Starting phenix.real_space_refine on Sat Jan 18 13:36:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xuo_38679/01_2025/8xuo_38679.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xuo_38679/01_2025/8xuo_38679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xuo_38679/01_2025/8xuo_38679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xuo_38679/01_2025/8xuo_38679.map" model { file = "/net/cci-nas-00/data/ceres_data/8xuo_38679/01_2025/8xuo_38679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xuo_38679/01_2025/8xuo_38679.cif" } resolution = 2.84 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= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 58 5.16 5 C 7788 2.51 5 N 2102 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12254 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6064 Classifications: {'peptide': 752} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 715} Chain: "G" Number of atoms: 6064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6064 Classifications: {'peptide': 752} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 715} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.91, per 1000 atoms: 0.65 Number of scatterers: 12254 At special positions: 0 Unit cell: (106.25, 144.5, 96.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 16 15.00 O 2290 8.00 N 2102 7.00 C 7788 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 Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.7 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 15 sheets defined 43.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.587A pdb=" N ARG A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.754A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.777A pdb=" N HIS A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 240' Processing helix chain 'A' and resid 242 through 258 removed outlier: 3.528A pdb=" N GLU A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 277 removed outlier: 3.574A pdb=" N TRP A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.698A pdb=" N ALA A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'A' and resid 332 through 347 removed outlier: 4.118A pdb=" N LEU A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.542A pdb=" N SER A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 removed outlier: 4.043A pdb=" N ASN A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 400 " --> pdb=" O MET A 396 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.710A pdb=" N ALA A 407 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 423 through 434 Processing helix chain 'A' and resid 443 through 458 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 509 through 516 removed outlier: 3.987A pdb=" N THR A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.599A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 580 through 586 removed outlier: 3.841A pdb=" N LEU A 586 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 removed outlier: 4.014A pdb=" N LEU A 609 " --> pdb=" O MET A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 677 through 684 removed outlier: 3.578A pdb=" N THR A 684 " --> pdb=" O VAL A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 Processing helix chain 'A' and resid 704 through 710 removed outlier: 3.869A pdb=" N LEU A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 713 No H-bonds generated for 'chain 'A' and resid 711 through 713' Processing helix chain 'A' and resid 737 through 741 Processing helix chain 'A' and resid 759 through 766 removed outlier: 3.675A pdb=" N LEU A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 766 " --> pdb=" O ILE A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.724A pdb=" N PHE A 813 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 837 Processing helix chain 'A' and resid 849 through 869 Processing helix chain 'G' and resid 158 through 168 Processing helix chain 'G' and resid 188 through 198 Processing helix chain 'G' and resid 199 through 206 Processing helix chain 'G' and resid 219 through 232 removed outlier: 3.615A pdb=" N LEU G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE G 231 " --> pdb=" O ILE G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 258 Processing helix chain 'G' and resid 269 through 278 removed outlier: 3.990A pdb=" N ILE G 278 " --> pdb=" O GLU G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.672A pdb=" N ALA G 299 " --> pdb=" O ASP G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 327 Processing helix chain 'G' and resid 332 through 346 removed outlier: 3.506A pdb=" N VAL G 336 " --> pdb=" O PRO G 332 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU G 337 " --> pdb=" O PRO G 333 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER G 338 " --> pdb=" O GLU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 364 Processing helix chain 'G' and resid 366 through 381 Processing helix chain 'G' and resid 387 through 401 removed outlier: 3.634A pdb=" N ASN G 391 " --> pdb=" O PRO G 387 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG G 400 " --> pdb=" O MET G 396 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 401 " --> pdb=" O SER G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 412 removed outlier: 3.675A pdb=" N ALA G 407 " --> pdb=" O TYR G 403 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 415 No H-bonds generated for 'chain 'G' and resid 413 through 415' Processing helix chain 'G' and resid 423 through 434 Processing helix chain 'G' and resid 443 through 458 Processing helix chain 'G' and resid 478 through 