Starting phenix.real_space_refine on Wed Mar 4 02:16:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a92_11682/03_2026/7a92_11682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a92_11682/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7a92_11682/03_2026/7a92_11682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a92_11682/03_2026/7a92_11682.map" model { file = "/net/cci-nas-00/data/ceres_data/7a92_11682/03_2026/7a92_11682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a92_11682/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.91, per 1000 atoms: 0.29 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: 0.78 Conformation dependent library (CDL) restraints added in 647.5 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: 0.28 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: 1.26 Time building geometry restraints manager: 1.06 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: 5591 17.99 - 35.98: 458 35.98 - 53.97: 121 53.97 - 71.97: 20 71.97 - 89.96: 12 Dihedral angle restraints: 6202 sinusoidal: 2593 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 6199 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: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.190 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 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 : 14.642 89.957 3847 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 covalent geometry : bond 0.00676 (10311) covalent geometry : angle 0.84368 (14023) SS BOND : bond 0.00651 ( 13) SS BOND : angle 2.12785 ( 26) hydrogen bonds : bond 0.14205 ( 383) hydrogen bonds : angle 6.66995 ( 1056) metal coordination : bond 0.00192 ( 2) link_BETA1-4 : bond 0.00018 ( 1) link_BETA1-4 : angle 1.65423 ( 3) link_NAG-ASN : bond 0.00522 ( 8) link_NAG-ASN : angle 3.05948 ( 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 : 0.289 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: 0.0825 time to fit residues: 17.9686 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 : 0.335 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: D 24 GLN D 287 GLN D 325 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 580 GLN A 658 ASN A 675 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.073290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.050128 restraints weight = 73095.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.050316 restraints weight = 35572.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051272 restraints weight = 23226.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051247 restraints weight = 21394.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.051484 restraints weight = 18199.842| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 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 = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10335 Z= 0.167 Angle : 0.669 12.105 14076 Z= 0.348 Chirality : 0.046 0.235 1531 Planarity : 0.005 0.052 1801 Dihedral : 6.939 56.660 1526 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % 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: -1.45 (0.23), residues: 1223 helix: -0.20 (0.26), residues: 386 sheet: -0.07 (0.34), residues: 217 loop : -1.82 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 161 TYR 0.020 0.002 TYR A 421 PHE 0.015 0.002 PHE A 377 TRP 0.019 0.002 TRP A 152 HIS 0.010 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00359 (10311) covalent geometry : angle 0.65551 (14023) SS BOND : bond 0.00271 ( 13) SS BOND : angle 1.96297 ( 26) hydrogen bonds : bond 0.04802 ( 383) hydrogen bonds : angle 5.35891 ( 1056) metal coordination : bond 0.00193 ( 2) link_BETA1-4 : bond 0.00000 ( 1) link_BETA1-4 : angle 1.92180 ( 3) link_NAG-ASN : bond 0.00437 ( 8) link_NAG-ASN : angle 2.65441 ( 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 71 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.9613 (ttp) cc_final: 0.9380 (ttp) REVERT: D 267 LEU cc_start: 0.9222 (mt) cc_final: 0.8946 (mm) REVERT: D 557 MET cc_start: 0.9263 (tmm) cc_final: 0.8820 (tmm) REVERT: D 595 LEU cc_start: 0.9399 (mt) cc_final: 0.9076 (tp) REVERT: D 599 ASN cc_start: 0.8173 (m-40) cc_final: 0.7795 (p0) REVERT: A 79 PHE cc_start: 0.8534 (t80) cc_final: 0.7679 (t80) REVERT: A 101 ILE cc_start: 0.8825 (pt) cc_final: 0.8487 (mp) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.0679 time to fit residues: 7.8568 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 : 0.391 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 121 optimal weight: 7.9990 chunk 88 optimal weight: 0.1980 chunk 66 optimal weight: 0.0770 chunk 98 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.073378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047536 restraints weight = 73871.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049956 restraints weight = 33436.