Starting phenix.real_space_refine on Tue Mar 3 16:02:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a64_15205/03_2026/8a64_15205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a64_15205/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8a64_15205/03_2026/8a64_15205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a64_15205/03_2026/8a64_15205.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a64_15205/03_2026/8a64_15205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a64_15205/03_2026/8a64_15205.map" } 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-5986/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.44, 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: 0.58 Conformation dependent library (CDL) restraints added in 255.3 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: 0.24 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: 1.25 Time building geometry restraints manager: 0.71 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 - 22.51: 3955 22.51 - 45.01: 1 45.01 - 67.52: 3 67.52 - 90.02: 6 90.02 - 112.53: 4 Dihedral angle restraints: 3969 sinusoidal: 64 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=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -64.91 112.53 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 176.83 111.88 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 3966 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.130 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 10.170 112.526 1415 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 covalent geometry : bond 0.00771 ( 6734) covalent geometry : angle 0.86284 ( 9375) hydrogen bonds : bond 0.20874 ( 375) hydrogen bonds : angle 9.76324 ( 1005) link_BETA1-4 : bond 0.03058 ( 2) link_BETA1-4 : angle 9.01551 ( 6) link_NAG-ASN : bond 0.01855 ( 1) link_NAG-ASN : angle 16.89220 ( 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 : 0.170 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0324 time to fit residues: 1.5548 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 : 0.231 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.031461 restraints weight = 89745.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.031461 restraints weight = 85517.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.031461 restraints weight = 85517.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.031461 restraints weight = 85517.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.031461 restraints weight = 85517.495| |-----------------------------------------------------------------------------| r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6737 Z= 0.259 Angle : 0.688 18.899 9384 Z= 0.381 Chirality : 0.046 0.430 1293 Planarity : 0.003 0.015 1354 Dihedral : 7.704 65.102 1412 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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: -1.04 (0.23), residues: 1348 helix: -0.21 (0.28), residues: 322 sheet: -1.20 (0.29), residues: 298 loop : -0.57 (0.24), residues: 728 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 covalent geometry : bond 0.00373 ( 6734) covalent geometry : angle 0.63327 ( 9375) hydrogen bonds : bond 0.04641 ( 375) hydrogen bonds : angle 8.11972 ( 1005) link_BETA1-4 : bond 0.02607 ( 2) link_BETA1-4 : angle 8.64173 ( 6) link_NAG-ASN : bond 0.01948 ( 1) link_NAG-ASN : angle 8.95315 ( 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 : 0.160 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0240 time to fit residues: 1.1108 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 : 0.230 ------------------------------------------------------------------------------- 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: 9.9990 chunk 57 optimal weight: 50.0000 chunk 11 optimal weight: 50.0000 chunk 25 optimal weight: 50.0000 chunk 91 optimal weight: 30.0000 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 50.0000 chunk 79 optimal weight: 50.0000 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 17 optimal weight: 0.0980 overall best weight: 14.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.052189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.031009 restraints weight = 89944.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.030758 restraints weight = 96566.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.030541 restraints weight = 91705.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.030492 restraints weight = 92901.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.030482 restraints weight = 89079.072| |-----------------------------------------------------------------------------| r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 6737 Z= 0.306 Angle : 0.732 17.120 9384 Z= 0.405 Chirality : 0.047 0.424 1293 Planarity : 0.004 0.020 1354 Dihedral : 6.826 40.003 1412 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 50.00 % Allowed : 0.00 % 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: -1.34 (0.23), residues: 1348 helix: 0.14 (0.29), residues: 319 sheet: -1.80 (0.29), residues: 297 loop : -0.87 (0.24), residues: 732 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 covalent geometry : bond 0.00454 ( 6734) covalent geometry : angle 0.68889 ( 9375) hydrogen bonds : bond 0.05385 ( 375) hydrogen bonds : angle 8.40824 ( 1005) link_BETA1-4 : bond 0.02773 ( 2) link_BETA1-4 : angle 8.51388 ( 6) link_NAG-ASN : bond 0.01049 ( 1) link_NAG-ASN : angle 7.08471 ( 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 21 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.193 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0313 time to fit residues: 1.5429 Evaluate side-chains 21 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 30.0000 chunk 55 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 131 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.052638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.030308 restraints weight = 89572.