Starting phenix.real_space_refine on Thu Jul 2 05:14:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8a64_15205/07_2026/8a64_15205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a64_15205/07_2026/8a64_15205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a64_15205/07_2026/8a64_15205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a64_15205/07_2026/8a64_15205.map" model { file = "/net/cci-nas-00/data/ceres_data/8a64_15205/07_2026/8a64_15205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a64_15205/07_2026/8a64_15205.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8a64_15205/07_2026/8a64_15205.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8a64_15205/07_2026/8a64_15205.cif" } resolution = 4.6 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= 0.006 sd= 0.041 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: 3 Type Number sf(0) Gaussians C 4010 2.51 5 N 1357 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6737 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 4639 Classifications: {'peptide': 940} Incomplete info: {'truncation_to_alanine': 819} Link IDs: {'PTRANS': 39, 'TRANS': 900} Unresolved chain link angles: 39 Unresolved non-hydrogen bonds: 2967 Unresolved non-hydrogen angles: 3779 Unresolved non-hydrogen dihedrals: 2486 Unresolved non-hydrogen chiralities: 249 Planarities with less than four sites: {'ASP:plan': 75, 'HIS:plan': 14, 'TYR:plan': 37, 'GLU:plan': 64, 'ASN:plan1': 51, 'PHE:plan': 34, 'GLN:plan1': 35, 'ARG:plan': 31, 'TRP:plan': 12} Unresolved non-hydrogen planarities: 1570 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1032 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 191} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 189} Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 673 Unresolved non-hydrogen angles: 868 Unresolved non-hydrogen dihedrals: 576 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 10, 'ARG:plan': 6, 'GLU:plan': 14, 'HIS:plan': 6, 'ASN:plan1': 10, 'TRP:plan': 4, 'TYR:plan': 9, 'GLN:plan1': 9} Unresolved non-hydrogen planarities: 353 Chain: "C" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1027 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 189} Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 875 Unresolved non-hydrogen dihedrals: 579 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 10, 'ARG:plan': 6, 'GLU:plan': 14, 'HIS:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 4, 'TYR:plan': 9, 'GLN:plan1': 9} Unresolved non-hydrogen planarities: 356 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.42, per 1000 atoms: 0.21 Number of scatterers: 6737 At special positions: 0 Unit cell: (135.708, 87.316, 139.916, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1370 8.00 N 1357 7.00 C 4010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN B 297 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 351.3 milliseconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 22 sheets defined 30.2% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.545A pdb=" N SER A 52 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 53 " --> pdb=" O ILE A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 57 through 70 Processing helix chain 'A' and resid 76 through 98 removed outlier: 3.937A pdb=" N GLU A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 158 through 167 removed outlier: 4.515A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 223 through 226 Processing helix chain 'A' and resid 247 through 263 Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.403A pdb=" N GLU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 434 through 446 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.814A pdb=" N LEU A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 519 through 523 Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.952A pdb=" N LYS A 528 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 605 through 622 Processing helix chain 'A' and resid 660 through 665 Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 780 through 788 removed outlier: 4.326A pdb=" N LYS A 786 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A 787 " --> pdb=" O ASN A 783 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 removed outlier: 4.053A pdb=" N ARG A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 866 through 868 No H-bonds generated for 'chain 'A' and resid 866 through 868' Processing helix chain 'A' and resid 926 through 943 Processing helix chain 'A' and resid 948 through 966 removed outlier: 3.830A pdb=" N GLU A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 987 removed outlier: 4.519A pdb=" N ILE A 976 " --> pdb=" O ASP A 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 432 through 436 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 117 removed outlier: 6.267A pdb=" N TYR A 114 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 148 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY A 116 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 179 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP A 231 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG A 181 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP A 233 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 183 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 230 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP A 279 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 232 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU A 301 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N MET A 278 