Starting phenix.real_space_refine on Wed Sep 17 23:51:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xuo_38679/09_2025/8xuo_38679.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xuo_38679/09_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_38679/09_2025/8xuo_38679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xuo_38679/09_2025/8xuo_38679.map" model { file = "/net/cci-nas-00/data/ceres_data/8xuo_38679/09_2025/8xuo_38679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xuo_38679/09_2025/8xuo_38679.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.58, per 1000 atoms: 0.29 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: 1.19 Conformation dependent library (CDL) restraints added in 837.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.44 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: 2.34 Time building geometry restraints manager: 1.60 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: 0.02 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: 2.960 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- 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= 0.247 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 : 8.69 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG G 683 TYR 0.016 0.001 TYR A 591 PHE 0.021 0.001 PHE G 779 TRP 0.015 0.001 TRP G 754 HIS 0.006 0.001 HIS G 638 Details of bonding type rmsd covalent geometry : bond 0.00422 (12518) covalent geometry : angle 0.83183 (16952) hydrogen bonds : bond 0.19062 ( 439) hydrogen bonds : angle 6.65755 ( 1224) *********************** 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 : 0.433 Fit side-chains 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: 0.4512 time to fit residues: 90.0296 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 : 0.506 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 287 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.228151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.185342 restraints weight = 15821.900| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 3.22 r_work: 0.4174 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1952 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= 0.226 Angle : 0.857 14.182 16952 Z= 0.402 Chirality : 0.050 0.483 1892 Planarity : 0.005 0.049 2134 Dihedral : 12.262 178.848 1769 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 6.60 % Allowed : 23.31 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.21), residues: 1500 helix: 0.90 (0.22), residues: 520 sheet: 0.52 (0.36), residues: 216 loop : -0.53 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 683 TYR 0.027 0.002 TYR G 591 PHE 0.016 0.002 PHE G 583 TRP 0.019 0.002 TRP G 211 HIS 0.006 0.002 HIS G 638 Details of bonding type rmsd covalent geometry : bond 0.00540 (12518) covalent geometry : angle 0.85696 (16952) hydrogen bonds : bond 0.05243 ( 439) hydrogen bonds : angle 5.08221 ( 1224) *********************** 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 241 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 151 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8934 (t) cc_final: 0.8729 (m) REVERT: A 219 ARG cc_start: 0.6976 (mtp-110) cc_final: 0.6496 (mtp-110) REVERT: A 420 GLN cc_start: 0.8341 (mm110) cc_final: 0.8136 (mm110) REVERT: A 504 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6904 (pm20) REVERT: A 610 TRP cc_start: 0.3255 (OUTLIER) cc_final: 0.2053 (m-90) REVERT: A 772 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8335 (tt) REVERT: A 777 ASN cc_start: 0.7144 (m-40) cc_final: 0.6859 (t0) REVERT: A 800 ARG cc_start: 0.6545 (tpt-90) cc_final: 0.6002 (tpm170) REVERT: A 844 MET cc_start: 0.7070 (tmm) cc_final: 0.6797 (tmm) REVERT: G 204 TYR cc_start: 0.5668 (OUTLIER) cc_final: 0.5430 (t80) REVERT: G 294 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8165 (ptm160) REVERT: G 579 PHE cc_start: 0.5774 (m-80) cc_final: 0.5274 (m-80) REVERT: G 581 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6787 (ptt180) REVERT: G 687 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6758 (mp) REVERT: G 718 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.5537 (mm-30) REVERT: G 732 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7667 (ptmt) outliers start: 90 outliers final: 34 residues processed: 223 average time/residue: 0.5477 time to fit residues: 133.4566 Evaluate side-chains 161 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 356 ILE 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 583 PHE 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 204 TYR 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 591 TYR 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 Chi-restraints excluded: chain G residue 817 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 93 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN G 380 HIS G 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.229770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.189054 restraints weight = 16080.189| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.05 r_work: 0.4153 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12518 Z= 0.128 Angle : 0.641 9.766 16952 Z= 0.313 