492 Processing helix chain 'G' and resid 509 through 515 removed outlier: 3.764A pdb=" N THR G 515 " --> pdb=" O ARG G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 531 removed outlier: 3.583A pdb=" N THR G 531 " --> pdb=" O ASP G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 563 Processing helix chain 'G' and resid 580 through 586 removed outlier: 3.629A pdb=" N LEU G 586 " --> pdb=" O PHE G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 608 Processing helix chain 'G' and resid 672 through 676 Processing helix chain 'G' and resid 677 through 684 removed outlier: 3.517A pdb=" N THR G 684 " --> pdb=" O VAL G 680 " (cutoff:3.500A) Processing helix chain 'G' and resid 695 through 701 removed outlier: 4.307A pdb=" N LEU G 699 " --> pdb=" O LYS G 695 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 711 Processing helix chain 'G' and resid 737 through 741 Processing helix chain 'G' and resid 756 through 758 No H-bonds generated for 'chain 'G' and resid 756 through 758' Processing helix chain 'G' and resid 759 through 766 Processing helix chain 'G' and resid 809 through 813 removed outlier: 3.542A pdb=" N PHE G 813 " --> pdb=" O ALA G 810 " (cutoff:3.500A) Processing helix chain 'G' and resid 831 through 837 removed outlier: 3.578A pdb=" N LEU G 834 " --> pdb=" O PRO G 831 " (cutoff:3.500A) Processing helix chain 'G' and resid 849 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.760A pdb=" N THR A 208 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N VAL A 263 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A 210 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASP A 265 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 212 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR A 260 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 290 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 262 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR A 292 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 264 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU A 177 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU A 291 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL A 179 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR A 293 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A 181 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A 307 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.821A pdb=" N ILE A 472 " --> pdb=" O ARG A 466 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG A 466 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 474 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 497 through 498 removed outlier: 3.553A pdb=" N LEU A 542 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 541 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLU A 572 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 549 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 498 removed outlier: 3.553A pdb=" N LEU A 542 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 541 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLU A 572 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER A 595 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER A 573 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 615 " --> pdb=" O HIS A 638 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 602 removed outlier: 3.715A pdb=" N ILE A 626 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 690 through 694 removed outlier: 6.456A pdb=" N LEU A 748 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LYS A 775 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 750 " --> pdb=" O LYS A 775 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 796 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE A 822 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 798 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 819 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLN A 846 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 821 " --> pdb=" O GLN A 846 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET A 843 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 755 through 756 removed outlier: 5.380A pdb=" N LEU A 755 " --> pdb=" O SER A 780 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AA9, first strand: chain 'G' and resid 208 through 213 removed outlier: 6.794A pdb=" N THR G 208 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL G 263 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE G 210 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASP G 265 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL G 212 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR G 260 " --> pdb=" O PRO G 286 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N HIS G 175 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL G 289 " --> pdb=" O HIS G 175 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU G 177 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU G 291 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL G 179 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR G 293 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL G 181 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N HIS G 307 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 421 through 422 removed outlier: 6.612A pdb=" N GLU G 465 " --> pdb=" O LYS G 473 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N CYS G 475 " --> pdb=" O VAL G 463 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL G 463 " --> pdb=" O CYS G 475 