Starting phenix.real_space_refine on Tue Mar 11 23:46:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a64_15205/03_2025/8a64_15205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a64_15205/03_2025/8a64_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_15205/03_2025/8a64_15205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a64_15205/03_2025/8a64_15205.map" model { file = "/net/cci-nas-00/data/ceres_data/8a64_15205/03_2025/8a64_15205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a64_15205/03_2025/8a64_15205.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 35, 'ARG:plan': 31, 'TYR:plan': 37, 'ASN:plan1': 51, 'TRP:plan': 12, 'HIS:plan': 14, 'PHE:plan': 34, 'GLU:plan': 64, 'ASP:plan': 75} 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: {'GLN:plan1': 9, 'ASP:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 6} 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: {'GLN:plan1': 9, 'ASP:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 11, 'TRP:plan': 4, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 6} 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: 5.21, per 1000 atoms: 0.77 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: 2.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.51 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: 3.37 Time building geometry restraints manager: 2.87 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: 0.330 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: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.200 Process input model: 25.400 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.670 ------------------------------------------------------------------------------- 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 6734 Z= 0.575 Angle : 0.863 8.616 9375 Z= 0.574 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** 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 : 0.839 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0686 time to fit residues: 3.5523 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 : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 54 optimal weight: 50.0000 chunk 105 optimal weight: 30.0000 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 overall best weight: 5.8188 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.055409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.033659 restraints weight = 87156.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.033181 restraints weight = 84975.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.033181 restraints weight = 81011.119| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6734 Z= 0.168 Angle : 0.545 9.834 9375 Z= 0.310 Chirality : 0.045 0.409 1293 Planarity : 0.003 0.013 1354 Dihedral : 7.481 68.129 1412 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1348 helix: 0.25 (0.29), residues: 323 sheet: -1.09 (0.28), residues: 326 loop : -0.27 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** 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 : 0.734 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0606 time to fit residues: 3.3342 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 : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 90 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 65 optimal weight: 50.0000 chunk 44 optimal weight: 50.0000 chunk 121 optimal weight: 0.1980 chunk 13 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 123 optimal weight: 20.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.054297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.032026 restraints weight = 87527.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.032026 restraints weight = 83247.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.032026 restraints weight = 83247.624| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6734 Z= 0.145 Angle : 0.479 9.932 9375 Z= 0.269 Chirality : 0.044 0.242 1293 Planarity : 0.002 0.012 1354 Dihedral : 5.379 48.810 1412 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1348 helix: 1.19 (0.30), residues: 338 sheet: -1.15 (0.28), residues: 322 loop : -0.08 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** 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 : 0.844 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0662 time to fit residues: 3.7231 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 : 0.719 ------------------------------------------------------------------------------- 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 52 optimal weight: 40.0000 chunk 123 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 92 optimal weight: 50.0000 chunk 104 optimal weight: 50.0000 chunk 71 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 50.0000 chunk 89 optimal weight: 1.9990 overall best weight: 4.8168 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.053975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.031595 restraints weight = 88965.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.031600 restraints weight = 83783.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.031600 restraints weight = 80331.153| |-----------------------------------------------------------------------------| r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6734 Z= 0.139 Angle : 0.457 11.187 9375 Z= 0.256 Chirality : 0.045 0.501 1293 Planarity : 0.002 0.011 1354 Dihedral : 4.962 47.504 1412 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1348 helix: 1.60 (0.31), residues: 333 sheet: -1.31 (0.28), residues: 307 loop : -0.03 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** 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 : 0.764 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0654 time to fit residues: 3.5745 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 : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 31 optimal weight: 50.0000 chunk 13 optimal weight: 30.0000 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 0.0370 chunk 85 optimal weight: 50.0000 chunk 125 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 overall best weight: 4.9664 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.053560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031375 restraints weight = 89561.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031374 restraints weight = 84717.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031374 restraints weight = 84597.497| |-----------------------------------------------------------------------------| r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6734 Z= 0.134 Angle : 0.431 11.605 9375 Z= 0.246 Chirality : 0.044 0.399 1293 Planarity : 0.002 0.011 1354 Dihedral : 4.815 48.644 1412 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1348 helix: 1.80 (0.31), residues: 339 sheet: -1.42 (0.28), residues: 301 loop : -0.01 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** 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 : 0.678 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0600 time to fit residues: 3.2918 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 : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 3 optimal weight: 8.9990 chunk 69 optimal weight: 30.0000 chunk 83 optimal weight: 50.0000 chunk 106 optimal weight: 50.0000 chunk 82 optimal weight: 40.0000 chunk 99 optimal weight: 50.0000 chunk 124 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 50.0000 overall best weight: 15.1994 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.051520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.031411 restraints weight = 91838.