Chirality : 0.043 0.350 1892 Planarity : 0.004 0.041 2134 Dihedral : 10.817 163.336 1739 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.91 % Allowed : 24.49 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.22), residues: 1500 helix: 1.23 (0.23), residues: 528 sheet: 0.71 (0.37), residues: 220 loop : -0.40 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 815 TYR 0.014 0.001 TYR G 591 PHE 0.017 0.001 PHE G 779 TRP 0.013 0.001 TRP A 757 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00296 (12518) covalent geometry : angle 0.64125 (16952) hydrogen bonds : bond 0.03788 ( 439) hydrogen bonds : angle 4.64936 ( 1224) *********************** 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 205 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 138 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.8807 (t) cc_final: 0.8556 (p) REVERT: A 219 ARG cc_start: 0.6954 (mtp-110) cc_final: 0.6468 (mtp-110) REVERT: A 239 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.6811 (m90) REVERT: A 301 GLN cc_start: 0.6760 (mt0) cc_final: 0.6433 (mt0) REVERT: A 539 ARG cc_start: 0.5758 (mmt-90) cc_final: 0.5550 (mmt180) REVERT: A 695 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8126 (mtpt) REVERT: A 777 ASN cc_start: 0.7164 (m-40) cc_final: 0.6872 (m-40) REVERT: A 800 ARG cc_start: 0.6453 (tpt-90) cc_final: 0.5894 (tpm170) REVERT: A 841 GLN cc_start: 0.5761 (OUTLIER) cc_final: 0.5417 (mm-40) REVERT: A 844 MET cc_start: 0.6969 (tmm) cc_final: 0.6702 (tmm) REVERT: G 491 LYS cc_start: 0.7727 (tttt) cc_final: 0.7461 (ttpt) REVERT: G 579 PHE cc_start: 0.5701 (m-80) cc_final: 0.5322 (m-80) REVERT: G 581 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6736 (ptt180) REVERT: G 785 GLU cc_start: 0.7846 (mp0) cc_final: 0.7624 (mp0) outliers start: 67 outliers final: 21 residues processed: 191 average time/residue: 0.5662 time to fit residues: 118.2744 Evaluate side-chains 145 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 370 TRP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 841 GLN 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 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 671 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 75 optimal weight: 40.0000 chunk 110 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 640 HIS A 666 GLN ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.226806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.185713 restraints weight = 16052.407| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 3.00 r_work: 0.4111 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12518 Z= 0.155 Angle : 0.651 8.806 16952 Z= 0.318 Chirality : 0.044 0.225 1892 Planarity : 0.005 0.087 2134 Dihedral : 9.482 145.370 1728 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.01 % Allowed : 24.71 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.22), residues: 1500 helix: 1.23 (0.23), residues: 522 sheet: 0.63 (0.36), residues: 220 loop : -0.43 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 815 TYR 0.021 0.001 TYR G 591 PHE 0.022 0.002 PHE G 876 TRP 0.023 0.001 TRP G 754 HIS 0.005 0.001 HIS G 638 Details of bonding type rmsd covalent geometry : bond 0.00366 (12518) covalent geometry : angle 0.65072 (16952) hydrogen bonds : bond 0.03998 ( 439) hydrogen bonds : angle 4.61238 ( 1224) *********************** 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 222 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 140 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.6888 (m90) REVERT: A 301 GLN cc_start: 0.6819 (mt0) cc_final: 0.6603 (mt0) REVERT: A 610 TRP cc_start: 0.3292 (OUTLIER) cc_final: 0.2023 (m-90) REVERT: A 695 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8122 (mtpt) REVERT: A 777 ASN cc_start: 0.7327 (m-40) cc_final: 0.7010 (m-40) REVERT: A 785 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6675 (mp0) REVERT: A 800 ARG cc_start: 0.6533 (tpt-90) cc_final: 0.5943 (tpm170) REVERT: A 841 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5732 (mm-40) REVERT: A 844 MET cc_start: 0.7207 (tmm) cc_final: 0.6731 (tmt) REVERT: G 294 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8147 (ptm160) REVERT: G 491 LYS cc_start: 0.7699 (tttt) cc_final: 0.7497 (ttpt) REVERT: G 579 PHE cc_start: 0.5761 (m-80) cc_final: 0.5392 (m-80) REVERT: G 718 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.5560 (mm-30) REVERT: G 732 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7458 (ptmt) REVERT: G 766 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7446 (tt) REVERT: G 815 ARG cc_start: 0.7339 (mmm-85) cc_final: 0.6340 (mtt90) REVERT: G 823 CYS cc_start: 0.7420 (t) cc_final: 0.6876 (t) outliers start: 82 outliers final: 31 residues processed: 206 average time/residue: 0.5277 time to fit residues: 119.9071 Evaluate side-chains 160 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 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 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 469 ASP 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 687 LEU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 841 GLN 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 525 VAL