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU G 477 " --> pdb=" O VAL G 461 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL G 461 " --> pdb=" O LEU G 477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 497 through 498 removed outlier: 3.515A pdb=" N LEU G 542 " --> pdb=" O LEU G 519 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE G 541 " --> pdb=" O ASP G 570 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLU G 572 " --> pdb=" O PHE G 541 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 497 through 498 removed outlier: 3.515A pdb=" N LEU G 542 " --> pdb=" O LEU G 519 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE G 541 " --> pdb=" O ASP G 570 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLU G 572 " --> pdb=" O PHE G 541 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER G 595 " --> pdb=" O VAL G 571 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER G 573 " --> pdb=" O SER G 595 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE G 594 " --> pdb=" O ILE G 616 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 601 through 602 removed outlier: 7.366A pdb=" N LEU G 624 " --> pdb=" O LYS G 646 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 667 through 671 removed outlier: 4.314A pdb=" N THR G 667 " --> pdb=" O LYS G 689 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY G 691 " --> pdb=" O THR G 667 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N SER G 669 " --> pdb=" O GLY G 691 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG G 693 " --> pdb=" O SER G 669 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE G 671 " --> pdb=" O ARG G 693 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU G 748 " --> pdb=" O LYS G 773 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS G 775 " --> pdb=" O LEU G 748 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU G 750 " --> pdb=" O LYS G 775 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU G 772 " --> pdb=" O TRP G 797 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLU G 799 " --> pdb=" O LEU G 772 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N MET G 774 " --> pdb=" O GLU G 799 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU G 819 " --> pdb=" O MET G 844 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N GLN G 846 " --> pdb=" O LEU G 819 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU G 821 " --> pdb=" O GLN G 846 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET G 843 " --> pdb=" O SER G 879 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 783 through 785 removed outlier: 6.941A pdb=" N TRP G 784 " --> pdb=" O LYS G 807 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 445 hydrogen bonds defined for protein. 1224 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: 4.46 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2011 1.32 - 1.44: 3167 1.44 - 1.57: 7236 1.57 - 1.69: 18 1.69 - 1.82: 86 Bond restraints: 12518 Sorted by residual: bond pdb=" N VAL A 830 " pdb=" CA VAL A 830 " ideal model delta sigma weight residual 1.457 1.490 -0.033 9.00e-03 1.23e+04 1.36e+01 bond pdb=" N ILE A 431 " pdb=" CA ILE A 431 " ideal model delta sigma weight residual 1.461 1.503 -0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" N LEU A 429 " pdb=" CA LEU A 429 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.28e-02 6.10e+03 1.24e+01 bond pdb=" C ARG A 428 " pdb=" O ARG A 428 " ideal model delta sigma weight residual 1.237 1.196 0.040 1.17e-02 7.31e+03 1.19e+01 bond pdb=" C PRO A 422 " pdb=" O PRO A 422 " ideal model delta sigma weight residual 1.233 1.193 0.040 1.23e-02 6.61e+03 1.08e+01 ... (remaining 12513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 16404 2.09 - 4.17: 445 4.17 - 6.26: 82 6.26 - 8.34: 16 8.34 - 10.43: 5 Bond angle restraints: 16952 Sorted by residual: angle pdb=" O TRP A 430 " pdb=" C TRP A 430 " pdb=" N ILE A 431 " ideal model delta sigma weight residual 122.09 116.21 5.88 1.08e+00 8.57e-01 2.96e+01 angle pdb=" N GLU A 433 " pdb=" CA GLU A 433 " pdb=" C GLU A 433 " ideal model delta sigma weight residual 111.28 105.43 5.85 1.09e+00 8.42e-01 2.88e+01 angle pdb=" N PRO G 648 " pdb=" CA PRO G 648 " pdb=" C PRO G 648 " ideal model delta sigma weight residual 111.14 103.39 7.75 1.56e+00 4.11e-01 2.47e+01 angle pdb=" CA TRP A 430 " pdb=" C TRP A 430 " pdb=" N ILE A 431 " ideal model delta sigma weight residual 117.17 122.73 -5.56 1.18e+00 7.18e-01 2.22e+01 angle pdb=" CA LEU A 426 " pdb=" C LEU A 426 " pdb=" O LEU A 426 " ideal model delta sigma weight residual 120.55 115.60 4.95 1.06e+00 8.90e-01 2.18e+01 ... (remaining 16947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 7326 35.53 - 71.07: 319 71.07 - 106.60: 36 106.60 - 142.14: 14 142.14 - 177.67: 5 Dihedral angle restraints: 7700 sinusoidal: 3292 harmonic: 4408 Sorted by residual: dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 117.67 -177.67 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual 300.00 122.98 177.02 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP G 901 " pdb=" O3A ADP G 901 " pdb=" PB ADP G 901 " pdb=" PA ADP G 901 " ideal model delta sinusoidal sigma weight residual -60.00 84.01 -144.02 1 2.00e+01 2.50e-03 4.34e+01 ... (remaining 7697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 1885 1.004 - 2.007: 0 2.007 - 3.011: 0 3.011 - 4.014: 0 4.014 - 5.018: 7 Chirality restraints: 1892 Sorted by residual: chirality pdb=" C2 IHP A 902 " pdb=" C1 IHP A 902 " pdb=" C3 IHP A 902 " pdb=" O12 IHP A 902 " both_signs ideal model delta sigma weight residual False -2.52 