Starting phenix.real_space_refine on Thu Jul 2 20:13:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a92_11682/07_2026/7a92_11682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a92_11682/07_2026/7a92_11682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7a92_11682/07_2026/7a92_11682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a92_11682/07_2026/7a92_11682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a92_11682/07_2026/7a92_11682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a92_11682/07_2026/7a92_11682.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7a92_11682/07_2026/7a92_11682.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a92_11682/07_2026/7a92_11682.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 51 5.16 5 C 6424 2.51 5 N 1658 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10040 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4815 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 bond proxies already assigned to first conformer: 4917 Chain: "A" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5098 Classifications: {'peptide': 643} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 609} Chain breaks: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.26, per 1000 atoms: 0.23 Number of scatterers: 10040 At special positions: 0 Unit cell: (89.474, 104.566, 168.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 51 16.00 O 1906 8.00 N 1658 7.00 C 6424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 701 " - " ASN A 343 " " NAG A 702 " - " ASN A 331 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG J 1 " - " ASN D 546 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 391.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 706 " pdb="ZN ZN D 706 " - pdb=" NE2 HIS D 374 " pdb="ZN ZN D 706 " - pdb=" NE2 HIS D 378 " 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 13 sheets defined 35.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.516A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 81 removed outlier: 3.537A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.794A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.866A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 3.528A pdb=" N LEU D 162 " --> pdb=" O TYR D 158 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.701A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.603A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.508A pdb=" N TYR D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 3.815A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.125A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.909A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.574A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.853A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.552A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.718A pdb=" N TRP D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.696A pdb=" N TRP D 477 " --> pdb=" O TRP D 473 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.519A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.951A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.978A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.540A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.792A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 343' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.892A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.238A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.946A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.173A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.026A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.839A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 163 removed outlier: 6.521A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.810A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.600A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.263A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1056 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: 1.31 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3144 1.34 - 1.46: 2382 1.46 - 1.58: 4711 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 10311 Sorted by residual: bond pdb=" N LYS A 558 " pdb=" CA LYS A 558 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.27e-02 6.20e+03 1.16e+01 bond pdb=" CA SER A 591 " pdb=" CB SER A 591 " ideal model delta sigma weight residual 1.537 1.488 0.049 1.45e-02 4.76e+03 1.14e+01 bond pdb=" N CYS A 590 " pdb=" CA CYS A 590 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.10e+01 bond pdb=" N VAL A 595 " pdb=" CA VAL A 595 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL A 597 " pdb=" CA VAL A 597 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.75e+00 ... (remaining 10306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 13457 1.95 - 3.89: 495 3.89 - 5.84: 55 5.84 - 7.79: 14 7.79 - 9.73: 