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.030308 restraints weight = 81949.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.030308 restraints weight = 81949.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.030308 restraints weight = 81949.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.030308 restraints weight = 81949.668| |-----------------------------------------------------------------------------| r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 6737 Z= 0.172 Angle : 0.591 17.823 9384 Z= 0.317 Chirality : 0.045 0.443 1293 Planarity : 0.002 0.012 1354 Dihedral : 6.014 46.922 1412 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % 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: -1.13 (0.24), residues: 1348 helix: 0.56 (0.29), residues: 333 sheet: -2.08 (0.29), residues: 286 loop : -0.71 (0.25), residues: 729 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 covalent geometry : bond 0.00267 ( 6734) covalent geometry : angle 0.52820 ( 9375) hydrogen bonds : bond 0.03512 ( 375) hydrogen bonds : angle 7.51715 ( 1005) link_BETA1-4 : bond 0.02800 ( 2) link_BETA1-4 : angle 8.49560 ( 6) link_NAG-ASN : bond 0.01465 ( 1) link_NAG-ASN : angle 8.72864 ( 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 : 0.202 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0237 time to fit residues: 1.1476 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 : 0.150 ------------------------------------------------------------------------------- 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: 50.0000 chunk 121 optimal weight: 50.0000 chunk 86 optimal weight: 0.0070 chunk 13 optimal weight: 20.0000 chunk 102 optimal weight: 50.0000 chunk 3 optimal weight: 50.0000 chunk 11 optimal weight: 50.0000 chunk 18 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 overall best weight: 14.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.051765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.031286 restraints weight = 92309.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.030555 restraints weight = 91164.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.029793 restraints weight = 105099.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.029468 restraints weight = 112425.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.029601 restraints weight = 102269.174| |-----------------------------------------------------------------------------| r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 6737 Z= 0.289 Angle : 0.682 18.535 9384 Z= 0.387 Chirality : 0.045 0.436 1293 Planarity : 0.003 0.018 1354 Dihedral : 6.676 38.168 1412 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % 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: -1.63 (0.23), residues: 1348 helix: 0.37 (0.29), residues: 324 sheet: -2.35 (0.28), residues: 289 loop : -1.15 (0.24), 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 covalent geometry : bond 0.00433 ( 6734) covalent geometry : angle 0.63426 ( 9375) hydrogen bonds : bond 0.04799 ( 375) hydrogen bonds : angle 8.42942 ( 1005) link_BETA1-4 : bond 0.03191 ( 2) link_BETA1-4 : angle 8.49839 ( 6) link_NAG-ASN : bond 0.01384 ( 1) link_NAG-ASN : angle 7.23727 ( 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 : 0.238 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0307 time to fit residues: 1.4886 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 : 0.232 ------------------------------------------------------------------------------- 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: 50.0000 chunk 40 optimal weight: 50.0000 chunk 127 optimal weight: 40.0000 chunk 123 optimal weight: 50.0000 chunk 68 optimal weight: 30.0000 chunk 11 optimal weight: 50.0000 chunk 22 optimal weight: 40.0000 chunk 109 optimal weight: 4.9990 chunk 107 optimal weight: 50.0000 chunk 47 optimal weight: 0.0570 chunk 95 optimal weight: 0.1980 overall best weight: 15.0508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.030620 restraints weight = 93093.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.030014 restraints weight = 88720.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.029699 restraints weight = 100548.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.029747 restraints weight = 94940.