2.50 -5.02 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C2 IHP G 902 " pdb=" C1 IHP G 902 " pdb=" C3 IHP G 902 " pdb=" O12 IHP G 902 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C5 IHP A 902 " pdb=" C4 IHP A 902 " pdb=" C6 IHP A 902 " pdb=" O15 IHP A 902 " both_signs ideal model delta sigma weight residual False -2.42 2.56 -4.98 2.00e-01 2.50e+01 6.20e+02 ... (remaining 1889 not shown) Planarity restraints: 2134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 833 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ALA G 833 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA G 833 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU G 834 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 825 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ASP G 825 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP G 825 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN G 826 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 645 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C ALA G 645 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA G 645 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS G 646 " -0.017 2.00e-02 2.50e+03 ... (remaining 2131 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 119 2.56 - 3.14: 10144 3.14 - 3.73: 18814 3.73 - 4.31: 25832 4.31 - 4.90: 42921 Nonbonded interactions: 97830 Sorted by model distance: nonbonded pdb=" O LYS A 712 " pdb=" NZ LYS A 712 " model vdw 1.970 3.120 nonbonded pdb=" O LYS A 758 " pdb=" NZ LYS A 758 " model vdw 2.103 3.120 nonbonded pdb=" O LYS G 712 " pdb=" NZ LYS G 712 " model vdw 2.112 3.120 nonbonded pdb=" N GLU G 504 " pdb=" OE1 GLU G 504 " model vdw 2.176 3.120 nonbonded pdb=" N GLU G 785 " pdb=" OE1 GLU G 785 " model vdw 2.209 3.120 ... (remaining 97825 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.410 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.120 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 : 0.004 0.045 12518 Z= 0.271 Angle : 0.832 10.425 16952 Z= 0.464 Chirality : 0.301 5.018 1892 Planarity : 0.005 0.058 2134 Dihedral : 20.563 177.671 4828 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 2.71 % Allowed : 26.98 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1500 helix: 0.70 (0.22), residues: 520 sheet: 0.31 (0.36), residues: 216 loop : -0.31 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 754 HIS 0.006 0.001 HIS G 638 PHE 0.021 0.001 PHE G 779 TYR 0.016 0.001 TYR A 591 ARG 0.006 0.001 ARG G 683 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 MET cc_start: 0.7209 (ttt) cc_final: 0.6935 (ttp) REVERT: G 606 MET cc_start: 0.5930 (tpt) cc_final: 0.5705 (tpt) outliers start: 37 outliers final: 27 residues processed: 179 average time/residue: 0.9611 time to fit residues: 192.6790 Evaluate side-chains 146 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 591 TYR Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 635 ARG Chi-restraints excluded: chain G residue 697 SER Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 804 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.0270 chunk 113 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 380 HIS A 642 ASN A 666 GLN A 710 ASN G 451 ASN G 522 HIS G 537 HIS G 640 HIS G 710 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.229224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.186127 restraints weight = 15783.289| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 3.22 r_work: 0.4185 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12518 Z= 0.317 Angle : 0.835 13.061 16952 Z= 0.390 Chirality : 0.049 0.488 1892 Planarity : 0.005 0.047 2134 Dihedral : 12.116 179.450 1769 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 6.45 % Allowed : 23.09 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.21), residues: 1500 helix: 0.98 (0.22), residues: 520 sheet: 0.54 (0.36), residues: 216 loop : -0.50 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 211 HIS 0.006 0.001 HIS A 638 PHE 0.015 0.002 PHE G 583 TYR 0.024 0.002 TYR G 591 ARG 0.005 0.001 ARG G 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 145 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.8884 (t) cc_final: 0.8679 (m) REVERT: A 219 ARG cc_start: 0.7008 (mtp-110) cc_final: 0.6476 (mtp-110) REVERT: A 420 GLN cc_start: 0.8303 (mm110) cc_final: 0.8100 (mm110) REVERT: A 610 TRP cc_start: 0.3144 (OUTLIER) cc_final: 0.1962 (m-90) REVERT: A 772 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 777 ASN cc_start: 0.7057 (m-40) cc_final: 0.6773 (t0) REVERT: A 800 ARG cc_start: 0.6523 (tpt-90) cc_final: 0.5992 (tpm170) REVERT: A 844 MET cc_start: 0.7099 (tmm) cc_final: 0.6829 (tmm) REVERT: G 294 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8154 (ptm160) REVERT: G 579 PHE cc_start: 0.5764 (m-80) cc_final: 0.5259 (m-80) REVERT: G 581 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6739 (ptt180) REVERT: G 687 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6900 (mp) REVERT: G 718 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6968 (mm-30) outliers start: 88 outliers final: 30 residues processed: 214 average time/residue: 1.1383 time to fit residues: 267.0027 Evaluate side-chains 154 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 370 TRP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 581 ARG Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 622 ARG Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 718 GLU Chi-restraints excluded: chain G residue 779 PHE Chi-restraints excluded: chain G residue 804 