2 Bond angle restraints: 14023 Sorted by residual: angle pdb=" N VAL A 320 " pdb=" CA VAL A 320 " pdb=" C VAL A 320 " ideal model delta sigma weight residual 112.80 108.00 4.80 1.15e+00 7.56e-01 1.75e+01 angle pdb=" N PRO A 217 " pdb=" CA PRO A 217 " pdb=" C PRO A 217 " ideal model delta sigma weight residual 111.22 116.90 -5.68 1.40e+00 5.10e-01 1.64e+01 angle pdb=" C ASP A 578 " pdb=" CA ASP A 578 " pdb=" CB ASP A 578 " ideal model delta sigma weight residual 109.42 115.64 -6.22 1.57e+00 4.06e-01 1.57e+01 angle pdb=" CA ASN D 90 " pdb=" C ASN D 90 " pdb=" O ASN D 90 " ideal model delta sigma weight residual 120.55 116.40 4.15 1.06e+00 8.90e-01 1.54e+01 angle pdb=" CA ASN A 317 " pdb=" C ASN A 317 " pdb=" O ASN A 317 " ideal model delta sigma weight residual 121.87 117.65 4.22 1.16e+00 7.43e-01 1.32e+01 ... (remaining 14018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5428 17.99 - 35.98: 450 35.98 - 53.97: 109 53.97 - 71.97: 14 71.97 - 89.96: 12 Dihedral angle restraints: 6013 sinusoidal: 2404 harmonic: 3609 Sorted by residual: dihedral pdb=" CA SER D 425 " pdb=" C SER D 425 " pdb=" N PRO D 426 " pdb=" CA PRO D 426 " ideal model delta harmonic sigma weight residual 180.00 -154.67 -25.33 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 131.58 -38.58 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA TYR D 252 " pdb=" C TYR D 252 " pdb=" N PRO D 253 " pdb=" CA PRO D 253 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 6010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1185 0.062 - 0.125: 303 0.125 - 0.187: 33 0.187 - 0.249: 7 0.249 - 0.311: 3 Chirality restraints: 1531 Sorted by residual: chirality pdb=" CA ILE A 312 " pdb=" N ILE A 312 " pdb=" C ILE A 312 " pdb=" CB ILE A 312 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LEU A 216 " pdb=" N LEU A 216 " pdb=" C LEU A 216 " pdb=" CB LEU A 216 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ASP A 215 " pdb=" N ASP A 215 " pdb=" C ASP A 215 " pdb=" CB ASP A 215 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1528 not shown) Planarity restraints: 1809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 451 " -0.016 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C PRO D 451 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO D 451 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE D 452 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 161 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C ARG D 161 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG D 161 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 162 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 368 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ASP D 368 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP D 368 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE D 369 " 0.013 2.00e-02 2.50e+03 ... (remaining 1806 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1623 2.76 - 3.29: 8995 3.29 - 3.83: 15235 3.83 - 4.36: 18612 4.36 - 4.90: 32588 Nonbonded interactions: 77053 Sorted by model distance: nonbonded pdb=" OG SER D 19 " pdb=" OE1 GLU D 23 " model vdw 2.222 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.227 3.040 nonbonded pdb=" O ASP D 225 " pdb=" OG1 THR D 229 " model vdw 2.230 3.040 nonbonded pdb=" O LEU D 85 " pdb=" NZ LYS D 94 " model vdw 2.269 3.120 nonbonded pdb=" OH TYR D 41 " pdb=" OG1 THR A 500 " model vdw 2.272 3.040 ... (remaining 77048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.000 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 10335 Z= 0.334 Angle : 0.857 9.732 14076 Z= 0.487 Chirality : 0.056 0.311 1531 Planarity : 0.006 0.054 1801 Dihedral : 14.527 89.957 3658 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 1.19 % Allowed : 4.87 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -2.44 (0.22), residues: 1223 helix: -1.66 (0.24), residues: 387 sheet: -0.12 (0.34), residues: 214 loop : -2.15 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 518 TYR 0.018 0.002 TYR A 421 PHE 0.024 0.003 PHE A 543 TRP 0.036 0.003 TRP D 594 HIS 0.007 0.002 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.33 (10311) covalent geometry : angle 0.84368 / 0.48 (14023) SS BOND : bond 0.00651 / 0.47 ( 13) SS BOND : angle 2.12785 / 1.31 ( 26) hydrogen bonds : bond 0.14205 / 9.14 ( 383) hydrogen bonds : angle 6.66995 / 4.63 ( 1056) metal coordination : bond 0.00192 / 0.10 ( 2) link_BETA1-4 : bond 0.00018 / 0.01 ( 1) link_BETA1-4 : angle 1.65423 / 0.87 ( 3) link_NAG-ASN : bond 0.00522 / 0.39 ( 8) link_NAG-ASN : angle 3.05948 / 1.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 350 ASP cc_start: 0.8324 (t0) cc_final: 0.7849 (p0) REVERT: A 322 PRO cc_start: 0.5932 (Cg_exo) cc_final: 0.5647 (Cg_endo) outliers start: 13 outliers final: 2 residues processed: 147 average time/residue: 0.0718 time to fit residues: 15.8695 Evaluate side-chains 64 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 24 GLN D 287 GLN D 325 GLN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN A 66 HIS A 115 GLN A 164 ASN A 218 GLN A 239 GLN A 317 ASN A 321 GLN A 439 ASN A 580 GLN A 658 ASN A 675 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.072715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049577 restraints weight = 72635.