERT: B 570 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8043 (mm) REVERT: B 785 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7110 (pp) outliers start: 81 outliers final: 46 residues processed: 187 average time/residue: 0.0901 time to fit residues: 24.6536 Evaluate side-chains 174 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 118 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 785 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [36, 54, 66, 117, 75, 71, 37, 65, 57, 106, 52] chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 0.0370 chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN A 641 HIS B 565 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105715 restraints weight = 12761.569| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.94 r_work: 0.3018 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10834 Z= 0.112 Angle : 0.575 5.818 14716 Z= 0.304 Chirality : 0.042 0.168 1726 Planarity : 0.005 0.051 1786 Dihedral : 8.742 128.339 1509 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.24 % Rotamer: Outliers : 5.36 % Allowed : 25.95 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.21), residues: 1316 helix: -3.21 (0.16), residues: 728 sheet: -0.20 (0.53), residues: 108 loop : -2.32 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 600 TYR 0.016 0.001 TYR A 158 PHE 0.013 0.001 PHE B 638 TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS A 654 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10834) covalent geometry : angle 0.57501 / 0.30 (14716) hydrogen bonds : bond 0.04651 / 2.96 ( 263) hydrogen bonds : angle 4.82750 / 3.26 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 128 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8218 (mp) REVERT: A 167 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7946 (tp) REVERT: A 201 ASP cc_start: 0.7613 (p0) cc_final: 0.7267 (p0) REVERT: A 222 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: A 425 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7358 (mm) REVERT: A 491 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: A 492 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6983 (mmm) REVERT: A 570 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7991 (mm) REVERT: A 718 GLU cc_start: 0.7871 (tt0) cc_final: 0.7210 (tp30) REVERT: B 116 PHE cc_start: 0.8101 (m-10) cc_final: 0.7872 (m-10) REVERT: B 119 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8174 (mp) REVERT: B 193 MET cc_start: 0.8133 (ttm) cc_final: 0.7855 (ttt) REVERT: B 222 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: B 385 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8407 (tp40) REVERT: B 570 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8009 (mm) outliers start: 62 outliers final: 36 residues processed: 174 average time/residue: 0.0950 time to fit residues: 23.9367 Evaluate side-chains 167 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 718 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [78, 22, 99, 45, 5, 62, 104, 86, 80, 72, 53] chunk 78 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 524 GLN B 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.103626 restraints weight = 12979.313| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.95 r_work: 0.2989 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10834 Z= 0.125 Angle : 0.584 5.996 14716 Z= 0.305 Chirality : 0.043 0.165 1726 Planarity : 0.005 0.047 1786 Dihedral : 8.356 116.737 1501 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.67 % Favored : 92.25 % Rotamer: Outliers : 5.71 % Allowed : 25.52 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.21), residues: 1316 helix: -3.03 (0.16), residues: 738 sheet: -0.18 (0.53), residues: 108 loop : -2.25 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 541 TYR 0.015 0.001 TYR A 158 PHE 0.015 0.001 PHE A 502 TRP 0.007 0.001 TRP A 258 HIS 0.002 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10834) covalent geometry : angle 0.58402 / 0.31 (14716) hydrogen bonds : bond 0.04933 / 3.11 ( 263) hydrogen bonds : angle 4.66220 / 3.16 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 121 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8193 (mp) REVERT: A 167 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7996 (tp) REVERT: A 222 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: A 425 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7405 (mm) REVERT: A 491 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: A 492 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6946 (mmm) REVERT: A 570 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7968 (mm) REVERT: A 718 GLU cc_start: 0.7841 (tt0) cc_final: 0.7173 (tp30) REVERT: B 119 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 222 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: B 385 GLN cc_start: 0.8699 (tp-100) cc_final: 0.8414 (tp40) REVERT: B 570 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8003 (mm) outliers start: 66 outliers final: 41 residues processed: 172 average time/residue: 0.0942 time to fit residues: 23.9124 Evaluate side-chains 167 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 718 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [100, 87, 114, 78, 14, 85, 44, 66, 31, 19, 59] chunk 100 optimal weight: 0.0980 chunk 87 optimal weight: 0.2980 chunk 114 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104226 restraints weight = 