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLN A 303 " --> pdb=" O MET A 278 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 300 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY A 344 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 302 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N SER A 346 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR A 341 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE A 400 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 343 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR A 402 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 345 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU A 113 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER A 401 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY A 115 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 removed outlier: 3.542A pdb=" N VAL A 242 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 487 removed outlier: 5.665A pdb=" N LEU A 507 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER A 560 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU A 509 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 517 through 518 removed outlier: 6.721A pdb=" N LEU A 518 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 531 removed outlier: 3.878A pdb=" N GLY A 530 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 638 through 639 Processing sheet with id=AA8, first strand: chain 'A' and resid 649 through 651 Processing sheet with id=AA9, first strand: chain 'A' and resid 657 through 659 Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 removed outlier: 6.755A pdb=" N TYR A 922 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE A 819 " --> pdb=" O TYR A 922 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU A 818 " --> pdb=" O ASN A 892 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN A 892 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS A 820 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 773 through 775 removed outlier: 3.667A pdb=" N ILE A 810 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N TYR A 897 " --> pdb=" O PHE A 847 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE A 847 " --> pdb=" O TYR A 897 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA A 842 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR A 875 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 844 " --> pdb=" O VAL A 873 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.519A pdb=" N VAL B 302 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 277 through 279 removed outlier: 4.104A pdb=" N TRP B 277 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 319 through 323 Processing sheet with id=AB6, first strand: chain 'B' and resid 347 through 351 removed outlier: 5.551A pdb=" N SER B 364 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 412 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N THR B 366 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 410 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 368 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER B 408 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS B 370 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 406 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 347 through 351 removed outlier: 5.551A pdb=" N SER B 364 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 412 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N THR B 366 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 410 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 368 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER B 408 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS B 370 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 406 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 386 through 387 Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 243 removed outlier: 4.047A pdb=" N ASP C 265 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR C 300 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG C 301 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG C 292 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL C 303 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 282 through 284 Processing sheet with id=AC2, first strand: chain 'C' and resid 347 through 351 removed outlier: 5.408A pdb=" N THR C 366 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 410 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU C 368 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER C 408 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYS C 370 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU C 406 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 347 through 351 removed outlier: 5.408A pdb=" N THR C 366 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 410 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU C 368 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER C 408 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYS C 370 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU C 406 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 379 through 380 391 hydrogen bonds defined for protein. 