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS A 666 GLN G 380 HIS G 487 GLN G 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.228328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.187556 restraints weight = 16071.377| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 3.52 r_work: 0.4104 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12518 Z= 0.229 Angle : 0.661 10.088 16952 Z= 0.323 Chirality : 0.044 0.358 1892 Planarity : 0.004 0.048 2134 Dihedral : 10.869 161.741 1737 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.57 % Allowed : 24.05 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.22), residues: 1500 helix: 1.19 (0.23), residues: 528 sheet: 0.76 (0.36), residues: 218 loop : -0.47 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 757 HIS 0.003 0.001 HIS G 638 PHE 0.015 0.002 PHE A 790 TYR 0.016 0.001 TYR G 591 ARG 0.005 0.001 ARG G 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 143 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8889 (t) cc_final: 0.8644 (m) REVERT: A 219 ARG cc_start: 0.6958 (mtp-110) cc_final: 0.6509 (mtp-110) REVERT: A 239 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.6799 (m90) REVERT: A 610 TRP cc_start: 0.3076 (OUTLIER) cc_final: 0.1864 (m-90) REVERT: A 695 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8111 (mtpt) REVERT: A 772 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 777 ASN cc_start: 0.7268 (m-40) cc_final: 0.6966 (m-40) REVERT: A 800 ARG cc_start: 0.6466 (tpt-90) cc_final: 0.5895 (tpm170) REVERT: A 844 MET cc_start: 0.6917 (tmm) cc_final: 0.6612 (tmm) REVERT: G 204 TYR cc_start: 0.5765 (OUTLIER) cc_final: 0.5492 (t80) REVERT: G 579 PHE cc_start: 0.5767 (m-80) cc_final: 0.5346 (m-80) REVERT: G 581 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6787 (ptt180) REVERT: G 687 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6694 (mp) REVERT: G 785 GLU cc_start: 0.7836 (mp0) cc_final: 0.7608 (mp0) outliers start: 76 outliers final: 27 residues processed: 200 average time/residue: 1.1720 time to fit residues: 256.3708 Evaluate side-chains 150 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 204 TYR Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 581 ARG Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 817 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 710 ASN G 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.222811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.181525 restraints weight = 15801.223| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.99 r_work: 0.4052 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12518 Z= 0.302 Angle : 0.711 8.949 16952 Z= 0.350 Chirality : 0.046 0.222 1892 Planarity : 0.005 0.050 2134 Dihedral : 9.584 145.629 1728 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.60 % Allowed : 24.34 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1500 helix: 0.92 (0.23), residues: 532 sheet: 0.36 (0.34), residues: 254 loop : -0.60 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 754 HIS 0.006 0.001 HIS G 638 PHE 0.021 0.002 PHE G 876 TYR 0.027 0.002 TYR A 591 ARG 0.010 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 147 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.7054 (m90) REVERT: A 270 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: A 274 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: A 610 TRP cc_start: 0.3412 (OUTLIER) cc_final: 0.2073 (m-90) REVERT: A 695 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8132 (mtpt) REVERT: A 772 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8333 (tt) REVERT: A 777 ASN cc_start: 0.7483 (m-40) cc_final: 0.7171 (m-40) REVERT: A 785 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6887 (mp0) REVERT: A 800 ARG cc_start: 0.6513 (tpt-90) cc_final: 0.5905 (tpm170) REVERT: A 844 MET cc_start: 0.6938 (tmm) cc_final: 0.6549 (tmm) REVERT: G 239 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.7005 (m90) REVERT: G 246 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7143 (mt) REVERT: G 294 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8227 (ptm160) REVERT: G 370 TRP cc_start: 0.6987 (m100) cc_final: 0.6771 (t-100) REVERT: G 579 PHE cc_start: 0.5947 (m-80) cc_final: 0.5648 (m-80) REVERT: G 718 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.5786 (mm-30) REVERT: G 732 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7490 (ptmt) REVERT: G 766 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7479 (tt) REVERT: G 815 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.6551 (mtt90) REVERT: G 816 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6865 (tt) REVERT: G 823 CYS cc_start: 0.7470 (t) cc_final: 0.6870 (t) outliers start: 90 outliers final: 38 residues processed: 221 average time/residue: 1.0732 time to fit residues: 262.7461 Evaluate side-chains 173 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 718 GLU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 779 PHE Chi-restraints excluded: chain G residue 816 LEU Chi-restraints excluded: chain G residue 817 LYS Chi-restraints excluded: chain G residue 855 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN A 386 HIS A 666 GLN A 818 HIS G 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.226443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.185622 restraints weight = 15884.541| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 3.02 r_work: 0.4138 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12518 Z= 0.192 Angle : 0.616 7.400 16952 Z= 0.302 Chirality : 0.042 0.241 1892 Planarity : 0.004 0.049 