12809.880| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.95 r_work: 0.3044 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10834 Z= 0.104 Angle : 0.547 5.764 14716 Z= 0.285 Chirality : 0.042 0.159 1726 Planarity : 0.004 0.047 1786 Dihedral : 7.940 107.407 1498 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 5.02 % Allowed : 25.95 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.22), residues: 1316 helix: -2.74 (0.17), residues: 740 sheet: 0.15 (0.53), residues: 104 loop : -2.16 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 541 TYR 0.013 0.001 TYR A 158 PHE 0.012 0.001 PHE A 502 TRP 0.006 0.001 TRP A 258 HIS 0.001 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (10834) covalent geometry : angle 0.54653 / 0.29 (14716) hydrogen bonds : bond 0.04057 / 2.56 ( 263) hydrogen bonds : angle 4.51852 / 3.07 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8256 (mp) REVERT: A 120 GLN cc_start: 0.8845 (mm110) cc_final: 0.8549 (mm-40) REVERT: A 167 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8006 (tp) REVERT: A 201 ASP cc_start: 0.7673 (p0) cc_final: 0.7402 (p0) REVERT: A 222 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: A 425 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7465 (mm) REVERT: A 491 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: A 492 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6927 (mmm) REVERT: A 718 GLU cc_start: 0.7821 (tt0) cc_final: 0.7082 (tp30) REVERT: B 119 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8236 (mp) REVERT: B 193 MET cc_start: 0.8198 (ttm) cc_final: 0.7933 (ttt) REVERT: B 222 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: B 324 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8156 (ttm-80) REVERT: B 385 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8457 (tp40) REVERT: B 425 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7584 (mm) REVERT: B 651 HIS cc_start: 0.6976 (OUTLIER) cc_final: 0.6525 (t-90) REVERT: B 785 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6700 (pp) outliers start: 58 outliers final: 34 residues processed: 169 average time/residue: 0.0914 time to fit residues: 22.6678 Evaluate side-chains 168 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 785 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [65, 4, 97, 112, 90, 60, 78, 111, 80, 95, 25] chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 111 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105711 restraints weight = 12813.576| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.96 r_work: 0.3042 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 10834 Z= 0.107 Angle : 0.552 6.980 14716 Z= 0.287 Chirality : 0.042 0.156 1726 Planarity : 0.004 0.045 1786 Dihedral : 7.486 99.778 1490 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.53 % Favored : 93.39 % Rotamer: Outliers : 4.58 % Allowed : 25.95 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.22), residues: 1316 helix: -2.55 (0.17), residues: 746 sheet: -0.10 (0.52), residues: 108 loop : -2.09 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 541 TYR 0.013 0.001 TYR A 158 PHE 0.012 0.001 PHE A 588 TRP 0.006 0.001 TRP A 258 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10834) covalent geometry : angle 0.55213 / 0.29 (14716) hydrogen bonds : bond 0.04183 / 2.63 ( 263) hydrogen bonds : angle 4.46233 / 3.05 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8216 (mp) REVERT: A 120 GLN cc_start: 0.8816 (mm110) cc_final: 0.8506 (mm-40) REVERT: A 167 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8029 (tp) REVERT: A 175 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6952 (mm-30) REVERT: A 201 ASP cc_start: 0.7592 (p0) cc_final: 0.7080 (p0) REVERT: A 222 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: A 491 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 492 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6859 (mmm) REVERT: A 718 GLU cc_start: 0.7753 (tt0) cc_final: 0.7121 (tp30) REVERT: B 119 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 222 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: B 385 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8422 (tp40) REVERT: B 570 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8025 (mm) REVERT: B 651 HIS cc_start: 0.6944 (OUTLIER) cc_final: 0.6476 (t-90) REVERT: B 785 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6523 (pp) outliers start: 53 outliers final: 34 residues processed: 158 average time/residue: 0.0953 time to fit residues: 21.9306 Evaluate side-chains 163 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 785 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [5, 123, 49, 126, 32, 62, 96, 84, 124, 50, 13] chunk 5 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 126 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 96 optimal weight: 0.0970 chunk 84 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 HIS A 524 GLN B 524 GLN B 565 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.108231 restraints weight = 12705.900| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.95 r_work: 0.3080 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 10834 Z= 0.091 Angle : 0.515 6.211 14716 Z= 0.266 Chirality : 0.041 0.149 1726 Planarity : 0.004 0.044 1786 Dihedral : 6.876 86.571 1490 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.07 % Allowed : 26.64 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.22), residues: 1316 helix: -2.23 (0.18), residues: 738 