1005 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: 1.23 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 1357 1.28 - 1.35: 1347 1.35 - 1.42: 9 1.42 - 1.49: 1372 1.49 - 1.56: 2649 Bond restraints: 6734 Sorted by residual: bond pdb=" C VAL A 901 " pdb=" N PHE A 902 " ideal model delta sigma weight residual 1.329 1.296 0.033 1.36e-02 5.41e+03 5.87e+00 bond pdb=" C THR C 350 " pdb=" N LEU C 351 " ideal model delta sigma weight residual 1.333 1.296 0.036 1.59e-02 3.96e+03 5.14e+00 bond pdb=" N THR B 394 " pdb=" CA THR B 394 " ideal model delta sigma weight residual 1.453 1.474 -0.021 9.20e-03 1.18e+04 5.11e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" CA ASN A 848 " pdb=" C ASN A 848 " ideal model delta sigma weight residual 1.523 1.552 -0.029 1.34e-02 5.57e+03 4.60e+00 ... (remaining 6729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 8931 1.72 - 3.45: 410 3.45 - 5.17: 26 5.17 - 6.89: 6 6.89 - 8.62: 2 Bond angle restraints: 9375 Sorted by residual: angle pdb=" CA THR B 299 " pdb=" C THR B 299 " pdb=" O THR B 299 " ideal model delta sigma weight residual 122.31 117.15 5.16 1.31e+00 5.83e-01 1.55e+01 angle pdb=" C VAL A 169 " pdb=" CA VAL A 169 " pdb=" CB VAL A 169 " ideal model delta sigma weight residual 114.00 109.08 4.92 1.31e+00 5.83e-01 1.41e+01 angle pdb=" C LYS A 268 " pdb=" N GLY A 269 " pdb=" CA GLY A 269 " ideal model delta sigma weight residual 122.69 118.98 3.71 1.08e+00 8.57e-01 1.18e+01 angle pdb=" N GLY A 269 " pdb=" CA GLY A 269 " pdb=" C GLY A 269 " ideal model delta sigma weight residual 112.10 117.66 -5.56 1.82e+00 3.02e-01 9.34e+00 angle pdb=" N GLU A 102 " pdb=" CA GLU A 102 " pdb=" C GLU A 102 " ideal model delta sigma weight residual 110.28 105.92 4.36 1.48e+00 4.57e-01 8.67e+00 ... (remaining 9370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.09: 3283 4.09 - 8.19: 395 8.19 - 12.28: 178 12.28 - 16.38: 44 16.38 - 20.47: 8 Dihedral angle restraints: 3908 sinusoidal: 3 harmonic: 3905 Sorted by residual: dihedral pdb=" CA SER B 337 " pdb=" C SER B 337 " pdb=" N LYS B 338 " pdb=" CA LYS B 338 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ALA A 417 " pdb=" C ALA A 417 " pdb=" N LYS A 418 " pdb=" CA LYS A 418 " ideal model delta harmonic sigma weight residual 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA TYR A 909 " pdb=" C TYR A 909 " pdb=" N SER A 910 " pdb=" CA SER A 910 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1208 0.103 - 0.206: 83 0.206 - 0.310: 1 0.310 - 0.413: 0 0.413 - 0.516: 1 Chirality restraints: 1293 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 297 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.92 0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.47 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1290 not shown) Planarity restraints: 1355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 297 " 0.127 2.00e-02 2.50e+03 1.74e-01 3.80e+02 pdb=" CG ASN B 297 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN B 297 " 0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN B 297 " -0.299 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 100 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C ILE A 100 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE A 100 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO A 101 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 297 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ASN B 297 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN B 297 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 298 " -0.010 2.00e-02 2.50e+03 ... (remaining 1352 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 225 2.67 - 3.23: 7294 3.23 - 3.78: 10133 3.78 - 4.34: 11868 4.34 - 4.90: 17827 Nonbonded interactions: 47347 Sorted by model distance: nonbonded pdb=" O LEU A 509 " pdb=" N SER A 560 " model vdw 2.112 3.120 nonbonded pdb=" O ILE A 261 " pdb=" N ILE A 265 " model vdw 2.132 3.120 nonbonded pdb=" O ILE A 343 " pdb=" N PHE A 400 " model vdw 2.132 3.120 nonbonded pdb=" O LEU A 485 " pdb=" N ASP A 508 " model vdw 2.144 3.120 nonbonded pdb=" N ASP C 399 " pdb=" O SER C 403 " model vdw 2.190 3.120 ... (remaining 47342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 237 through 280 and (name N or name CA or name C or name \ O or name CB )) or (resid 281 through 315 and (name N or name CA or name C or na \ me O or name CB )) or resid 316 through 443)) selection = chain 'C' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.350 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.008 0.054 6737 Z= 0.556 Angle : 0.942 23.465 9384 Z= 0.588 Chirality : 0.056 0.516 1293 Planarity : 0.006 0.024 1354 Dihedral : 5.840 20.473 1354 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.55 (0.22), residues: 1348 helix: -1.30 (0.27), residues: 306 sheet: -1.02 (0.28), residues: 316 loop : -0.80 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.56 ( 6734) covalent geometry : angle 0.86284 / 0.57 ( 9375) hydrogen bonds : bond 0.20874 / 15.65 ( 375) hydrogen bonds : angle 9.76324 / 7.21 ( 1005) link_BETA1-4 : bond 0.03058 / 2.03 ( 2) link_BETA1-4 : angle 9.01551 / 3.40 ( 6) link_NAG-ASN : bond 0.01855 / 1.24 ( 1) link_NAG-ASN : angle 16.89220 / 13.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.266 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0299 time to fit residues: 1.4702 Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 50.0000 chunk 55 optimal weight: 9.9990 overall best weight: 11.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.053775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.031581 restraints weight = 89754.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.031581 restraints weight = 84846.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.031581 restraints weight = 84844.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.031581 restraints weight = 84844.