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.029772 restraints weight = 86718.603| |-----------------------------------------------------------------------------| r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 6737 Z= 0.285 Angle : 0.685 18.749 9384 Z= 0.379 Chirality : 0.044 0.256 1293 Planarity : 0.003 0.014 1354 Dihedral : 6.966 58.926 1412 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % 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: -1.87 (0.23), residues: 1348 helix: 0.03 (0.29), residues: 330 sheet: -2.59 (0.29), residues: 271 loop : -1.24 (0.24), residues: 747 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 covalent geometry : bond 0.00420 ( 6734) covalent geometry : angle 0.62731 ( 9375) hydrogen bonds : bond 0.04542 ( 375) hydrogen bonds : angle 8.45584 ( 1005) link_BETA1-4 : bond 0.03501 ( 2) link_BETA1-4 : angle 9.27285 ( 6) link_NAG-ASN : bond 0.02610 ( 1) link_NAG-ASN : angle 8.15231 ( 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 : 0.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0288 time to fit residues: 1.3813 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 : 0.163 ------------------------------------------------------------------------------- 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: 0.0970 chunk 99 optimal weight: 50.0000 chunk 103 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 96 optimal weight: 40.0000 chunk 102 optimal weight: 50.0000 chunk 123 optimal weight: 50.0000 chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 30.0000 chunk 124 optimal weight: 50.0000 overall best weight: 5.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.052310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.031091 restraints weight = 90317.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.030450 restraints weight = 86426.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.030183 restraints weight = 94459.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.030213 restraints weight = 86866.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.030235 restraints weight = 78599.030| |-----------------------------------------------------------------------------| r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 6737 Z= 0.130 Angle : 0.552 19.298 9384 Z= 0.291 Chirality : 0.044 0.382 1293 Planarity : 0.002 0.010 1354 Dihedral : 5.809 46.495 1412 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % 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: -1.23 (0.24), residues: 1348 helix: 0.91 (0.30), residues: 334 sheet: -2.43 (0.31), residues: 247 loop : -1.01 (0.24), residues: 767 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 covalent geometry : bond 0.00201 ( 6734) covalent geometry : angle 0.48236 ( 9375) hydrogen bonds : bond 0.03000 ( 375) hydrogen bonds : angle 7.22919 ( 1005) link_BETA1-4 : bond 0.02612 ( 2) link_BETA1-4 : angle 8.61714 ( 6) link_NAG-ASN : bond 0.01065 ( 1) link_NAG-ASN : angle 8.86882 ( 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 : 0.246 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0258 time to fit residues: 1.2450 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 : 0.235 ------------------------------------------------------------------------------- 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: 9.9990 chunk 124 optimal weight: 50.0000 chunk 31 optimal weight: 6.9990 chunk 39 optimal weight: 0.0270 chunk 45 optimal weight: 50.0000 chunk 129 optimal weight: 0.0570 chunk 41 optimal weight: 40.0000 chunk 83 optimal weight: 10.0000 chunk 120 optimal weight: 40.0000 overall best weight: 5.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.052192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.029178 restraints weight = 91712.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.029178 restraints weight = 85921.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.029178 restraints weight = 85921.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.029178 restraints weight = 85921.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.029178 restraints weight = 85921.840| |-----------------------------------------------------------------------------| r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 6737 Z= 0.135 Angle : 0.525 18.448 9384 Z= 0.276 Chirality : 0.044 0.374 1293 Planarity : 0.002 0.009 1354 Dihedral : 5.283 48.222 1412 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % 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: -0.98 (0.25), residues: 1348 helix: 1.25 (0.30), residues: 348 sheet: -2.43 (0.30), residues: 278 loop : -0.80 (0.25), residues: 722 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 covalent geometry : bond 0.00204 ( 6734) covalent geometry : angle 0.46059 ( 9375) hydrogen bonds : bond 0.02762 ( 375) hydrogen bonds : angle 6.71429 ( 1005) link_BETA1-4 : bond 0.02769 ( 2) link_BETA1-4 : angle 8.27004 ( 6) link_NAG-ASN : bond 0.00780 ( 1) link_NAG-ASN : angle 7.89263 ( 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 : 0.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0277 time to fit residues: 1.3838 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 : 0.160 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 50.0000 chunk 84 optimal weight: 50.0000 chunk 2 optimal weight: 50.0000 chunk 18 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 chunk 124 optimal weight: 50.0000 chunk 113 optimal weight: 30.0000 chunk 71 optimal weight: 40.0000 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 40.0000 overall best weight: 21.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030672 restraints weight = 94294.