Chi-restraints excluded: chain G residue 592 VAL 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 718 GLU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 779 PHE Chi-restraints excluded: chain G residue 817 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 141 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 93 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 HIS A 666 GLN A 818 HIS ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.221554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.178577 restraints weight = 16047.532| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.37 r_work: 0.4099 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12518 Z= 0.207 Angle : 0.705 8.725 16952 Z= 0.348 Chirality : 0.046 0.216 1892 Planarity : 0.006 0.090 2134 Dihedral : 9.351 144.902 1728 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.65 % Allowed : 25.95 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.22), residues: 1500 helix: 0.94 (0.23), residues: 534 sheet: 0.37 (0.34), residues: 252 loop : -0.64 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 511 TYR 0.029 0.002 TYR G 591 PHE 0.022 0.002 PHE G 876 TRP 0.012 0.001 TRP G 211 HIS 0.005 0.001 HIS G 638 Details of bonding type rmsd covalent geometry : bond 0.00506 (12518) covalent geometry : angle 0.70511 (16952) hydrogen bonds : bond 0.04685 ( 439) hydrogen bonds : angle 4.76606 ( 1224) *********************** 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 216 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 139 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7597 (OUTLIER) cc_final: 0.7044 (m90) REVERT: A 542 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7600 (mt) REVERT: A 610 TRP cc_start: 0.3324 (OUTLIER) cc_final: 0.1993 (m-90) REVERT: A 695 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8118 (mtpt) REVERT: A 772 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8361 (tt) REVERT: A 785 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7013 (mp0) REVERT: A 800 ARG cc_start: 0.6468 (tpt-90) cc_final: 0.5812 (tpm170) REVERT: A 841 GLN cc_start: 0.6449 (OUTLIER) cc_final: 0.6240 (mp10) REVERT: A 844 MET cc_start: 0.7345 (tmm) cc_final: 0.6831 (tmt) REVERT: G 239 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.6964 (m90) REVERT: G 294 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8208 (ptm160) REVERT: G 579 PHE cc_start: 0.6030 (m-80) cc_final: 0.5721 (m-80) REVERT: G 718 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.5678 (mm-30) REVERT: G 732 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7423 (ptmt) REVERT: G 785 GLU cc_start: 0.7861 (mp0) cc_final: 0.7546 (mp0) REVERT: G 816 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6815 (tt) REVERT: G 823 CYS cc_start: 0.7517 (t) cc_final: 0.6922 (t) outliers start: 77 outliers final: 36 residues processed: 202 average time/residue: 0.5471 time to fit residues: 121.0206 Evaluate side-chains 170 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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 356 ILE 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 542 LEU 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 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 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 841 GLN 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 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 301 GLN 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 680 VAL 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 816 LEU Chi-restraints excluded: chain G residue 855 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 10 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 128 optimal weight: 0.3980 chunk 106 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 818 HIS G 174 ASN 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 = 0.4681 r_free = 0.4681 target = 0.227561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.186888 restraints weight = 16063.096| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 3.02 r_work: 0.4154 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12518 Z= 0.116 Angle : 0.613 7.823 16952 Z= 0.300 Chirality : 0.042 0.236 1892 Planarity : 0.004 0.070 2134 Dihedral : 8.872 143.388 1728 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.25 % Allowed : 27.71 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1500 helix: 1.29 (0.23), residues: 522 sheet: 0.35 (0.33), residues: 274 loop : -0.38 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 288 TYR 0.008 0.001 TYR G 591 PHE 0.028 0.001 PHE G 876 TRP 0.011 0.001 TRP A 631 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00274 (12518) covalent geometry : angle 0.61338 (16952) hydrogen bonds : bond 0.03198 ( 439) hydrogen bonds : angle 4.41069 ( 1224) *********************** 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 202 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 144 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7092 (m90) REVERT: A 246 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6937 (mt) REVERT: A 610 TRP cc_start: 0.3264 (OUTLIER) cc_final: 0.1912 (m-90) REVERT: A 695 