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.031581 restraints weight = 84844.220| |-----------------------------------------------------------------------------| r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6737 Z= 0.261 Angle : 0.659 18.173 9384 Z= 0.370 Chirality : 0.046 0.386 1293 Planarity : 0.003 0.014 1354 Dihedral : 5.560 23.414 1351 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.05 (0.23), residues: 1348 helix: -0.26 (0.28), residues: 322 sheet: -1.14 (0.29), residues: 313 loop : -0.56 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.26 ( 6734) covalent geometry : angle 0.62218 / 0.36 ( 9375) hydrogen bonds : bond 0.04895 / 3.67 ( 375) hydrogen bonds : angle 8.10542 / 6.10 ( 1005) link_BETA1-4 : bond 0.03158 / 2.09 ( 2) link_BETA1-4 : angle 8.20924 / 3.26 ( 6) link_NAG-ASN : bond 0.01361 / 0.91 ( 1) link_NAG-ASN : angle 3.75864 / 2.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.187 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0200 time to fit residues: 0.9742 Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 93 optimal weight: 8.9990 chunk 57 optimal weight: 50.0000 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 50.0000 chunk 91 optimal weight: 40.0000 chunk 118 optimal weight: 7.9990 chunk 48 optimal weight: 50.0000 chunk 79 optimal weight: 50.0000 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 17 optimal weight: 5.9990 overall best weight: 11.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030254 restraints weight = 88962.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030254 restraints weight = 83657.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030254 restraints weight = 83657.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030254 restraints weight = 83657.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030254 restraints weight = 83657.532| |-----------------------------------------------------------------------------| r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 6737 Z= 0.245 Angle : 0.650 13.705 9384 Z= 0.356 Chirality : 0.046 0.424 1293 Planarity : 0.003 0.015 1354 Dihedral : 5.336 22.850 1351 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.98 (0.23), residues: 1348 helix: 0.45 (0.29), residues: 326 sheet: -1.64 (0.29), residues: 303 loop : -0.62 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.24 ( 6734) covalent geometry : angle 0.61325 / 0.35 ( 9375) hydrogen bonds : bond 0.04616 / 3.46 ( 375) hydrogen bonds : angle 7.69350 / 5.78 ( 1005) link_BETA1-4 : bond 0.01960 / 1.30 ( 2) link_BETA1-4 : angle 6.95685 / 2.82 ( 6) link_NAG-ASN : bond 0.00157 / 0.10 ( 1) link_NAG-ASN : angle 6.94261 / 4.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.243 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0296 time to fit residues: 1.4107 Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 50.0000 chunk 39 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 55 optimal weight: 40.0000 chunk 10 optimal weight: 50.0000 chunk 45 optimal weight: 40.0000 chunk 83 optimal weight: 0.0060 chunk 105 optimal weight: 9.9990 chunk 131 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 overall best weight: 9.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.051989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.029900 restraints weight = 91366.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.030001 restraints weight = 86189.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.030083 restraints weight = 81552.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.030091 restraints weight = 79245.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.030136 restraints weight = 78740.797| |-----------------------------------------------------------------------------| r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6737 Z= 0.197 Angle : 0.577 18.209 9384 Z= 0.315 Chirality : 0.046 0.528 1293 Planarity : 0.002 0.012 1354 Dihedral : 4.942 21.805 1351 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.84 (0.24), residues: 1348 helix: 0.98 (0.30), residues: 326 sheet: -1.95 (0.29), residues: 282 loop : -0.60 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.20 ( 6734) covalent geometry : angle 0.52614 / 0.31 ( 9375) hydrogen bonds : bond 0.03515 / 2.64 ( 375) hydrogen bonds : angle 7.10423 / 5.32 ( 1005) link_BETA1-4 : bond 0.03051 / 2.03 ( 2) link_BETA1-4 : angle 8.26947 / 3.31 ( 6) link_NAG-ASN : bond 0.01281 / 0.85 ( 1) link_NAG-ASN : angle 6.17882 / 3.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.288 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0330 time to fit residues: 1.5729 Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 7 optimal weight: 50.0000 chunk 2 optimal weight: 30.0000 chunk 121 optimal weight: 40.0000 chunk 86 optimal weight: 0.0030 chunk 13 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 3 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 overall best weight: 6.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.052994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.031547 restraints weight = 91405.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.030987 restraints weight = 87607.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.030806 restraints weight = 86333.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.030834 restraints weight = 80212.