Starting phenix.real_space_refine on Sun Jun 29 19:32:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvz_37880/06_2025/8wvz_37880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvz_37880/06_2025/8wvz_37880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wvz_37880/06_2025/8wvz_37880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvz_37880/06_2025/8wvz_37880.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvz_37880/06_2025/8wvz_37880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvz_37880/06_2025/8wvz_37880.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 6 5.21 5 S 159 5.16 5 C 22191 2.51 5 N 5856 2.21 5 O 6368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34621 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5347 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 613} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5347 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 613} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5347 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 613} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 5333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5333 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 611} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 7148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 7148 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 828} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5347 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 613} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.90, per 1000 atoms: 0.57 Number of scatterers: 34621 At special positions: 0 Unit cell: (151.11, 153.3, 176.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 159 16.00 P 41 15.00 Mg 6 11.99 O 6368 8.00 N 5856 7.00 C 22191 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: 8.20 Conformation dependent library (CDL) restraints added in 4.1 seconds 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7868 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 29 sheets defined 49.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.615A pdb=" N LEU A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 removed outlier: 4.384A pdb=" N ARG A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.736A pdb=" N TYR A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 through 353 removed outlier: 3.982A pdb=" N THR A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 375 through 386 removed outlier: 3.514A pdb=" N MET A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 409 removed outlier: 3.570A pdb=" N TYR A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 476 through 494 removed outlier: 4.125A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 494 " --> pdb=" O TYR A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 removed outlier: 3.582A pdb=" N ASN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 520 through 535 removed outlier: 4.215A pdb=" N PHE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.613A pdb=" N THR A 620 " --> pdb=" O PHE A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 654 removed outlier: 3.771A pdb=" N LEU A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 746 through 752 removed outlier: 3.559A pdb=" N TRP A 750 " --> pdb=" O ASP A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 810 Processing helix chain 'A' and resid 823 through 831 Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 854 through 870 removed outlier: 4.024A pdb=" N VAL A 858 " --> pdb=" O ASN A 854 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 868 " --> pdb=" O GLU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 882 removed outlier: 4.480A pdb=" N GLN A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 296 through 309 removed outlier: 4.125A pdb=" N ALA B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 317 Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 335 through 344 removed outlier: 3.639A pdb=" N GLN B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 377 through 386 removed outlier: 4.017A pdb=" N HIS B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 409 Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.516A pdb=" N ILE B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 476 Processing helix chain 'B' and resid 476 through 494 removed outlier: 3.928A pdb=" N VAL B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 494 " --> pdb=" O TYR B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.726A pdb=" N LEU B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 497 through 502' Processing helix chain 'B' and resid 502 through 516 removed outlier: 4.367A pdb=" N SER B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 520 through 535 removed outlier: 4.255A pdb=" N PHE B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.700A pdb=" N THR B 620 " --> pdb=" O PHE B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 654 Processing helix chain 'B' and resid 663 through 668 removed outlier: 4.182A pdb=" N SER B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 748 through 751 removed outlier: 3.878A pdb=" N ARG B 751 " --> pdb=" O GLY B 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 751' Processing helix chain 'B' and resid 778 through 783 Processing helix chain 'B' and resid 787 through 808 removed outlier: 3.734A pdb=" N GLN B 791 " --> pdb=" O ASP B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 831 Processing helix chain 'B' and resid 833 through 843 Processing helix chain 'B' and resid 854 through 870 removed outlier: 3.831A pdb=" N VAL B 858 " --> pdb=" O ASN B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 887 removed outlier: 3.819A pdb=" N LEU B 880 " --> pdb=" O ILE B 876 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 886 " --> pdb=" O GLN B 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 