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049835 restraints weight = 35688.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050805 restraints weight = 22858.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050800 restraints weight = 20933.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051085 restraints weight = 18210.409| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10335 Z= 0.164 Angle : 0.672 10.579 14076 Z= 0.348 Chirality : 0.046 0.212 1531 Planarity : 0.005 0.054 1801 Dihedral : 5.144 26.567 1337 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.47 (0.22), residues: 1223 helix: -0.20 (0.26), residues: 386 sheet: -0.09 (0.35), residues: 211 loop : -1.82 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 161 TYR 0.021 0.002 TYR D 199 PHE 0.015 0.002 PHE A 318 TRP 0.020 0.002 TRP A 152 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (10311) covalent geometry : angle 0.65926 / 0.34 (14023) SS BOND : bond 0.00273 / 0.17 ( 13) SS BOND : angle 1.87497 / 1.13 ( 26) hydrogen bonds : bond 0.04579 / 2.92 ( 383) hydrogen bonds : angle 5.33988 / 3.75 ( 1056) metal coordination : bond 0.00195 / 0.10 ( 2) link_BETA1-4 : bond 0.00128 / 0.07 ( 1) link_BETA1-4 : angle 1.98745 / 1.06 ( 3) link_NAG-ASN : bond 0.00480 / 0.33 ( 8) link_NAG-ASN : angle 2.62641 / 1.67 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.9586 (ttp) cc_final: 0.9305 (ttp) REVERT: D 557 MET cc_start: 0.9303 (tmm) cc_final: 0.9021 (tmm) REVERT: A 79 PHE cc_start: 0.8533 (t80) cc_final: 0.7647 (t80) REVERT: A 101 ILE cc_start: 0.8881 (pt) cc_final: 0.8545 (mp) outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.0625 time to fit residues: 7.0838 Evaluate side-chains 46 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 96 GLN ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN A 641 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.072034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.046070 restraints weight = 75012.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048426 restraints weight = 33907.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049917 restraints weight = 21155.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.050673 restraints weight = 15630.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051448 restraints weight = 13102.033| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10335 Z= 0.135 Angle : 0.586 6.648 14076 Z= 0.302 Chirality : 0.044 0.183 1531 Planarity : 0.004 0.052 1801 Dihedral : 4.720 25.985 1337 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.86 (0.24), residues: 1223 helix: 0.52 (0.27), residues: 379 sheet: 0.23 (0.36), residues: 210 loop : -1.57 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 219 TYR 0.027 0.001 TYR A 396 PHE 0.011 0.001 PHE D 512 TRP 0.017 0.001 TRP D 271 HIS 0.005 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10311) covalent geometry : angle 0.57300 / 0.30 (14023) SS BOND : bond 0.00210 / 0.14 ( 13) SS BOND : angle 1.70902 / 1.10 ( 26) hydrogen bonds : bond 0.03999 / 2.52 ( 383) hydrogen bonds : angle 4.93967 / 3.43 ( 1056) metal coordination : bond 0.00198 / 0.10 ( 2) link_BETA1-4 : bond 0.00262 / 0.14 ( 1) link_BETA1-4 : angle 1.46101 / 0.79 ( 3) link_NAG-ASN : bond 0.00439 / 0.31 ( 8) link_NAG-ASN : angle 2.40850 / 1.54 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 222 LEU cc_start: 0.9596 (tp) cc_final: 0.9385 (tp) REVERT: D 557 MET cc_start: 0.9294 (tmm) cc_final: 0.8912 (tmm) REVERT: A 79 PHE cc_start: 0.8390 (t80) cc_final: 0.7634 (t80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0660 time to fit residues: 6.7742 Evaluate side-chains 46 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 121 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 63 optimal weight: 8.9990 chunk 94 optimal weight: 0.0470 chunk 83 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.071863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.045800 restraints weight = 92156.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.049165 restraints weight = 42099.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051162 restraints weight = 19905.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051161 restraints weight = 16327.