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.030831 restraints weight = 77453.745| |-----------------------------------------------------------------------------| r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 6737 Z= 0.144 Angle : 0.528 17.118 9384 Z= 0.281 Chirality : 0.044 0.360 1293 Planarity : 0.002 0.009 1354 Dihedral : 4.467 18.097 1351 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.64 (0.24), residues: 1348 helix: 1.33 (0.30), residues: 341 sheet: -2.03 (0.29), residues: 282 loop : -0.51 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.14 ( 6734) covalent geometry : angle 0.46766 / 0.27 ( 9375) hydrogen bonds : bond 0.03057 / 2.30 ( 375) hydrogen bonds : angle 6.61121 / 4.93 ( 1005) link_BETA1-4 : bond 0.02897 / 1.92 ( 2) link_BETA1-4 : angle 7.85629 / 2.99 ( 6) link_NAG-ASN : bond 0.01051 / 0.70 ( 1) link_NAG-ASN : angle 8.02744 / 4.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.244 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0222 time to fit residues: 1.1078 Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 129 optimal weight: 0.0040 chunk 40 optimal weight: 50.0000 chunk 127 optimal weight: 40.0000 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 50.0000 chunk 11 optimal weight: 50.0000 chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 95 optimal weight: 0.0570 overall best weight: 3.0116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.053566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.031849 restraints weight = 90872.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.031579 restraints weight = 91318.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.031053 restraints weight = 95217.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.031082 restraints weight = 96379.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.031096 restraints weight = 90391.235| |-----------------------------------------------------------------------------| r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6737 Z= 0.094 Angle : 0.482 17.917 9384 Z= 0.251 Chirality : 0.044 0.469 1293 Planarity : 0.002 0.009 1354 Dihedral : 3.940 15.675 1351 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.25), residues: 1348 helix: 1.69 (0.30), residues: 348 sheet: -1.85 (0.30), residues: 265 loop : -0.43 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00144 / 0.09 ( 6734) covalent geometry : angle 0.42063 / 0.24 ( 9375) hydrogen bonds : bond 0.02304 / 1.73 ( 375) hydrogen bonds : angle 5.89180 / 4.39 ( 1005) link_BETA1-4 : bond 0.02701 / 1.79 ( 2) link_BETA1-4 : angle 7.85792 / 2.90 ( 6) link_NAG-ASN : bond 0.01165 / 0.78 ( 1) link_NAG-ASN : angle 7.01762 / 4.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.253 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0287 time to fit residues: 1.4073 Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 47 optimal weight: 0.1980 chunk 99 optimal weight: 50.0000 chunk 103 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 111 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 42 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.053416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.030063 restraints weight = 89693.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.030063 restraints weight = 84457.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.030063 restraints weight = 84457.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.030063 restraints weight = 84457.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.030063 restraints weight = 84457.318| |-----------------------------------------------------------------------------| r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6737 Z= 0.101 Angle : 0.466 17.016 9384 Z= 0.244 Chirality : 0.044 0.418 1293 Planarity : 0.002 0.008 1354 Dihedral : 3.671 14.464 1351 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.18 (0.25), residues: 1348 helix: 1.89 (0.30), residues: 348 sheet: -1.92 (0.29), residues: 284 loop : -0.26 (0.26), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00155 / 0.10 ( 6734) covalent geometry : angle 0.41063 / 0.23 ( 9375) hydrogen bonds : bond 0.02237 / 1.68 ( 375) hydrogen bonds : angle 5.56604 / 4.14 ( 1005) link_BETA1-4 : bond 0.02546 / 1.69 ( 2) link_BETA1-4 : angle 7.41585 / 2.69 ( 6) link_NAG-ASN : bond 0.00827 / 0.55 ( 1) link_NAG-ASN : angle 6.61561 / 4.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0270 time to fit residues: 1.3219 Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 50.0000 chunk 65 optimal weight: 50.0000 chunk 124 optimal weight: 8.9990 chunk 31 optimal weight: 50.0000 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 50.0000 chunk 129 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 83 optimal weight: 50.0000 chunk 120 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.030112 restraints weight = 91605.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.029727 restraints weight = 86653.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.029798 restraints weight = 81734.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.029798 restraints weight = 77449.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.029798 restraints weight = 77449.069| |-----------------------------------------------------------------------------| r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 6737 Z= 0.135 Angle : 0.500 16.881 9384 Z= 0.264 Chirality : 0.044 0.396 1293 Planarity : 0.002 0.013 1354 Dihedral : 3.918 17.909 1351 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.22 (0.25), residues: 1348 helix: 1.98 (0.31), residues: 341 sheet: -1.81 (0.30), residues: 272 loop : -0.43 (0.26), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.13 ( 6734) covalent geometry : angle 0.43650 / 0.25 ( 9375) hydrogen bonds : bond 0.02546 / 1.91 ( 375) hydrogen bonds : angle 5.86646 / 4.37 ( 1005) link_BETA1-4 : bond 0.03062 / 2.02 ( 2) link_BETA1-4 : angle 7.52605 / 2.82 ( 6) link_NAG-ASN : bond 0.01375 / 0.92 ( 1) link_NAG-ASN : angle 8.56797 / 5.