Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 02:48:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2023/8a64_15205.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2023/8a64_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2023/8a64_15205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2023/8a64_15205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2023/8a64_15205.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2023/8a64_15205.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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 chiralities: 3 Time building chain proxies: 4.59, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 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: 3.17 Conformation dependent library (CDL) restraints added in 1.7 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: 1.13 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: 2.95 Time building geometry restraints manager: 3.36 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: 101.78 - 106.87: 111 106.87 - 111.96: 3446 111.96 - 117.06: 1271 117.06 - 122.15: 3040 122.15 - 127.24: 1507 Bond angle restraints: 9375 Sorted by residual: angle pdb=" CA THR B 299 " pdb=" C THR B 299 " pdb=" O THR B 299 " ideal model delta sigma weight residual 122.31 117.15 5.16 1.31e+00 5.83e-01 1.55e+01 angle pdb=" C VAL A 169 " pdb=" CA VAL A 169 " pdb=" CB VAL A 169 " ideal model delta sigma weight residual 114.00 109.08 4.92 1.31e+00 5.83e-01 1.41e+01 angle pdb=" C LYS A 268 " pdb=" N GLY A 269 " pdb=" CA GLY A 269 " ideal model delta sigma weight residual 122.69 118.98 3.71 1.08e+00 8.57e-01 1.18e+01 angle pdb=" N GLY A 269 " pdb=" CA GLY A 269 " pdb=" C GLY A 269 " ideal model delta sigma weight residual 112.10 117.66 -5.56 1.82e+00 3.02e-01 9.34e+00 angle pdb=" N GLU A 102 " pdb=" CA GLU A 102 " pdb=" C GLU A 102 " ideal model delta sigma weight residual 110.28 105.92 4.36 1.48e+00 4.57e-01 8.67e+00 ... (remaining 9370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.09: 3283 4.09 - 8.19: 395 8.19 - 12.28: 178 12.28 - 16.38: 44 16.38 - 20.47: 8 Dihedral angle restraints: 3908 sinusoidal: 3 harmonic: 3905 Sorted by residual: dihedral pdb=" CA SER B 337 " pdb=" C SER B 337 " pdb=" N LYS B 338 " pdb=" CA LYS B 338 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ALA A 417 " pdb=" C ALA A 417 " pdb=" N LYS A 418 " pdb=" CA LYS A 418 " ideal model delta harmonic sigma weight residual 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA TYR A 909 " pdb=" C TYR A 909 " pdb=" N SER A 910 " pdb=" CA SER A 910 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1208 0.103 - 0.206: 83 0.206 - 0.310: 1 0.310 - 0.413: 0 0.413 - 0.516: 1 Chirality restraints: 1293 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 297 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.92 0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.47 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1290 not shown) Planarity restraints: 1355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 297 " 0.127 2.00e-02 2.50e+03 1.74e-01 3.80e+02 pdb=" CG ASN B 297 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN B 297 " 0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN B 297 " -0.299 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 100 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C ILE A 100 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE A 100 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO A 101 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 297 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ASN B 297 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN B 297 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 298 " -0.010 2.00e-02 2.50e+03 ... (remaining 1352 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 225 2.67 - 3.23: 7294 3.23 - 3.78: 10133 3.78 - 4.34: 11868 4.34 - 4.90: 17827 Nonbonded interactions: 47347 Sorted by model distance: nonbonded pdb=" O LEU A 509 " pdb=" N SER A 560 " model vdw 2.112 2.520 nonbonded pdb=" O ILE A 261 " pdb=" N ILE A 265 " model vdw 2.132 2.520 nonbonded pdb=" O ILE A 343 " pdb=" N PHE A 400 " model vdw 2.132 2.520 nonbonded pdb=" O LEU A 485 " pdb=" N ASP A 508 " model vdw 2.144 2.520 nonbonded pdb=" N ASP C 399 " pdb=" O SER C 403 " model vdw 2.190 2.520 ... (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 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: 0.340 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: 1.870 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 24.990 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- 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 : 5.840 20.473 1354 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.00 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.840 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0660 time to fit residues: 3.6292 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9830 ------------------------------------------------------------------------------- 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: 8.9990 chunk 56 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 68 optimal weight: 40.0000 chunk 54 optimal weight: 50.0000 chunk 105 optimal weight: 50.0000 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 121 optimal weight: 20.