2134 Dihedral : 9.032 143.959 1728 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.18 % Allowed : 27.49 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.22), residues: 1500 helix: 1.24 (0.23), residues: 528 sheet: 0.51 (0.34), residues: 254 loop : -0.48 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 631 HIS 0.002 0.001 HIS A 175 PHE 0.025 0.001 PHE G 876 TYR 0.011 0.001 TYR G 591 ARG 0.010 0.001 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 142 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7003 (m90) REVERT: A 610 TRP cc_start: 0.3256 (OUTLIER) cc_final: 0.1936 (m-90) REVERT: A 695 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8114 (mtpt) REVERT: A 772 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8391 (tt) REVERT: A 777 ASN cc_start: 0.7474 (m-40) cc_final: 0.7161 (m-40) REVERT: A 785 GLU cc_start: 0.7572 (tm-30) cc_final: 0.6992 (mp0) REVERT: A 800 ARG cc_start: 0.6537 (tpt-90) cc_final: 0.5919 (tpm170) REVERT: A 844 MET cc_start: 0.6693 (tmm) cc_final: 0.6457 (tmm) REVERT: G 294 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8122 (ptm160) REVERT: G 579 PHE cc_start: 0.5832 (m-80) cc_final: 0.5540 (m-80) REVERT: G 622 ARG cc_start: 0.7908 (mtm180) cc_final: 0.7690 (mtp-110) REVERT: G 785 GLU cc_start: 0.7843 (mp0) cc_final: 0.7539 (mp0) REVERT: G 823 CYS cc_start: 0.7413 (t) cc_final: 0.6914 (t) outliers start: 57 outliers final: 21 residues processed: 185 average time/residue: 1.0944 time to fit residues: 223.2288 Evaluate side-chains 155 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 680 VAL Chi-restraints excluded: chain G residue 779 PHE Chi-restraints excluded: chain G residue 817 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 127 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 666 GLN ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN G 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.219555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.178009 restraints weight = 16123.196| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 3.05 r_work: 0.4005 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 12518 Z= 0.375 Angle : 0.750 9.837 16952 Z= 0.370 Chirality : 0.047 0.215 1892 Planarity : 0.006 0.085 2134 Dihedral : 9.428 143.983 1727 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 6.01 % Allowed : 26.76 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.22), residues: 1500 helix: 0.79 (0.23), residues: 532 sheet: 0.09 (0.34), residues: 258 loop : -0.76 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 211 HIS 0.005 0.001 HIS G 638 PHE 0.021 0.002 PHE G 876 TYR 0.032 0.002 TYR A 591 ARG 0.010 0.001 ARG G 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 139 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7183 (m90) REVERT: A 274 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: A 542 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7660 (mt) REVERT: A 610 TRP cc_start: 0.3421 (OUTLIER) cc_final: 0.1991 (m-90) REVERT: A 695 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8123 (mtpt) REVERT: A 768 HIS cc_start: 0.8122 (m170) cc_final: 0.7779 (m90) REVERT: A 772 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8396 (tt) REVERT: A 785 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7144 (mp0) REVERT: A 800 ARG cc_start: 0.6476 (tpt-90) cc_final: 0.6147 (mmm160) REVERT: A 815 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7170 (mtm-85) REVERT: A 823 CYS cc_start: 0.7442 (t) cc_final: 0.7095 (t) REVERT: G 294 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8215 (ptm160) REVERT: G 622 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7729 (mtp-110) REVERT: G 718 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6015 (mp0) REVERT: G 785 GLU cc_start: 0.7866 (mp0) cc_final: 0.7566 (mp0) REVERT: G 815 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.7173 (mtp85) REVERT: G 823 CYS cc_start: 0.7601 (t) cc_final: 0.6998 (t) outliers start: 82 outliers final: 40 residues processed: 201 average time/residue: 1.1510 time to fit residues: 253.6258 Evaluate side-chains 178 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 622 ARG Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 680 VAL Chi-restraints excluded: chain G residue 699 LEU Chi-restraints excluded: chain G residue 718 GLU Chi-restraints excluded: chain G residue 779 PHE Chi-restraints excluded: chain G residue 817 LYS Chi-restraints excluded: chain G residue 855 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN G 768 HIS G 865 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.222209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.180279 restraints weight = 16086.825| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 3.01 r_work: 0.4110 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12518 Z= 0.255 Angle : 0.670 7.657 16952 Z= 0.329 Chirality : 0.043 0.225 1892 Planarity : 0.005 0.073 2134 Dihedral : 9.184 141.301 1727 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.69 % Allowed : 28.37 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.22), residues: 1500 helix: 1.05 (0.23), residues: 522 sheet: 0.16 (0.34), residues: 256 loop : -0.69 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 754 HIS 0.003 0.001 HIS G 638 PHE 0.027 0.002 PHE G 876 TYR 0.017 0.001 TYR A 591 ARG 0.009 0.001 ARG G 511 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 136 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7090 (m90) REVERT: A 610 TRP cc_start: 0.3316 (OUTLIER) cc_final: 0.1887 (m-90) REVERT: A 695 