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0242 time to fit residues: 1.1488 Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 99 optimal weight: 9.9990 chunk 40 optimal weight: 50.0000 chunk 84 optimal weight: 0.0170 chunk 2 optimal weight: 50.0000 chunk 18 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 109 optimal weight: 50.0000 chunk 60 optimal weight: 30.0000 overall best weight: 9.4028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.052142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.030912 restraints weight = 92017.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.030385 restraints weight = 86853.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.030431 restraints weight = 84009.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.030120 restraints weight = 81238.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.030120 restraints weight = 76277.393| |-----------------------------------------------------------------------------| r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6737 Z= 0.198 Angle : 0.554 17.816 9384 Z= 0.303 Chirality : 0.045 0.450 1293 Planarity : 0.002 0.010 1354 Dihedral : 4.463 18.344 1351 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.33 (0.25), residues: 1348 helix: 2.10 (0.31), residues: 328 sheet: -1.86 (0.31), residues: 260 loop : -0.61 (0.25), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.20 ( 6734) covalent geometry : angle 0.50047 / 0.29 ( 9375) hydrogen bonds : bond 0.03440 / 2.57 ( 375) hydrogen bonds : angle 6.52405 / 4.83 ( 1005) link_BETA1-4 : bond 0.02386 / 1.59 ( 2) link_BETA1-4 : angle 7.65709 / 2.79 ( 6) link_NAG-ASN : bond 0.00596 / 0.40 ( 1) link_NAG-ASN : angle 7.83196 / 4.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0303 time to fit residues: 1.5012 Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 33 optimal weight: 8.9990 chunk 19 optimal weight: 50.0000 chunk 5 optimal weight: 0.2980 chunk 31 optimal weight: 8.9990 chunk 9 optimal weight: 40.0000 chunk 38 optimal weight: 50.0000 chunk 99 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 0.0470 chunk 86 optimal weight: 10.0000 overall best weight: 4.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.031219 restraints weight = 90418.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.031003 restraints weight = 86400.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.030762 restraints weight = 88703.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.030503 restraints weight = 84258.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.030506 restraints weight = 79922.168| |-----------------------------------------------------------------------------| r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6737 Z= 0.113 Angle : 0.487 17.199 9384 Z= 0.255 Chirality : 0.044 0.396 1293 Planarity : 0.002 0.008 1354 Dihedral : 3.940 17.041 1351 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1348 helix: 2.07 (0.30), residues: 343 sheet: -1.92 (0.30), residues: 280 loop : -0.37 (0.26), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.11 ( 6734) covalent geometry : angle 0.42590 / 0.24 ( 9375) hydrogen bonds : bond 0.02407 / 1.81 ( 375) hydrogen bonds : angle 5.92373 / 4.37 ( 1005) link_BETA1-4 : bond 0.02691 / 1.78 ( 2) link_BETA1-4 : angle 7.45675 / 2.69 ( 6) link_NAG-ASN : bond 0.01179 / 0.79 ( 1) link_NAG-ASN : angle 7.91629 / 5.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.280 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0302 time to fit residues: 1.5186 Evaluate side-chains 20 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 0 optimal weight: 50.0000 chunk 128 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 44 optimal weight: 50.0000 chunk 94 optimal weight: 50.0000 chunk 131 optimal weight: 30.0000 chunk 31 optimal weight: 0.5980 chunk 102 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 49 optimal weight: 0.0010 chunk 41 optimal weight: 3.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.053572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.030364 restraints weight = 89820.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.030364 restraints weight = 82900.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.030364 restraints weight = 82900.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.030364 restraints weight = 82900.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.030364 restraints weight = 82900.079| |-----------------------------------------------------------------------------| r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.037 6737 Z= 0.072 Angle : 0.452 17.042 9384 Z= 0.232 Chirality : 0.044 0.399 1293 Planarity : 0.001 0.009 1354 Dihedral : 3.356 12.039 1351 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.01 (0.25), residues: 1348 helix: 2.19 (0.30), residues: 349 sheet: -1.94 (0.30), residues: 285 loop : -0.16 (0.27), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 55 PHE 0.000 0.000 PHE A 64 TRP 0.000 0.000 TRP A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00107 / 0.07 ( 6734) covalent geometry : angle 0.38924 / 0.22 ( 9375) hydrogen bonds : bond 0.01814 / 1.36 ( 375) hydrogen bonds : angle 5.13822 / 3.78 ( 1005) link_BETA1-4 : bond 0.02677 / 1.77 ( 2) link_BETA1-4 : angle 7.33892 / 2.63 ( 6) link_NAG-ASN : bond 0.00909 / 0.61 ( 1) link_NAG-ASN : angle 7.60488 / 4.90 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1250.47 seconds wall clock time: 21 minutes 57.76 seconds (1317.76 seconds total)