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.030802 restraints weight = 87284.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.030468 restraints weight = 94964.336| |-----------------------------------------------------------------------------| r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 6734 Z= 0.344 Angle : 0.632 10.169 9375 Z= 0.375 Chirality : 0.045 0.352 1293 Planarity : 0.003 0.016 1354 Dihedral : 6.034 39.927 1412 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1348 helix: 1.33 (0.30), residues: 319 sheet: -1.84 (0.28), residues: 298 loop : -0.45 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** 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 : 0.831 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0671 time to fit residues: 3.7256 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 : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 13 optimal weight: 50.0000 chunk 114 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 10 optimal weight: 40.0000 chunk 76 optimal weight: 40.0000 chunk 88 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.052955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031046 restraints weight = 87729.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.031038 restraints weight = 83183.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.030799 restraints weight = 77944.310| |-----------------------------------------------------------------------------| r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6734 Z= 0.137 Angle : 0.445 10.434 9375 Z= 0.256 Chirality : 0.044 0.436 1293 Planarity : 0.002 0.009 1354 Dihedral : 5.201 47.493 1412 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1348 helix: 1.66 (0.30), residues: 334 sheet: -1.79 (0.28), residues: 294 loop : -0.30 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** 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 : 0.748 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0644 time to fit residues: 3.4819 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 : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 85 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 66 optimal weight: 40.0000 chunk 65 optimal weight: 2.9990 chunk 99 optimal weight: 50.0000 chunk 47 optimal weight: 0.0370 chunk 111 optimal weight: 50.0000 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 overall best weight: 2.8242 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.053599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.032025 restraints weight = 90034.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.031654 restraints weight = 90999.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.031288 restraints weight = 93747.455| |-----------------------------------------------------------------------------| r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.037 6734 Z= 0.107 Angle : 0.405 10.399 9375 Z= 0.230 Chirality : 0.044 0.404 1293 Planarity : 0.001 0.008 1354 Dihedral : 4.657 50.670 1412 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1348 helix: 1.99 (0.30), residues: 341 sheet: -1.84 (0.28), residues: 306 loop : -0.06 (0.26), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** 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 : 0.815 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0675 time to fit residues: 3.6810 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 : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 128 optimal weight: 50.0000 chunk 62 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 132 optimal weight: 50.0000 chunk 34 optimal weight: 40.0000 chunk 124 optimal weight: 50.0000 chunk 93 optimal weight: 10.0000 chunk 27 optimal weight: 40.0000 chunk 37 optimal weight: 20.0000 chunk 44 optimal weight: 50.0000 overall best weight: 15.5998 ------------------------------------------------------------------------------- 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 = 0.3201 r_free = 0.3201 target = 0.051794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.029412 restraints weight = 91865.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.029412 restraints weight = 85558.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.029412 restraints weight = 85558.627| |-----------------------------------------------------------------------------| r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 6734 Z= 0.336 Angle : 0.627 9.835 9375 Z= 0.379 Chirality : 0.045 0.442 1293 Planarity : 0.003 0.018 1354 Dihedral : 6.218 38.101 1412 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.24), residues: 1348 helix: 1.34 (0.30), residues: 320 sheet: -2.17 (0.29), residues: 284 loop : -0.65 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** 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 : 0.763 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0649 time to fit residues: 3.5411 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 : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 129 optimal weight: 0.0070 chunk 6 optimal weight: 50.0000 chunk 82 optimal weight: 2.9990 chunk 83 optimal weight: 40.0000 chunk 65 optimal weight: 0.4980 chunk 56 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 72 optimal weight: 40.0000 chunk 18 optimal weight: 40.0000 chunk 118 optimal weight: 40.0000 chunk 40 optimal weight: 50.0000 overall best weight: 6.7008 ------------------------------------------------------------------------------- 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 = 0.052475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.031085 restraints weight = 92571.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.030629 restraints weight = 89351.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.030495 restraints weight = 86103.915| |-----------------------------------------------------------------------------| r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 6734 Z= 0.165 Angle : 0.468 10.257 9375 Z= 0.269 Chirality : 0.044 0.416 1293 Planarity : 0.002 0.009 1354 Dihedral : 5.478 45.292 1412 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1348 helix: 1.64 (0.30), residues: 334 sheet: -1.83 (0.32), residues: 249 loop : -0.61 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 ********************** 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 : 0.753 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0628 time to fit residues: 3.4058 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 : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 122 optimal weight: 30.0000 chunk 114 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 50.0000 chunk 48 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3243 r_free = 0.3243 target = 0.053136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.031607 restraints weight = 90250.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.031081 restraints weight = 86815.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.030915 restraints weight = 88873.394| |-----------------------------------------------------------------------------| r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.033 6734 Z= 0.102 Angle : 0.406 10.616 9375 Z= 0.229 Chirality : 0.044 0.408 1293 Planarity : 0.001 0.008 1354 Dihedral : 4.889 52.256 1412 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1348 helix: 2.10 (0.30), residues: 342 sheet: -1.91 (0.31), residues: 263 loop : -0.36 (0.26), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2283.80 seconds wall clock time: 39 minutes 39.71 seconds (2379.71 seconds total)