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8102 (mtpt) REVERT: A 772 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8431 (tt) REVERT: A 785 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7010 (mp0) REVERT: A 800 ARG cc_start: 0.6477 (tpt-90) cc_final: 0.5839 (tpm170) REVERT: A 844 MET cc_start: 0.7090 (tmm) cc_final: 0.6763 (tmt) REVERT: G 239 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6966 (m90) REVERT: G 294 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8068 (ptm160) REVERT: G 572 GLU cc_start: 0.7785 (tp30) cc_final: 0.7496 (tp30) REVERT: G 579 PHE cc_start: 0.5794 (m-80) cc_final: 0.5468 (m-80) REVERT: G 622 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7661 (mtp-110) REVERT: G 732 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7438 (ptmt) REVERT: G 766 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7345 (tt) REVERT: G 785 GLU cc_start: 0.7882 (mp0) cc_final: 0.7556 (mp0) REVERT: G 815 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.6636 (mtt90) REVERT: G 823 CYS cc_start: 0.7464 (t) cc_final: 0.6963 (t) outliers start: 58 outliers final: 23 residues processed: 192 average time/residue: 0.5076 time to fit residues: 107.7470 Evaluate side-chains 159 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU 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 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 G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL 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 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 630 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 A 818 HIS G 287 ASN G 487 GLN G 613 GLN G 638 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.217956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.177183 restraints weight = 15976.059| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.91 r_work: 0.4056 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 12518 Z= 0.270 Angle : 0.809 11.285 16952 Z= 0.400 Chirality : 0.048 0.230 1892 Planarity : 0.006 0.059 2134 Dihedral : 9.598 144.555 1727 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.13 % Allowed : 28.01 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.22), residues: 1500 helix: 0.67 (0.22), residues: 530 sheet: -0.00 (0.33), residues: 258 loop : -0.85 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 590 TYR 0.037 0.003 TYR G 591 PHE 0.023 0.003 PHE G 876 TRP 0.014 0.002 TRP G 211 HIS 0.005 0.001 HIS G 638 Details of bonding type rmsd covalent geometry : bond 0.00665 (12518) covalent geometry : angle 0.80927 (16952) hydrogen bonds : bond 0.05699 ( 439) hydrogen bonds : angle 5.03471 ( 1224) *********************** 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 209 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 139 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7274 (m90) REVERT: A 270 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: A 274 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: A 581 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7493 (ptm-80) REVERT: A 610 TRP cc_start: 0.3587 (OUTLIER) cc_final: 0.2110 (m-90) REVERT: A 695 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8162 (mtpt) REVERT: A 765 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7954 (mt0) REVERT: A 768 HIS cc_start: 0.8097 (m170) cc_final: 0.7730 (m90) REVERT: A 785 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7243 (mp0) REVERT: A 800 ARG cc_start: 0.6431 (tpt-90) cc_final: 0.5987 (mmm160) REVERT: A 823 CYS cc_start: 0.7252 (t) cc_final: 0.6936 (t) REVERT: A 844 MET cc_start: 0.6960 (tmm) cc_final: 0.6731 (tmt) REVERT: G 239 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.7282 (m90) REVERT: G 294 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8320 (ptm160) REVERT: G 718 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6291 (mp0) REVERT: G 732 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7467 (ptmt) REVERT: G 766 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7397 (tt) REVERT: G 815 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7306 (mtp85) REVERT: G 823 CYS cc_start: 0.7676 (t) cc_final: 0.7065 (t) outliers start: 70 outliers final: 34 residues processed: 194 average time/residue: 0.5529 time to fit residues: 117.0309 Evaluate side-chains 167 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 356 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 579 PHE 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 687 LEU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 805 SER 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 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 622 ARG Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 667 THR 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 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 35 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 818 HIS G 487 GLN G 613 GLN G 865 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.221887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.181486 restraints weight = 15879.321| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.95 r_work: 0.4087 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4656 