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030119 restraints weight = 94017.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.029583 restraints weight = 112504.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.029514 restraints weight = 108742.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.029631 restraints weight = 101555.642| |-----------------------------------------------------------------------------| r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 6737 Z= 0.407 Angle : 0.773 18.613 9384 Z= 0.449 Chirality : 0.046 0.406 1293 Planarity : 0.004 0.021 1354 Dihedral : 6.964 39.022 1412 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.87 % Favored : 86.13 % 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: -2.03 (0.23), residues: 1348 helix: 0.08 (0.29), residues: 324 sheet: -2.90 (0.28), residues: 282 loop : -1.31 (0.24), residues: 742 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 covalent geometry : bond 0.00606 ( 6734) covalent geometry : angle 0.73002 ( 9375) hydrogen bonds : bond 0.05685 ( 375) hydrogen bonds : angle 8.89709 ( 1005) link_BETA1-4 : bond 0.02478 ( 2) link_BETA1-4 : angle 8.37771 ( 6) link_NAG-ASN : bond 0.01569 ( 1) link_NAG-ASN : angle 7.89573 ( 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 : 0.179 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0274 time to fit residues: 1.3023 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 : 0.141 ------------------------------------------------------------------------------- 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: 40.0000 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 50.0000 chunk 38 optimal weight: 50.0000 chunk 99 optimal weight: 40.0000 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.052295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.030957 restraints weight = 90437.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.030425 restraints weight = 87543.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.030267 restraints weight = 85312.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.030089 restraints weight = 83823.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.030091 restraints weight = 79014.504| |-----------------------------------------------------------------------------| r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6933 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= 0.115 Angle : 0.538 18.227 9384 Z= 0.284 Chirality : 0.044 0.362 1293 Planarity : 0.002 0.009 1354 Dihedral : 5.521 47.726 1412 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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: -1.23 (0.25), residues: 1348 helix: 1.02 (0.30), residues: 344 sheet: -2.64 (0.30), residues: 278 loop : -0.89 (0.25), 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 covalent geometry : bond 0.00173 ( 6734) covalent geometry : angle 0.47563 ( 9375) hydrogen bonds : bond 0.02715 ( 375) hydrogen bonds : angle 6.93202 ( 1005) link_BETA1-4 : bond 0.02649 ( 2) link_BETA1-4 : angle 8.26058 ( 6) link_NAG-ASN : bond 0.00527 ( 1) link_NAG-ASN : angle 7.80587 ( 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 : 0.192 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0274 time to fit residues: 1.3764 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 : 0.228 ------------------------------------------------------------------------------- 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: 60.0000 chunk 128 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 44 optimal weight: 30.0000 chunk 94 optimal weight: 50.0000 chunk 131 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 95 optimal weight: 0.0980 chunk 49 optimal weight: 40.0000 chunk 41 optimal weight: 20.0000 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.052112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.029560 restraints weight = 91553.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.029316 restraints weight = 85452.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.029341 restraints weight = 81560.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.029341 restraints weight = 80172.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.029341 restraints weight = 80170.063| |-----------------------------------------------------------------------------| r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6737 Z= 0.124 Angle : 0.516 18.433 9384 Z= 0.269 Chirality : 0.044 0.380 1293 Planarity : 0.002 0.009 1354 Dihedral : 5.152 47.966 1412 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % 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: -0.99 (0.25), residues: 1348 helix: 1.44 (0.30), residues: 343 sheet: -2.69 (0.29), residues: 283 loop : -0.76 (0.26), residues: 722 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 covalent geometry : bond 0.00191 ( 6734) covalent geometry : angle 0.45283 ( 9375) hydrogen bonds : bond 0.02625 ( 375) hydrogen bonds : angle 6.56381 ( 1005) link_BETA1-4 : bond 0.02760 ( 2) link_BETA1-4 : angle 8.19933 ( 6) link_NAG-ASN : bond 0.00856 ( 1) link_NAG-ASN : angle 7.53660 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1354.39 seconds wall clock time: 23 minutes 40.53 seconds (1420.53 seconds total)