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.051510 restraints weight = 20652.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.052503 restraints weight = 15163.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053168 restraints weight = 12386.832| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10335 Z= 0.112 Angle : 0.573 6.740 14076 Z= 0.296 Chirality : 0.044 0.192 1531 Planarity : 0.004 0.054 1801 Dihedral : 6.404 56.219 1526 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: -0.88 (0.23), residues: 1223 helix: 0.53 (0.27), residues: 378 sheet: 0.31 (0.36), residues: 205 loop : -1.62 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 161 TYR 0.027 0.001 TYR A 396 PHE 0.011 0.001 PHE A 592 TRP 0.013 0.001 TRP D 459 HIS 0.005 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00238 (10311) covalent geometry : angle 0.56060 (14023) SS BOND : bond 0.00312 ( 13) SS BOND : angle 1.63157 ( 26) hydrogen bonds : bond 0.03816 ( 383) hydrogen bonds : angle 4.92380 ( 1056) metal coordination : bond 0.00126 ( 2) link_BETA1-4 : bond 0.00519 ( 1) link_BETA1-4 : angle 1.49606 ( 3) link_NAG-ASN : bond 0.00503 ( 8) link_NAG-ASN : angle 2.39058 ( 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 76 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 222 LEU cc_start: 0.9590 (tp) cc_final: 0.9365 (tp) REVERT: D 323 MET cc_start: 0.9006 (tpp) cc_final: 0.8801 (mmm) REVERT: D 474 MET cc_start: 0.8754 (mmm) cc_final: 0.8488 (mmm) REVERT: D 557 MET cc_start: 0.9260 (tmm) cc_final: 0.8863 (tmm) REVERT: D 595 LEU cc_start: 0.9352 (mt) cc_final: 0.9025 (tp) REVERT: D 599 ASN cc_start: 0.7987 (m-40) cc_final: 0.7723 (p0) REVERT: A 79 PHE cc_start: 0.8336 (t80) cc_final: 0.7570 (t80) REVERT: A 101 ILE cc_start: 0.8859 (pt) cc_final: 0.8555 (mp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0678 time to fit residues: 8.2572 Evaluate side-chains 51 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 10.0000 chunk 118 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** 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 = 0.3624 r_free = 0.3624 target = 0.072356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.045956 restraints weight = 91195.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048517 restraints weight = 38332.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050178 restraints weight = 22840.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.051271 restraints weight = 16323.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.051970 restraints weight = 13111.463| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 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 = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10335 Z= 0.115 Angle : 0.554 7.325 14076 Z= 0.283 Chirality : 0.043 0.183 1531 Planarity : 0.004 0.054 1801 Dihedral : 5.836 55.684 1526 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -0.60 (0.24), residues: 1223 helix: 0.78 (0.28), residues: 380 sheet: 0.39 (0.36), residues: 213 loop : -1.45 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 161 TYR 0.018 0.001 TYR A 396 PHE 0.011 0.001 PHE D 504 TRP 0.011 0.001 TRP D 459 HIS 0.006 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00248 (10311) covalent geometry : angle 0.54359 (14023) SS BOND : bond 0.00160 ( 13) SS BOND : angle 1.21459 ( 26) hydrogen bonds : bond 0.03577 ( 383) hydrogen bonds : angle 4.71276 ( 1056) metal coordination : bond 0.00136 ( 2) link_BETA1-4 : bond 0.00412 ( 1) link_BETA1-4 : angle 1.46841 ( 3) link_NAG-ASN : bond 0.00409 ( 8) link_NAG-ASN : angle 2.29307 ( 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 65 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 557 MET cc_start: 0.9366 (tmm) cc_final: 0.8922 (tmm) REVERT: D 595 LEU cc_start: 0.9404 (mt) cc_final: 0.9094 (tp) REVERT: A 79 PHE cc_start: 0.8368 (t80) cc_final: 0.7642 (t80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0720 time to fit residues: 7.6822 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 : 0.370 ------------------------------------------------------------------------------- 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: 2.9990 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 60 optimal weight: 0.0020 chunk 50 optimal weight: 0.0070 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS A ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.072498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.046142 restraints weight = 91835.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.048688 restraints weight = 38061.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050323 restraints weight = 22801.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051399 restraints weight = 16427.