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= 0.162 Angle : 0.690 8.479 16952 Z= 0.340 Chirality : 0.044 0.228 1892 Planarity : 0.005 0.050 2134 Dihedral : 9.268 140.695 1727 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.67 % Allowed : 30.21 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.22), residues: 1500 helix: 1.02 (0.23), residues: 522 sheet: 0.09 (0.34), residues: 254 loop : -0.74 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 746 TYR 0.018 0.001 TYR G 591 PHE 0.028 0.002 PHE G 876 TRP 0.013 0.002 TRP G 754 HIS 0.002 0.001 HIS G 818 Details of bonding type rmsd covalent geometry : bond 0.00399 (12518) covalent geometry : angle 0.69041 (16952) hydrogen bonds : bond 0.03986 ( 439) hydrogen bonds : angle 4.63141 ( 1224) *********************** 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 187 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7189 (m90) REVERT: A 581 ARG cc_start: 0.7625 (mtm110) cc_final: 0.7392 (ptm-80) REVERT: A 610 TRP cc_start: 0.3526 (OUTLIER) cc_final: 0.2061 (m-90) REVERT: A 695 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8031 (mtpt) REVERT: A 765 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7963 (mt0) REVERT: A 768 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7669 (m90) REVERT: A 772 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 785 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7373 (mp0) REVERT: A 800 ARG cc_start: 0.6406 (tpt-90) cc_final: 0.6085 (mmm160) REVERT: A 817 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7054 (mttp) REVERT: A 823 CYS cc_start: 0.7208 (t) cc_final: 0.6887 (t) REVERT: A 836 ASP cc_start: 0.8028 (t0) cc_final: 0.7573 (t0) REVERT: A 838 ARG cc_start: 0.6801 (mpp-170) cc_final: 0.6518 (mmt180) REVERT: A 844 MET cc_start: 0.7041 (tmm) cc_final: 0.6705 (tmt) REVERT: G 239 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7164 (m90) REVERT: G 294 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8159 (ptm160) REVERT: G 622 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7728 (mtp-110) REVERT: G 718 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: G 766 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7361 (tt) REVERT: G 815 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.7225 (mtp85) REVERT: G 823 CYS cc_start: 0.7625 (t) cc_final: 0.7084 (t) outliers start: 50 outliers final: 23 residues processed: 177 average time/residue: 0.5206 time to fit residues: 101.9010 Evaluate side-chains 161 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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 579 PHE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP 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 772 LEU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 141 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 818 HIS G 487 GLN G 613 GLN G 858 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.220988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.181898 restraints weight = 15845.032| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 3.27 r_work: 0.4068 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12518 Z= 0.160 Angle : 0.681 9.142 16952 Z= 0.337 Chirality : 0.044 0.215 1892 Planarity : 0.005 0.052 2134 Dihedral : 9.151 139.250 1727 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.45 % Allowed : 30.43 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.22), residues: 1500 helix: 1.07 (0.23), residues: 522 sheet: 0.08 (0.34), residues: 258 loop : -0.71 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 746 TYR 0.020 0.002 TYR G 591 PHE 0.030 0.002 PHE G 876 TRP 0.015 0.001 TRP A 757 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00394 (12518) covalent geometry : angle 0.68055 (16952) hydrogen bonds : bond 0.04033 ( 439) hydrogen bonds : angle 4.60046 ( 1224) *********************** 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 180 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.4319 (OUTLIER) cc_final: 0.4008 (tm-30) REVERT: A 239 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7180 (m90) REVERT: A 581 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7403 (ptm-80) REVERT: A 610 TRP cc_start: 0.3651 (OUTLIER) cc_final: 0.2144 (m-90) REVERT: A 695 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8003 (mtpt) REVERT: A 765 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8054 (mt0) REVERT: A 768 HIS cc_start: 0.8077 (OUTLIER) cc_final: 0.7701 (m90) REVERT: A 785 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7480 (mp0) REVERT: A 800 ARG cc_start: 0.6385 (tpt-90) cc_final: 0.6066 (mmm160) REVERT: A 823 CYS cc_start: 0.7157 (t) cc_final: 0.6835 (t) REVERT: A 836 ASP cc_start: 0.8041 (t0) cc_final: 0.7427 (t0) REVERT: A 844 MET cc_start: 0.7055 (tmm) cc_final: 0.6704 (tmt) REVERT: G 239 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7143 (m90) REVERT: G 294 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8175 (ptm160) REVERT: G 622 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7787 (mtp-110) REVERT: G 718 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.5976 (mp0) REVERT: G 766 