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7986 (mtpt) REVERT: A 768 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7572 (m90) REVERT: A 772 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8388 (tt) REVERT: A 785 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7240 (mp0) REVERT: A 800 ARG cc_start: 0.6364 (tpt-90) cc_final: 0.5954 (mmm160) REVERT: A 815 ARG cc_start: 0.7733 (mtp85) cc_final: 0.7025 (mtm-85) REVERT: A 817 LYS cc_start: 0.7470 (ttmt) cc_final: 0.7096 (mttp) REVERT: A 823 CYS cc_start: 0.7359 (t) cc_final: 0.6968 (t) REVERT: A 836 ASP cc_start: 0.7570 (m-30) cc_final: 0.7288 (t0) REVERT: G 239 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7175 (m90) REVERT: G 294 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8144 (ptm160) REVERT: G 493 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: G 622 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7698 (mtp-110) REVERT: G 718 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.5885 (mp0) REVERT: G 766 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7298 (tt) REVERT: G 815 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7122 (mtp85) REVERT: G 823 CYS cc_start: 0.7599 (t) cc_final: 0.7056 (t) outliers start: 64 outliers final: 36 residues processed: 186 average time/residue: 1.0879 time to fit residues: 224.7583 Evaluate side-chains 177 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 493 GLU Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 680 VAL Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 699 LEU Chi-restraints excluded: chain G residue 718 GLU Chi-restraints excluded: chain G residue 750 LEU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 779 PHE Chi-restraints excluded: chain G residue 855 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 94 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN G 858 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.223396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.183006 restraints weight = 16031.498| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.43 r_work: 0.4106 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12518 Z= 0.193 Angle : 0.631 8.476 16952 Z= 0.309 Chirality : 0.042 0.221 1892 Planarity : 0.004 0.065 2134 Dihedral : 8.913 138.981 1727 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.89 % Allowed : 29.55 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1500 helix: 1.24 (0.24), residues: 522 sheet: 0.21 (0.33), residues: 276 loop : -0.48 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 757 HIS 0.002 0.001 HIS G 307 PHE 0.031 0.001 PHE G 876 TYR 0.011 0.001 TYR G 591 ARG 0.008 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 142 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.6428 (m-30) cc_final: 0.6218 (m-30) REVERT: A 239 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.7148 (m90) REVERT: A 450 ASP cc_start: 0.7402 (t0) cc_final: 0.6901 (m-30) REVERT: A 610 TRP cc_start: 0.3368 (OUTLIER) cc_final: 0.1935 (m-90) REVERT: A 695 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7958 (mtpt) REVERT: A 765 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7995 (mt0) REVERT: A 768 HIS cc_start: 0.7880 (m170) cc_final: 0.7516 (m90) REVERT: A 785 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7331 (mp0) REVERT: A 800 ARG cc_start: 0.6413 (tpt-90) cc_final: 0.6072 (mmm160) REVERT: A 815 ARG cc_start: 0.7591 (mtp85) cc_final: 0.6917 (mtm180) REVERT: A 823 CYS cc_start: 0.7271 (t) cc_final: 0.6897 (t) REVERT: A 836 ASP cc_start: 0.7585 (m-30) cc_final: 0.7116 (t0) REVERT: G 169 LEU cc_start: 0.5504 (OUTLIER) cc_final: 0.5211 (pt) REVERT: G 294 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8127 (ptm160) REVERT: G 622 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7755 (mtp-110) REVERT: G 688 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6045 (mmtt) REVERT: G 718 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.5824 (mp0) REVERT: G 766 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7340 (tt) REVERT: G 815 ARG cc_start: 0.7466 (mmm-85) cc_final: 0.7104 (mtp85) REVERT: G 823 CYS cc_start: 0.7597 (t) cc_final: 0.7052 (t) outliers start: 53 outliers final: 29 residues processed: 184 average time/residue: 1.0961 time to fit residues: 222.3414 Evaluate side-chains 162 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 688 LYS Chi-restraints excluded: chain G residue 718 GLU Chi-restraints excluded: chain G residue 750 LEU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 779 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.219960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179098 restraints weight = 15978.346| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.97 r_work: 0.4056 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12518 Z= 0.332 Angle : 0.738 10.812 16952 Z= 0.366 Chirality : 0.046 0.207 1892 Planarity : 0.005 0.069 2134 Dihedral : 9.303 141.240 1727 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.55 % Allowed : 29.25 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1500 helix: 0.96 (0.23), residues: 520 sheet: 0.13 (0.34), residues: 258 loop : -0.72 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 757 HIS 0.005 0.001 HIS G 638 PHE 0.027 0.002 PHE G 876 TYR 0.026 0.002 TYR A 591 ARG 0.008 0.001 ARG G 838 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 131 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7211 (m90) REVERT: A 610 TRP cc_start: 0.3691 (OUTLIER) cc_final: 0.2182 (m-90) REVERT: A 695 