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051929 restraints weight = 13243.718| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 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 = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3619 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= 0.101 Angle : 0.541 8.366 14076 Z= 0.275 Chirality : 0.043 0.183 1531 Planarity : 0.003 0.051 1801 Dihedral : 5.647 55.500 1526 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: -0.44 (0.24), residues: 1223 helix: 0.86 (0.28), residues: 383 sheet: 0.43 (0.36), residues: 215 loop : -1.32 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.016 0.001 TYR A 396 PHE 0.013 0.001 PHE D 315 TRP 0.013 0.001 TRP A 353 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00217 (10311) covalent geometry : angle 0.53030 (14023) SS BOND : bond 0.00120 ( 13) SS BOND : angle 1.23819 ( 26) hydrogen bonds : bond 0.03355 ( 383) hydrogen bonds : angle 4.59479 ( 1056) metal coordination : bond 0.00230 ( 2) link_BETA1-4 : bond 0.00133 ( 1) link_BETA1-4 : angle 1.57264 ( 3) link_NAG-ASN : bond 0.00487 ( 8) link_NAG-ASN : angle 2.34069 ( 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 61 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 595 LEU cc_start: 0.9402 (mt) cc_final: 0.9086 (tp) REVERT: A 79 PHE cc_start: 0.8360 (t80) cc_final: 0.7557 (t80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0771 time to fit residues: 7.5056 Evaluate side-chains 48 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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: 0.5980 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.071265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.048554 restraints weight = 68006.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.048638 restraints weight = 36561.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.049291 restraints weight = 24269.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.049304 restraints weight = 22669.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.049478 restraints weight = 19232.389| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4014 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= 0.129 Angle : 0.553 9.475 14076 Z= 0.281 Chirality : 0.043 0.206 1531 Planarity : 0.004 0.051 1801 Dihedral : 5.589 56.113 1526 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.14 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: -0.34 (0.24), residues: 1223 helix: 0.91 (0.27), residues: 384 sheet: 0.61 (0.37), residues: 209 loop : -1.27 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 204 TYR 0.017 0.001 TYR A 396 PHE 0.015 0.001 PHE D 315 TRP 0.012 0.001 TRP D 473 HIS 0.006 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00276 (10311) covalent geometry : angle 0.54337 (14023) SS BOND : bond 0.00548 ( 13) SS BOND : angle 1.21400 ( 26) hydrogen bonds : bond 0.03480 ( 383) hydrogen bonds : angle 4.54593 ( 1056) metal coordination : bond 0.00334 ( 2) link_BETA1-4 : bond 0.00203 ( 1) link_BETA1-4 : angle 1.55906 ( 3) link_NAG-ASN : bond 0.00399 ( 8) link_NAG-ASN : angle 2.25546 ( 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 53 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 249 MET cc_start: 0.8766 (mmt) cc_final: 0.8172 (mmm) REVERT: D 557 MET cc_start: 0.9354 (tmm) cc_final: 0.9071 (tmm) REVERT: D 595 LEU cc_start: 0.9494 (mt) cc_final: 0.9191 (tp) REVERT: A 79 PHE cc_start: 0.8628 (t80) cc_final: 0.7777 (t80) REVERT: A 229 LEU cc_start: 0.9227 (mt) cc_final: 0.8945 (tp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0674 time to fit residues: 5.9568 Evaluate side-chains 42 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 7.9990 chunk 102 optimal weight: 0.0270 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.0170 chunk 91 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 0.0070 chunk 95 optimal weight: 0.5980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.072261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.048871 restraints weight = 66254.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.049555 restraints weight = 35246.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.050135 restraints weight = 23174.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050307 restraints weight = 20442.