sheet: 0.13 (0.52), residues: 104 loop : -2.01 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 621 TYR 0.011 0.001 TYR A 158 PHE 0.011 0.001 PHE B 638 TRP 0.004 0.000 TRP A 258 HIS 0.001 0.000 HIS A 654 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (10834) covalent geometry : angle 0.51484 / 0.27 (14716) hydrogen bonds : bond 0.03213 / 2.03 ( 263) hydrogen bonds : angle 4.33055 / 2.95 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8182 (mp) REVERT: A 120 GLN cc_start: 0.8794 (mm110) cc_final: 0.8470 (mm-40) REVERT: A 154 GLU cc_start: -0.0441 (OUTLIER) cc_final: -0.1999 (tm-30) REVERT: A 167 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7867 (tp) REVERT: A 175 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6793 (mm-30) REVERT: A 222 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6898 (tt0) REVERT: A 491 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: A 492 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6924 (mmm) REVERT: A 718 GLU cc_start: 0.7530 (tt0) cc_final: 0.6947 (tp30) REVERT: B 119 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8144 (mp) REVERT: B 120 GLN cc_start: 0.8817 (mm110) cc_final: 0.8483 (mm-40) REVERT: B 193 MET cc_start: 0.8027 (ttm) cc_final: 0.7768 (ttt) REVERT: B 222 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: B 385 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8466 (tp40) REVERT: B 476 ASN cc_start: 0.7318 (t0) cc_final: 0.7116 (t0) REVERT: B 651 HIS cc_start: 0.6940 (OUTLIER) cc_final: 0.6488 (t-90) REVERT: B 785 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6430 (pp) outliers start: 47 outliers final: 31 residues processed: 163 average time/residue: 0.0898 time to fit residues: 21.6548 Evaluate side-chains 165 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 785 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [95, 112, 55, 82, 24, 16, 53, 1, 103, 4, 96] chunk 95 optimal weight: 0.0470 chunk 112 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN B 565 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120348 restraints weight = 12599.947| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.77 r_work: 0.3273 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10834 Z= 0.108 Angle : 0.541 6.031 14716 Z= 0.279 Chirality : 0.042 0.147 1726 Planarity : 0.004 0.044 1786 Dihedral : 6.815 83.413 1489 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.67 % Allowed : 25.95 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.22), residues: 1316 helix: -2.12 (0.18), residues: 742 sheet: -0.08 (0.52), residues: 108 loop : -2.01 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 527 TYR 0.011 0.001 TYR A 158 PHE 0.011 0.001 PHE B 638 TRP 0.005 0.001 TRP A 258 HIS 0.002 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (10834) covalent geometry : angle 0.54095 / 0.28 (14716) hydrogen bonds : bond 0.04014 / 2.52 ( 263) hydrogen bonds : angle 4.31488 / 2.94 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8637 (mp) REVERT: A 120 GLN cc_start: 0.9016 (mm110) cc_final: 0.8746 (mm-40) REVERT: A 167 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7975 (tp) REVERT: A 175 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 222 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: A 491 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: A 492 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7490 (mmm) REVERT: A 718 GLU cc_start: 0.7533 (tt0) cc_final: 0.7014 (tp30) REVERT: B 119 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8608 (mp) REVERT: B 120 GLN cc_start: 0.9048 (mm110) cc_final: 0.8782 (mm-40) REVERT: B 193 MET cc_start: 0.8592 (ttm) cc_final: 0.8359 (ttt) REVERT: B 222 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: B 324 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8449 (ttm-80) REVERT: B 491 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: B 570 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8183 (mm) REVERT: B 651 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6934 (t-90) REVERT: B 785 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6943 (pp) outliers start: 54 outliers final: 36 residues processed: 165 average time/residue: 0.0905 time to fit residues: 21.8386 Evaluate side-chains 170 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 517 MET Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 785 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [123, 38, 131, 126, 67, 32, 117, 55, 96, 107, 92] chunk 123 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119087 restraints weight = 12525.458| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.61 r_work: 0.3245 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10834 Z= 0.129 Angle : 0.571 5.976 14716 Z= 0.294 Chirality : 0.043 0.146 1726 Planarity : 0.004 0.045 1786 Dihedral : 6.961 82.987 1489 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.76 % Allowed : 25.17 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.22), residues: 1316 helix: -2.19 (0.17), residues: 756 sheet: -0.08 (0.52), residues: 108 loop : -2.04 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 541 TYR 0.012 0.001 TYR A 628 PHE 0.015 0.001 PHE A 588 TRP 0.006 0.001 TRP A 298 HIS 0.002 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (10834) covalent geometry : angle 0.57054 / 0.29 (14716) hydrogen bonds : bond 0.04764 / 2.98 ( 263) hydrogen bonds : angle 4.41529 / 3.01 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8633 (mp) REVERT: A 120 GLN cc_start: 0.9004 (mm110) cc_final: 0.8717 (mm-40) REVERT: A 167 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 175 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 222 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: A 491 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: A 492 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7465 (mmm) REVERT: A 718 GLU cc_start: 0.7571 (tt0) cc_final: 0.7067 (tp30) REVERT: B 119 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 120 GLN cc_start: 0.9024 (mm110) cc_final: 0.8742 (mm-40) REVERT: B 182 PHE cc_start: 0.8011 (t80) cc_final: 0.7525 (t80) REVERT: B 222 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: B 324 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8419 (ttm-80) REVERT: B 491 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: B 570 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8141 (mm) REVERT: B 619 MET cc_start: 0.8160 (mtp) cc_final: 0.7828 (mtm) REVERT: B 651 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6896 (t-90) REVERT: B 785 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6990 (pp) outliers start: 55 outliers final: 39 residues processed: 162 average time/residue: 0.0901 time to fit residues: 21.3622 Evaluate side-chains 174 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 517 MET Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 785 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [81, 13, 11, 7, 33, 83, 10, 16, 59, 30, 119] chunk 81 optimal weight: 0.0050 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 0.0270 chunk 30 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 overall best weight: 0.4652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120964 restraints weight = 12589.659| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.77 r_work: 0.3282 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10834 Z= 0.100 Angle : 0.529 6.156 14716 Z= 0.273 Chirality : 0.042 0.145 1726 Planarity : 0.004 0.043 1786 Dihedral : 6.575 71.908 1489 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.98 % Allowed : 26.12 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.22), residues: 1316 helix: -1.92 (0.18), residues: 744 sheet: 0.22 (0.52), residues: 104 loop : -2.00 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.011 0.001 TYR A 158 PHE 0.015 0.001 PHE B 116 TRP 0.005 0.001 TRP B 523 HIS 0.002 0.000 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (10834) covalent geometry : angle 0.52861 / 0.27 (14716) hydrogen bonds : bond 0.03694 / 2.33 ( 263) hydrogen bonds : angle 4.33990 / 2.95 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8624 (mp) REVERT: A 120 GLN cc_start: 0.9000 (mm110) cc_final: 0.8718 (mm-40) REVERT: A 167 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 175 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 222 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6846 (tt0) REVERT: A 491 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 492 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7491 (mmm) REVERT: A 718 GLU cc_start: 0.7522 (tt0) cc_final: 0.7037 (tp30) REVERT: B 119 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8614 (mp) REVERT: B 120 GLN cc_start: 0.9052 (mm110) cc_final: 0.8786 (mm-40) REVERT: B 169 ARG cc_start: 0.6468 (mtp-110) cc_final: 0.5735 (mtt180) REVERT: B 182 PHE cc_start: 0.8061 (t80) cc_final: 0.7584 (t80) REVERT: B 222 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: B 517 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8787 (mtp) REVERT: B 570 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8158 (mm) REVERT: B 619 MET cc_start: 0.8023 (mtp) cc_final: 0.7704 (mtm) REVERT: B 651 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6880 (t-90) REVERT: B 785 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.6928 (pp) outliers start: 46 outliers final: 31 residues processed: 160 average time/residue: 0.0992 time to fit residues: 22.9493 Evaluate side-chains 170 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 517 MET Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 785 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [48, 45, 128, 43, 87, 80, 105, 25, 118, 36, 68] chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 128 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 105 optimal weight: 0.0770 chunk 25 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113974 restraints weight = 12621.205| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.93 r_work: 0.3135 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 10834 Z= 0.099 Angle : 0.526 6.136 14716 Z= 0.271 Chirality : 0.042 0.144 1726 Planarity : 0.004 0.044 1786 Dihedral : 6.406 63.179 1489 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.89 % Allowed : 26.21 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.23), residues: 1316 helix: -1.75 (0.18), residues: 746 sheet: -0.03 (0.52), residues: 108 loop : -1.89 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 138 TYR 0.010 0.001 TYR A 158 PHE 0.013 0.001 PHE B 116 TRP 0.004 0.001 TRP A 370 HIS 0.002 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (10834) covalent geometry : angle 0.52558 / 0.27 (14716) hydrogen bonds : bond 0.03708 / 2.33 ( 263) hydrogen bonds : angle 4.28292 / 2.92 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2706.58 seconds wall clock time: 46 minutes 54.48 seconds (2814.48 seconds total)