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 6734 Z= 0.267 Angle : 0.621 12.139 9375 Z= 0.366 Chirality : 0.046 0.340 1293 Planarity : 0.003 0.016 1354 Dihedral : 5.480 20.561 1351 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 0.00 % 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: -1.00 (0.23), residues: 1348 helix: -0.23 (0.28), residues: 322 sheet: -1.11 (0.28), residues: 325 loop : -0.51 (0.25), residues: 701 *********************** 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.751 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0619 time to fit residues: 3.3672 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 82 optimal weight: 50.0000 chunk 33 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 131 optimal weight: 50.0000 chunk 108 optimal weight: 50.0000 chunk 120 optimal weight: 50.0000 chunk 41 optimal weight: 40.0000 chunk 97 optimal weight: 50.0000 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 6734 Z= 0.271 Angle : 0.618 12.481 9375 Z= 0.355 Chirality : 0.045 0.293 1293 Planarity : 0.003 0.016 1354 Dihedral : 5.484 22.333 1351 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer Outliers : 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: -0.89 (0.23), residues: 1348 helix: 0.44 (0.29), residues: 322 sheet: -1.38 (0.30), residues: 283 loop : -0.65 (0.24), residues: 743 *********************** 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 fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.769 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0669 time to fit residues: 3.8037 Evaluate side-chains 21 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.821 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0683 time to fit residues: 1.1644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 122 optimal weight: 50.0000 chunk 129 optimal weight: 0.1980 chunk 115 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 40.0000 overall best weight: 3.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 6734 Z= 0.127 Angle : 0.459 9.433 9375 Z= 0.263 Chirality : 0.045 0.472 1293 Planarity : 0.002 0.011 1354 Dihedral : 4.516 18.448 1351 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.00 % 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: 1.30 (0.30), residues: 326 sheet: -1.26 (0.28), residues: 314 loop : -0.29 (0.26), residues: 708 *********************** 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.810 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0702 time to fit residues: 3.8764 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 6.9990 chunk 1 optimal weight: 40.0000 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 50.0000 chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 chunk 116 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 overall best weight: 13.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 6734 Z= 0.280 Angle : 0.583 10.699 9375 Z= 0.343 Chirality : 0.046 0.405 1293 Planarity : 0.003 0.016 1354 Dihedral : 5.373 20.251 1351 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer Outliers : 0.00 % 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: -0.80 (0.24), residues: 1348 helix: 1.08 (0.30), residues: 322 sheet: -1.79 (0.30), residues: 279 loop : -0.68 (0.24), residues: 747 *********************** 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.779 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0655 time to fit residues: 3.5748 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 50.0000 chunk 25 optimal weight: 20.0000 chunk 76 optimal weight: 50.0000 chunk 31 optimal weight: 20.0000 chunk 129 optimal weight: 0.9980 chunk 107 optimal weight: 50.0000 chunk 60 optimal weight: 40.0000 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 68 optimal weight: 50.0000 chunk 124 optimal weight: 6.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 6734 Z= 0.191 Angle : 0.496 10.812 9375 Z= 0.286 Chirality : 0.045 0.496 1293 Planarity : 0.002 0.013 1354 Dihedral : 4.818 18.925 1351 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 0.00 % 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 (0.24), residues: 1348 helix: 1.46 (0.31), residues: 317 sheet: -1.86 (0.30), residues: 277 loop : -0.62 (0.25), residues: 754 *********************** 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.772 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0631 time to fit residues: 3.5080 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 50.0000 chunk 109 optimal weight: 50.0000 chunk 72 optimal weight: 0.0270 chunk 129 optimal weight: 0.0370 chunk 80 optimal weight: 9.9990 chunk 78 optimal weight: 40.0000 chunk 59 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 50.0000 overall best weight: 4.