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051059 restraints weight = 17413.574| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10335 Z= 0.090 Angle : 0.520 8.733 14076 Z= 0.261 Chirality : 0.043 0.185 1531 Planarity : 0.003 0.052 1801 Dihedral : 5.404 55.171 1526 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.09 % Allowed : 1.01 % Favored : 98.90 % 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: 1.19 (0.28), residues: 383 sheet: 0.80 (0.36), residues: 209 loop : -1.27 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.013 0.001 TYR A 396 PHE 0.015 0.001 PHE D 315 TRP 0.009 0.001 TRP D 459 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00188 (10311) covalent geometry : angle 0.51049 (14023) SS BOND : bond 0.00140 ( 13) SS BOND : angle 0.98974 ( 26) hydrogen bonds : bond 0.03024 ( 383) hydrogen bonds : angle 4.41121 ( 1056) metal coordination : bond 0.00107 ( 2) link_BETA1-4 : bond 0.00526 ( 1) link_BETA1-4 : angle 1.50631 ( 3) link_NAG-ASN : bond 0.00491 ( 8) link_NAG-ASN : angle 2.21568 ( 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 57 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: D 480 MET cc_start: 0.9502 (mmm) cc_final: 0.9298 (mmm) REVERT: D 557 MET cc_start: 0.9281 (tmm) cc_final: 0.8938 (tmm) REVERT: D 595 LEU cc_start: 0.9433 (mt) cc_final: 0.9109 (tp) REVERT: A 55 PHE cc_start: 0.8713 (m-10) cc_final: 0.8483 (m-10) REVERT: A 79 PHE cc_start: 0.8572 (t80) cc_final: 0.7738 (t80) REVERT: A 229 LEU cc_start: 0.9273 (mt) cc_final: 0.8995 (tp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0646 time to fit residues: 6.2447 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 : 0.345 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 0.0670 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 3 optimal weight: 0.0670 chunk 71 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 GLN D 535 HIS ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.070889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.044953 restraints weight = 97256.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.048417 restraints weight = 42582.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049661 restraints weight = 19101.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049576 restraints weight = 17529.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049702 restraints weight = 15514.662| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10335 Z= 0.127 Angle : 0.540 7.847 14076 Z= 0.275 Chirality : 0.043 0.195 1531 Planarity : 0.004 0.055 1801 Dihedral : 5.443 55.576 1526 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.09 % Allowed : 0.37 % 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: -0.05 (0.24), residues: 1223 helix: 1.27 (0.28), residues: 383 sheet: 0.75 (0.37), residues: 206 loop : -1.16 (0.24), residues: 634 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 0.012 0.001 PHE D 315 TRP 0.010 0.001 TRP D 473 HIS 0.007 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00275 (10311) covalent geometry : angle 0.52917 (14023) SS BOND : bond 0.00562 ( 13) SS BOND : angle 1.50504 ( 26) hydrogen bonds : bond 0.03290 ( 383) hydrogen bonds : angle 4.44948 ( 1056) metal coordination : bond 0.00271 ( 2) link_BETA1-4 : bond 0.00335 ( 1) link_BETA1-4 : angle 1.60552 ( 3) link_NAG-ASN : bond 0.00379 ( 8) link_NAG-ASN : angle 2.22265 ( 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 55 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: D 557 MET cc_start: 0.9291 (tmm) cc_final: 0.8912 (tmm) REVERT: D 595 LEU cc_start: 0.9469 (mt) cc_final: 0.9159 (tp) REVERT: A 79 PHE cc_start: 0.8569 (t80) cc_final: 0.7763 (t80) REVERT: A 229 LEU cc_start: 0.9236 (mt) cc_final: 0.8947 (tp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0731 time to fit residues: 6.6346 Evaluate side-chains 42 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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: 0.6980 chunk 64 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 71 optimal weight: 0.2980 chunk 43 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.071202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.044965 restraints weight = 92541.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047374 restraints weight = 39686.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048897 restraints weight = 24064.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.049883 restraints weight = 17664.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.050363 restraints weight = 14442.823| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10335 Z= 0.100 Angle : 0.519 7.909 14076 Z= 0.263 Chirality : 0.042 0.180 1531 Planarity : 0.003 0.053 1801 Dihedral : 5.392 55.576 1526 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.09 % Allowed : 0.73 % Favored : 99.17 % 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: 1.35 (0.28), residues: 384 sheet: 0.85 (0.36), residues: 208 loop : -1.13 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 460 TYR 0.014 0.001 TYR A 396 PHE 0.016 0.001 PHE D 315 TRP 0.010 0.001 TRP D 459 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00216 (10311) covalent geometry : angle 0.50730 (14023) SS BOND : bond 0.00186 ( 13) SS BOND : angle 1.43113 ( 26) hydrogen bonds : bond 0.03140 ( 383) hydrogen bonds : angle 4.38342 ( 1056) metal coordination : bond 0.00180 ( 2) link_BETA1-4 : bond 0.00410 ( 1) link_BETA1-4 : angle 1.53047 ( 3) link_NAG-ASN : bond 0.00456 ( 8) link_NAG-ASN : angle 2.26407 ( 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 55 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 266 LEU cc_start: 0.9223 (mt) cc_final: 0.9013 (mt) REVERT: D 557 MET cc_start: 0.9313 (tmm) cc_final: 0.8932 (tmm) REVERT: D 595 LEU cc_start: 0.9413 (mt) cc_final: 0.9110 (tp) REVERT: A 79 PHE cc_start: 0.8556 (t80) cc_final: 0.7763 (t80) REVERT: A 229 LEU cc_start: 0.9232 (mt) cc_final: 0.8937 (tp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0581 time to fit residues: 5.3786 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 : 0.296 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 0.0370 chunk 18 optimal weight: 0.0670 chunk 52 optimal weight: 0.6980 chunk 85 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.071745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045466 restraints weight = 97114.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.048008 restraints weight = 40258.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.049624 restraints weight = 23941.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.050668 restraints weight = 17186.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.051349 restraints weight = 13874.198| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10335 Z= 0.086 Angle : 0.520 8.368 14076 Z= 0.260 Chirality : 0.042 0.196 1531 Planarity : 0.003 0.049 1801 Dihedral : 5.262 54.616 1526 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.72 % 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: 0.10 (0.25), residues: 1223 helix: 1.42 (0.28), residues: 384 sheet: 0.89 (0.38), residues: 203 loop : -1.10 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 403 TYR 0.013 0.001 TYR A 396 PHE 0.018 0.001 PHE D 315 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00181 (10311) covalent geometry : angle 0.50934 (14023) SS BOND : bond 0.00254 ( 13) SS BOND : angle 1.32482 ( 26) hydrogen bonds : bond 0.02869 ( 383) hydrogen bonds : angle 4.29221 ( 1056) metal coordination : bond 0.00074 ( 2) link_BETA1-4 : bond 0.00667 ( 1) link_BETA1-4 : angle 1.56696 ( 3) link_NAG-ASN : bond 0.00515 ( 8) link_NAG-ASN : angle 2.17816 ( 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 62 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 266 LEU cc_start: 0.9248 (mt) cc_final: 0.9028 (mt) REVERT: D 297 MET cc_start: 0.8480 (ptt) cc_final: 0.7059 (tmm) REVERT: D 302 TRP cc_start: 0.6661 (m-10) cc_final: 0.6286 (m100) REVERT: D 557 MET cc_start: 0.9340 (tmm) cc_final: 0.8952 (tmm) REVERT: D 595 LEU cc_start: 0.9428 (mt) cc_final: 0.9093 (tp) REVERT: A 55 PHE cc_start: 0.8808 (m-10) cc_final: 0.8551 (m-10) REVERT: A 79 PHE cc_start: 0.8528 (t80) cc_final: 0.7725 (t80) REVERT: A 229 LEU cc_start: 0.9229 (mt) cc_final: 0.8898 (tp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0762 time to fit residues: 7.4153 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 : 0.230 ------------------------------------------------------------------------------- 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: 0.4980 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 121 optimal weight: 0.0270 chunk 77 optimal weight: 0.0170 chunk 58 optimal weight: 0.9980 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.072003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.049437 restraints weight = 68106.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049826 restraints weight = 36183.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049944 restraints weight = 25956.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050156 restraints weight = 23217.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.051096 restraints weight = 19472.711| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4757 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= 0.085 Angle : 0.521 8.006 14076 Z= 0.259 Chirality : 0.042 0.190 1531 Planarity : 0.003 0.044 1801 Dihedral : 5.146 54.232 1526 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % 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: 0.16 (0.25), residues: 1223 helix: 1.46 (0.28), residues: 384 sheet: 0.94 (0.38), residues: 203 loop : -1.07 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.012 0.001 TYR A 396 PHE 0.016 0.001 PHE D 315 TRP 0.009 0.001 TRP D 459 HIS 0.003 0.000 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00182 (10311) covalent geometry : angle 0.51053 (14023) SS BOND : bond 0.00179 ( 13) SS BOND : angle 1.32430 ( 26) hydrogen bonds : bond 0.02795 ( 383) hydrogen bonds : angle 4.28459 ( 1056) metal coordination : bond 0.00054 ( 2) link_BETA1-4 : bond 0.00300 ( 1) link_BETA1-4 : angle 1.51965 ( 3) link_NAG-ASN : bond 0.00515 ( 8) link_NAG-ASN : angle 2.17753 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.21 seconds wall clock time: 34 minutes 6.67 seconds (2046.67 seconds total)