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051324 restraints weight = 13660.652| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10335 Z= 0.111 Angle : 0.559 7.414 14076 Z= 0.286 Chirality : 0.043 0.183 1531 Planarity : 0.004 0.050 1801 Dihedral : 4.561 24.836 1337 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.68 (0.24), residues: 1223 helix: 0.67 (0.27), residues: 379 sheet: 0.39 (0.37), residues: 210 loop : -1.48 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 306 TYR 0.018 0.001 TYR A 396 PHE 0.010 0.001 PHE D 315 TRP 0.015 0.001 TRP D 302 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (10311) covalent geometry : angle 0.54858 / 0.28 (14023) SS BOND : bond 0.00205 / 0.16 ( 13) SS BOND : angle 1.38740 / 0.89 ( 26) hydrogen bonds : bond 0.03601 / 2.27 ( 383) hydrogen bonds : angle 4.77863 / 3.34 ( 1056) metal coordination : bond 0.00275 / 0.14 ( 2) link_BETA1-4 : bond 0.00447 / 0.24 ( 1) link_BETA1-4 : angle 1.37573 / 0.75 ( 3) link_NAG-ASN : bond 0.00412 / 0.29 ( 8) link_NAG-ASN : angle 2.33259 / 1.49 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 312 GLU cc_start: 0.9195 (tt0) cc_final: 0.8984 (tt0) REVERT: D 376 MET cc_start: 0.9176 (tpp) cc_final: 0.8952 (tpp) REVERT: D 557 MET cc_start: 0.9303 (tmm) cc_final: 0.8875 (tmm) REVERT: A 79 PHE cc_start: 0.8495 (t80) cc_final: 0.7670 (t80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0676 time to fit residues: 6.6220 Evaluate side-chains 47 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 0.0040 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 71 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 50 optimal weight: 0.0370 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.3270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 34 HIS A ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.072054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045725 restraints weight = 92547.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.048258 restraints weight = 39009.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049877 restraints weight = 23260.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.050939 restraints weight = 16797.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.051617 restraints weight = 13548.745| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10335 Z= 0.093 Angle : 0.529 7.718 14076 Z= 0.269 Chirality : 0.043 0.185 1531 Planarity : 0.003 0.053 1801 Dihedral : 4.315 23.219 1337 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.09 % Allowed : 1.10 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.46 (0.24), residues: 1223 helix: 0.88 (0.28), residues: 382 sheet: 0.51 (0.36), residues: 214 loop : -1.39 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.016 0.001 TYR A 396 PHE 0.012 0.001 PHE D 315 TRP 0.016 0.001 TRP A 353 HIS 0.005 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (10311) covalent geometry : angle 0.51957 / 0.27 (14023) SS BOND : bond 0.00416 / 0.24 ( 13) SS BOND : angle 0.96380 / 0.60 ( 26) hydrogen bonds : bond 0.03313 / 2.08 ( 383) hydrogen bonds : angle 4.58846 / 3.22 ( 1056) metal coordination : bond 0.00065 / 0.03 ( 2) link_BETA1-4 : bond 0.00441 / 0.23 ( 1) link_BETA1-4 : angle 1.36296 / 0.75 ( 3) link_NAG-ASN : bond 0.00483 / 0.33 ( 8) link_NAG-ASN : angle 2.28012 / 1.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: D 62 MET cc_start: 0.9115 (ttm) cc_final: 0.8893 (mtm) REVERT: A 55 PHE cc_start: 0.8842 (m-10) cc_final: 0.8592 (m-10) REVERT: A 79 PHE cc_start: 0.8396 (t80) cc_final: 0.7596 (t80) REVERT: A 229 LEU cc_start: 0.9244 (mt) cc_final: 0.8916 (tp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0764 time to fit residues: 7.3933 Evaluate side-chains 44 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.071397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.049001 restraints weight = 67999.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.048817 restraints weight = 34998.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049534 restraints weight = 24103.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.049970 restraints weight = 19642.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050102 restraints weight = 17642.978| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10335 Z= 0.105 Angle : 0.530 9.143 14076 Z= 0.268 Chirality : 0.043 0.191 1531 Planarity : 0.003 0.051 1801 Dihedral : 4.276 29.863 1337 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.09 % Allowed : 1.10 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.32 (0.24), residues: 1223 helix: 1.07 (0.28), residues: 382 sheet: 0.62 (0.36), residues: 209 loop : -1.35 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 204 TYR 0.015 0.001 TYR A 396 PHE 0.014 0.001 PHE D 327 TRP 0.013 0.001 TRP D 302 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (10311) covalent geometry : angle 0.51956 / 0.27 (14023) SS BOND : bond 0.00094 / 0.06 ( 13) SS BOND : angle 1.06083 / 0.69 ( 26) hydrogen bonds : bond 0.03277 / 2.04 ( 383) hydrogen bonds : angle 4.52037 / 3.18 ( 1056) metal coordination : bond 0.00195 / 0.10 ( 2) link_BETA1-4 : bond 0.00226 / 0.12 ( 1) link_BETA1-4 : angle 1.42649 / 0.78 ( 3) link_NAG-ASN : bond 0.00599 / 0.36 ( 8) link_NAG-ASN : angle 2.34795 / 1.