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7995 (mtpt) REVERT: A 765 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8060 (mt0) REVERT: A 768 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7674 (m90) REVERT: A 785 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7522 (mp0) REVERT: A 800 ARG cc_start: 0.6386 (tpt-90) cc_final: 0.5991 (mmm160) REVERT: A 815 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7093 (mtm-85) REVERT: A 817 LYS cc_start: 0.7606 (mtmm) cc_final: 0.7033 (mtpm) REVERT: A 823 CYS cc_start: 0.7342 (t) cc_final: 0.6981 (t) REVERT: A 836 ASP cc_start: 0.7683 (m-30) cc_final: 0.7210 (t0) REVERT: G 239 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7170 (m90) REVERT: G 294 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8216 (ptm160) REVERT: G 622 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7756 (mtp-110) REVERT: G 718 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.5938 (mp0) REVERT: G 744 LYS cc_start: 0.8324 (tptm) cc_final: 0.7998 (mppt) REVERT: G 766 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7343 (tt) REVERT: G 815 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7276 (mtp85) REVERT: G 823 CYS cc_start: 0.7666 (t) cc_final: 0.7077 (t) outliers start: 62 outliers final: 38 residues processed: 180 average time/residue: 1.1390 time to fit residues: 225.1691 Evaluate side-chains 168 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 599 ILE Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 680 VAL Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 699 LEU Chi-restraints excluded: chain G residue 718 GLU Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 779 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 131 optimal weight: 0.9980 chunk 79 optimal weight: 0.0270 chunk 34 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN G 174 ASN G 613 GLN ** G 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.223810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.184208 restraints weight = 15831.408| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 3.17 r_work: 0.4115 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12518 Z= 0.188 Angle : 0.653 9.735 16952 Z= 0.324 Chirality : 0.043 0.217 1892 Planarity : 0.005 0.057 2134 Dihedral : 8.911 136.278 1727 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.01 % Allowed : 30.94 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.23), residues: 1500 helix: 1.17 (0.24), residues: 524 sheet: 0.24 (0.34), residues: 272 loop : -0.54 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 757 HIS 0.002 0.001 HIS G 307 PHE 0.030 0.001 PHE G 876 TYR 0.009 0.001 TYR A 591 ARG 0.016 0.001 ARG A 746 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.6509 (m-30) cc_final: 0.6288 (m-30) REVERT: A 239 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.7173 (m90) REVERT: A 610 TRP cc_start: 0.3569 (OUTLIER) cc_final: 0.2089 (m-90) REVERT: A 622 ARG cc_start: 0.7700 (mtm180) cc_final: 0.7499 (mtp-110) REVERT: A 695 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7944 (mtpt) REVERT: A 701 ASP cc_start: 0.6923 (t0) cc_final: 0.6068 (p0) REVERT: A 765 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8088 (mt0) REVERT: A 768 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7594 (m90) REVERT: A 785 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7530 (mp0) REVERT: A 800 ARG cc_start: 0.6435 (tpt-90) cc_final: 0.6029 (mmm160) REVERT: A 815 ARG cc_start: 0.7432 (mtp85) cc_final: 0.6869 (mtm180) REVERT: A 817 LYS cc_start: 0.7611 (mtmm) cc_final: 0.7055 (mtpm) REVERT: A 823 CYS cc_start: 0.7246 (t) cc_final: 0.6872 (t) REVERT: A 836 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7209 (t0) REVERT: G 294 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8076 (ptm160) REVERT: G 572 GLU cc_start: 0.7828 (tp30) cc_final: 0.7519 (tp30) REVERT: G 622 ARG cc_start: 0.8000 (mtm180) cc_final: 0.7757 (mtp-110) REVERT: G 744 LYS cc_start: 0.8074 (tptm) cc_final: 0.7607 (mppt) REVERT: G 815 ARG cc_start: 0.7488 (mmm-85) cc_final: 0.7158 (mtp85) REVERT: G 823 CYS cc_start: 0.7624 (t) cc_final: 0.7097 (t) outliers start: 41 outliers final: 23 residues processed: 165 average time/residue: 1.1154 time to fit residues: 203.6214 Evaluate side-chains 158 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 599 ILE Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 779 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 103 optimal weight: 0.4980 chunk 138 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.0060 chunk 131 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 846 GLN G 613 GLN ** G 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.222146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.182586 restraints weight = 15947.429| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 3.14 r_work: 0.4094 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12518 Z= 0.230 Angle : 0.669 9.262 16952 Z= 0.332 Chirality : 0.043 0.201 1892 Planarity : 0.005 0.059 2134 Dihedral : 8.894 137.088 1726 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.01 % Allowed : 31.01 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.23), residues: 1500 helix: 1.18 (0.24), residues: 524 sheet: 0.23 (0.33), residues: 276 loop : -0.54 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 370 HIS 0.003 0.001 HIS G 175 PHE 0.029 0.002 PHE G 876 TYR 0.015 0.001 TYR A 591 ARG 0.013 0.001 ARG A 746 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8404.40 seconds wall clock time: 149 minutes 10.11 seconds (8950.11 seconds total)