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 6734 Z= 0.140 Angle : 0.448 9.322 9375 Z= 0.255 Chirality : 0.044 0.448 1293 Planarity : 0.002 0.009 1354 Dihedral : 4.251 15.039 1351 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 0.00 % 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: -0.34 (0.25), residues: 1348 helix: 1.82 (0.31), residues: 327 sheet: -1.81 (0.30), residues: 277 loop : -0.45 (0.25), residues: 744 *********************** 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.785 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0663 time to fit residues: 3.6342 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 50.0000 chunk 38 optimal weight: 20.0000 chunk 25 optimal weight: 50.0000 chunk 82 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 117 optimal weight: 50.0000 chunk 123 optimal weight: 50.0000 chunk 112 optimal weight: 30.0000 overall best weight: 12.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 6734 Z= 0.275 Angle : 0.569 11.003 9375 Z= 0.337 Chirality : 0.046 0.549 1293 Planarity : 0.003 0.016 1354 Dihedral : 5.154 20.488 1351 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer Outliers : 0.00 % 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: -0.72 (0.24), residues: 1348 helix: 1.63 (0.31), residues: 310 sheet: -1.98 (0.29), residues: 292 loop : -0.70 (0.25), residues: 746 *********************** 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.809 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0676 time to fit residues: 3.6826 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 52 optimal weight: 30.0000 chunk 94 optimal weight: 50.0000 chunk 36 optimal weight: 50.0000 chunk 108 optimal weight: 20.0000 chunk 113 optimal weight: 50.0000 chunk 119 optimal weight: 50.0000 chunk 79 optimal weight: 30.0000 chunk 127 optimal weight: 0.1980 overall best weight: 16.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.109 6734 Z= 0.328 Angle : 0.665 9.800 9375 Z= 0.393 Chirality : 0.045 0.467 1293 Planarity : 0.004 0.018 1354 Dihedral : 6.308 26.223 1351 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 29.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer Outliers : 0.00 % 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: -1.83 (0.23), residues: 1348 helix: 0.17 (0.30), residues: 322 sheet: -2.59 (0.29), residues: 275 loop : -1.24 (0.23), residues: 751 *********************** 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.701 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0646 time to fit residues: 3.4809 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 40.0000 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 133 optimal weight: 50.0000 chunk 122 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 40.0000 chunk 65 optimal weight: 40.0000 chunk 84 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.7066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 6734 Z= 0.250 Angle : 0.567 10.164 9375 Z= 0.330 Chirality : 0.045 0.497 1293 Planarity : 0.003 0.022 1354 Dihedral : 5.591 21.577 1351 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer Outliers : 0.00 % 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: -1.64 (0.24), residues: 1348 helix: 0.63 (0.31), residues: 317 sheet: -2.68 (0.29), residues: 283 loop : -1.14 (0.24), residues: 748 ********************** 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.723 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0648 time to fit residues: 3.4719 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 50.0000 chunk 109 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 40.0000 chunk 93 optimal weight: 8.9990 chunk 6 optimal weight: 50.0000 overall best weight: 5.8586 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.052102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.030798 restraints weight = 90863.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.030544 restraints weight = 90592.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.030213 restraints weight = 93273.386| |-----------------------------------------------------------------------------| r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.7097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 6734 Z= 0.156 Angle : 0.473 10.319 9375 Z= 0.269 Chirality : 0.044 0.449 1293 Planarity : 0.002 0.010 1354 Dihedral : 4.665 18.652 1351 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer Outliers : 0.00 % 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: -1.08 (0.24), residues: 1348 helix: 1.28 (0.31), residues: 319 sheet: -2.52 (0.30), residues: 280 loop : -0.81 (0.24), residues: 749 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1083.28 seconds wall clock time: 20 minutes 40.67 seconds (1240.67 seconds total)