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7390 (tt) REVERT: G 815 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7256 (mtp85) REVERT: G 823 CYS cc_start: 0.7693 (t) cc_final: 0.7131 (t) outliers start: 47 outliers final: 25 residues processed: 173 average time/residue: 0.5118 time to fit residues: 97.6759 Evaluate side-chains 161 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU 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 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 579 PHE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP 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 G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 128 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 818 HIS A 846 GLN 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 = 0.4611 r_free = 0.4611 target = 0.220460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.180369 restraints weight = 15949.594| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 3.21 r_work: 0.4063 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12518 Z= 0.168 Angle : 0.695 9.130 16952 Z= 0.345 Chirality : 0.044 0.211 1892 Planarity : 0.005 0.053 2134 Dihedral : 9.185 138.822 1727 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.23 % Allowed : 30.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.22), residues: 1500 helix: 1.00 (0.23), residues: 522 sheet: -0.07 (0.32), residues: 278 loop : -0.64 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 746 TYR 0.020 0.002 TYR G 591 PHE 0.029 0.002 PHE G 876 TRP 0.014 0.002 TRP A 757 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00414 (12518) covalent geometry : angle 0.69525 (16952) hydrogen bonds : bond 0.04126 ( 439) hydrogen bonds : angle 4.62262 ( 1224) ********************** 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 178 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7215 (m90) REVERT: A 581 ARG cc_start: 0.7587 (mtm110) cc_final: 0.7367 (ptm-80) REVERT: A 610 TRP cc_start: 0.3676 (OUTLIER) cc_final: 0.2121 (m-90) REVERT: A 695 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7994 (mtpt) REVERT: A 701 ASP cc_start: 0.6903 (t0) cc_final: 0.5954 (p0) REVERT: A 758 LYS cc_start: 0.9111 (tptp) cc_final: 0.8877 (ttpm) REVERT: A 765 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8165 (mt0) REVERT: A 768 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7694 (m90) REVERT: A 800 ARG cc_start: 0.6404 (tpt-90) cc_final: 0.6031 (mmm160) REVERT: A 817 LYS cc_start: 0.7796 (mtmt) cc_final: 0.7326 (mtpm) REVERT: A 823 CYS cc_start: 0.7214 (t) cc_final: 0.6863 (t) REVERT: A 844 MET cc_start: 0.7074 (tmm) cc_final: 0.6704 (tmt) REVERT: G 239 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7115 (m90) REVERT: G 294 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8185 (ptm160) REVERT: G 375 ASP cc_start: 0.8439 (m-30) cc_final: 0.8133 (p0) REVERT: G 622 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7758 (mtp-110) REVERT: G 718 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6047 (mp0) REVERT: G 744 LYS cc_start: 0.8282 (tptm) cc_final: 0.7966 (mppt) REVERT: G 746 ARG cc_start: 0.6919 (ttt-90) cc_final: 0.6638 (mtm110) REVERT: G 766 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7374 (tt) REVERT: G 815 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.7304 (mtp85) REVERT: G 823 CYS cc_start: 0.7677 (t) cc_final: 0.7122 (t) outliers start: 44 outliers final: 25 residues processed: 172 average time/residue: 0.5121 time to fit residues: 97.0288 Evaluate side-chains 163 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 525 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP 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 G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL 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 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 687 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 110 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 77 optimal weight: 0.0030 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 818 HIS G 487 GLN G 613 GLN G 710 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.220414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.181389 restraints weight = 15848.835| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 3.23 r_work: 0.4053 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12518 Z= 0.165 Angle : 0.686 8.885 16952 Z= 0.340 Chirality : 0.044 0.209 1892 Planarity : 0.005 0.054 2134 Dihedral : 9.171 137.730 1727 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.45 % Allowed : 30.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.22), residues: 1500 helix: 0.99 (0.23), residues: 522 sheet: -0.08 (0.32), residues: 278 loop : -0.64 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 746 TYR 0.020 0.002 TYR G 591 PHE 0.028 0.002 PHE G 876 TRP 0.016 0.001 TRP A 757 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00404 (12518) covalent geometry : angle 0.68620 (16952) hydrogen bonds : bond 0.04031 ( 439) hydrogen bonds : angle 4.64083 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4564.50 seconds wall clock time: 78 minutes 37.19 seconds (4717.19 seconds total)