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: D 62 MET cc_start: 0.9370 (ttm) cc_final: 0.9098 (mtm) REVERT: D 249 MET cc_start: 0.8706 (mmt) cc_final: 0.8134 (mmm) REVERT: D 557 MET cc_start: 0.9279 (tmm) cc_final: 0.9019 (tmm) REVERT: A 79 PHE cc_start: 0.8551 (t80) cc_final: 0.7719 (t80) REVERT: A 229 LEU cc_start: 0.9262 (mt) cc_final: 0.8996 (tp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0676 time to fit residues: 5.4969 Evaluate side-chains 41 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 60 optimal weight: 0.6980 chunk 102 optimal weight: 0.0060 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 91 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.071608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049242 restraints weight = 66610.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.049074 restraints weight = 34754.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049707 restraints weight = 24145.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050165 restraints weight = 19851.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.050307 restraints weight = 17751.555| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10335 Z= 0.097 Angle : 0.526 8.319 14076 Z= 0.267 Chirality : 0.042 0.181 1531 Planarity : 0.003 0.048 1801 Dihedral : 4.158 25.272 1337 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.09 % Allowed : 1.19 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.19 (0.24), residues: 1223 helix: 1.14 (0.28), residues: 384 sheet: 0.81 (0.36), residues: 209 loop : -1.30 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 306 TYR 0.014 0.001 TYR A 396 PHE 0.014 0.001 PHE D 428 TRP 0.008 0.001 TRP D 459 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (10311) covalent geometry : angle 0.51660 / 0.26 (14023) SS BOND : bond 0.00117 / 0.07 ( 13) SS BOND : angle 1.17866 / 0.72 ( 26) hydrogen bonds : bond 0.03142 / 1.95 ( 383) hydrogen bonds : angle 4.46380 / 3.15 ( 1056) metal coordination : bond 0.00265 / 0.14 ( 2) link_BETA1-4 : bond 0.00321 / 0.17 ( 1) link_BETA1-4 : angle 1.35637 / 0.74 ( 3) link_NAG-ASN : bond 0.00533 / 0.34 ( 8) link_NAG-ASN : angle 2.21273 / 1.40 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: D 557 MET cc_start: 0.9256 (tmm) cc_final: 0.8929 (tmm) REVERT: A 79 PHE cc_start: 0.8513 (t80) cc_final: 0.7722 (t80) REVERT: A 229 LEU cc_start: 0.9300 (mt) cc_final: 0.8983 (tp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0661 time to fit residues: 5.6162 Evaluate side-chains 41 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 71 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.070476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.043943 restraints weight = 96792.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046378 restraints weight = 40426.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047954 restraints weight = 24297.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048874 restraints weight = 17593.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049577 restraints weight = 14475.799| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10335 Z= 0.137 Angle : 0.550 7.933 14076 Z= 0.282 Chirality : 0.043 0.189 1531 Planarity : 0.004 0.042 1801 Dihedral : 4.212 26.198 1337 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.14 (0.24), residues: 1223 helix: 1.21 (0.28), residues: 385 sheet: 0.68 (0.36), residues: 212 loop : -1.24 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.015 0.001 TYR A 396 PHE 0.019 0.001 PHE D 315 TRP 0.016 0.001 TRP D 473 HIS 0.007 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (10311) covalent geometry : angle 0.53980 / 0.28 (14023) SS BOND : bond 0.00159 / 0.11 ( 13) SS BOND : angle 1.35939 / 0.90 ( 26) hydrogen bonds : bond 0.03463 / 2.17 ( 383) hydrogen bonds : angle 4.57281 / 3.22 ( 1056) metal coordination : bond 0.00321 / 0.17 ( 2) link_BETA1-4 : bond 0.00256 / 0.13 ( 1) link_BETA1-4 : angle 1.48484 / 0.81 ( 3) link_NAG-ASN : bond 0.00412 / 0.27 ( 8) link_NAG-ASN : angle 2.26667 / 1.44 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 557 MET cc_start: 0.9346 (tmm) cc_final: 0.8964 (tmm) REVERT: A 79 PHE cc_start: 0.8579 (t80) cc_final: 0.7776 (t80) REVERT: A 229 LEU cc_start: 0.9222 (mt) cc_final: 0.8905 (tp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0736 time to fit residues: 6.2957 Evaluate side-chains 40 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 72 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 71 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.070938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.044620 restraints weight = 92200.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.047025 restraints weight = 39521.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048579 restraints weight = 23952.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049594 restraints weight = 17396.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.050231 restraints weight = 14190.285| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10335 Z= 0.096 Angle : 0.514 8.009 14076 Z= 0.262 Chirality : 0.043 0.182 1531 Planarity : 0.003 0.048 1801 Dihedral : 4.114 24.170 1337 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.06 (0.24), residues: 1223 helix: 1.29 (0.28), residues: 386 sheet: 0.75 (0.36), residues: 209 loop : -1.20 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 460 TYR 0.013 0.001 TYR A 396 PHE 0.017 0.001 PHE D 315 TRP 0.009 0.001 TRP D 473 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (10311) covalent geometry : angle 0.50393 / 0.26 (14023) SS BOND : bond 0.00140 / 0.09 ( 13) SS BOND : angle 1.11321 / 0.73 ( 26) hydrogen bonds : bond 0.03194 / 2.01 ( 383) hydrogen bonds : angle 4.47931 / 3.17 ( 1056) metal coordination : bond 0.00167 / 0.09 ( 2) link_BETA1-4 : bond 0.00413 / 0.22 ( 1) link_BETA1-4 : angle 1.40834 / 0.78 ( 3) link_NAG-ASN : bond 0.00441 / 0.31 ( 8) link_NAG-ASN : angle 2.22695 / 1.41 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 557 MET cc_start: 0.9358 (tmm) cc_final: 0.9009 (tmm) REVERT: A 79 PHE cc_start: 0.8592 (t80) cc_final: 0.7779 (t80) REVERT: A 229 LEU cc_start: 0.9205 (mt) cc_final: 0.8888 (tp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0694 time to fit residues: 6.1185 Evaluate side-chains 40 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.070293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.043756 restraints weight = 98366.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.046159 restraints weight = 41221.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047764 restraints weight = 24734.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048774 restraints weight = 17895.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049389 restraints weight = 14530.943| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10335 Z= 0.113 Angle : 0.529 8.221 14076 Z= 0.269 Chirality : 0.042 0.183 1531 Planarity : 0.003 0.046 1801 Dihedral : 4.093 23.049 1337 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.04 (0.24), residues: 1223 helix: 1.34 (0.28), residues: 386 sheet: 0.72 (0.36), residues: 209 loop : -1.20 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 204 TYR 0.014 0.001 TYR A 396 PHE 0.013 0.001 PHE D 315 TRP 0.010 0.001 TRP D 610 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10311) covalent geometry : angle 0.51893 / 0.27 (14023) SS BOND : bond 0.00129 / 0.09 ( 13) SS BOND : angle 1.19339 / 0.78 ( 26) hydrogen bonds : bond 0.03251 / 2.05 ( 383) hydrogen bonds : angle 4.45867 / 3.14 ( 1056) metal coordination : bond 0.00269 / 0.14 ( 2) link_BETA1-4 : bond 0.00245 / 0.13 ( 1) link_BETA1-4 : angle 1.47727 / 0.81 ( 3) link_NAG-ASN : bond 0.00414 / 0.27 ( 8) link_NAG-ASN : angle 2.25813 / 1.43 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 557 MET cc_start: 0.9373 (tmm) cc_final: 0.8965 (tmm) REVERT: A 79 PHE cc_start: 0.8654 (t80) cc_final: 0.7826 (t80) REVERT: A 229 LEU cc_start: 0.9230 (mt) cc_final: 0.8912 (tp) REVERT: A 595 VAL cc_start: 0.7873 (t) cc_final: 0.7531 (t) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0564 time to fit residues: 4.6664 Evaluate side-chains 39 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 89 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.070023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.044626 restraints weight = 69126.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046665 restraints weight = 34251.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047995 restraints weight = 22271.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048645 restraints weight = 16925.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049366 restraints weight = 14430.633| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10335 Z= 0.118 Angle : 0.529 7.600 14076 Z= 0.269 Chirality : 0.043 0.179 1531 Planarity : 0.004 0.046 1801 Dihedral : 4.109 21.944 1337 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.02 (0.24), residues: 1223 helix: 1.34 (0.28), residues: 386 sheet: 0.67 (0.37), residues: 206 loop : -1.15 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.014 0.001 TYR A 396 PHE 0.015 0.001 PHE D 315 TRP 0.011 0.001 TRP D 610 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (10311) covalent geometry : angle 0.51820 / 0.27 (14023) SS BOND : bond 0.00158 / 0.11 ( 13) SS BOND : angle 1.19789 / 0.79 ( 26) hydrogen bonds : bond 0.03297 / 2.08 ( 383) hydrogen bonds : angle 4.43684 / 3.13 ( 1056) metal coordination : bond 0.00272 / 0.14 ( 2) link_BETA1-4 : bond 0.00254 / 0.13 ( 1) link_BETA1-4 : angle 1.46903 / 0.81 ( 3) link_NAG-ASN : bond 0.00402 / 0.27 ( 8) link_NAG-ASN : angle 2.34767 / 1.50 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.32 seconds wall clock time: 30 minutes 7.84 seconds (1807.84 seconds total)