297 removed outlier: 4.455A pdb=" N ASP C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 311 through 317 removed outlier: 3.841A pdb=" N TYR C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 331 Processing helix chain 'C' and resid 335 through 345 Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 354 through 367 Processing helix chain 'C' and resid 374 through 386 removed outlier: 3.716A pdb=" N ILE C 378 " --> pdb=" O THR C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 409 removed outlier: 3.747A pdb=" N GLU C 392 " --> pdb=" O GLN C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 425 removed outlier: 3.538A pdb=" N ILE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 Processing helix chain 'C' and resid 476 through 494 removed outlier: 3.795A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 516 removed outlier: 3.692A pdb=" N ASN C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 520 through 535 removed outlier: 4.281A pdb=" N PHE C 533 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 605 removed outlier: 3.574A pdb=" N ILE C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 621 through 623 No H-bonds generated for 'chain 'C' and resid 621 through 623' Processing helix chain 'C' and resid 641 through 657 removed outlier: 3.649A pdb=" N LEU C 645 " --> pdb=" O GLY C 641 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP C 655 " --> pdb=" O MET C 651 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N HIS C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 666 Processing helix chain 'C' and resid 705 through 710 Processing helix chain 'C' and resid 746 through 752 removed outlier: 4.122A pdb=" N ARG C 752 " --> pdb=" O GLY C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 787 through 809 removed outlier: 3.614A pdb=" N GLN C 791 " --> pdb=" O ASP C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 823 through 831 Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.938A pdb=" N ARG C 837 " --> pdb=" O ASP C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 870 removed outlier: 3.916A pdb=" N THR C 868 " --> pdb=" O GLU C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 882 removed outlier: 4.054A pdb=" N GLN C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 886 Processing helix chain 'C' and resid 888 through 891 removed outlier: 3.935A pdb=" N LYS C 891 " --> pdb=" O VAL C 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 888 through 891' Processing helix chain 'D' and resid 290 through 297 removed outlier: 3.681A pdb=" N HIS D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 309 removed outlier: 3.933A pdb=" N ARG D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 317 through 331 removed outlier: 4.004A pdb=" N THR D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 Processing helix chain 'D' and resid 347 through 351 removed outlier: 3.743A pdb=" N TRP D 350 " --> pdb=" O PRO D 347 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN D 351 " --> pdb=" O GLU D 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 347 through 351' Processing helix chain 'D' and resid 353 through 368 removed outlier: 3.822A pdb=" N LYS D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N HIS D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 388 through 409 Processing helix chain 'D' and resid 414 through 427 removed outlier: 3.554A pdb=" N ILE D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 476 Processing helix chain 'D' and resid 476 through 494 removed outlier: 4.175A pdb=" N VAL D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN D 494 " --> pdb=" O TYR D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 removed outlier: 4.121A pdb=" N LEU D 501 " --> pdb=" O GLU D 497 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 520 through 535 removed outlier: 4.218A pdb=" N PHE D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 605 removed outlier: 3.546A pdb=" N ILE D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.660A pdb=" N THR D 620 " --> pdb=" O PHE D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 654 removed outlier: 4.040A pdb=" N MET D 646 " --> pdb=" O LYS D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 666 Processing helix chain 'D' and resid 704 through 710 Processing helix chain 'D' and resid 746 through 752 removed outlier: 3.772A pdb=" N TRP D 750 " --> pdb=" O ASP D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 783 Processing helix chain 'D' and resid 787 through 810 removed outlier: 3.793A pdb=" N GLN D 791 " --> pdb=" O ASP D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 816 Processing helix chain 'D' and resid 819 through 831 removed outlier: 3.828A pdb=" N SER D 823 " --> pdb=" O PRO D 819 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR D 825 " --> pdb=" O ILE D 821 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 831 " --> pdb=" O ALA D 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 843 Processing helix chain 'D' and resid 854 through 870 removed outlier: 3.860A pdb=" N VAL D 858 " --> pdb=" O ASN D 854 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR D 860 " --> pdb=" O SER D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 886 Processing helix chain 'D' and resid 889 through 893 removed outlier: 3.507A pdb=" N TYR D 892 " --> pdb=" O LEU D 889 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 893 " --> pdb=" O GLU D 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 889 through 893' Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.576A pdb=" N GLU E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 79 Processing helix chain 'E' and resid 111 through 128 removed outlier: 4.304A pdb=" N ASN E 128 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.732A pdb=" N LYS E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 190 Processing helix chain 'E' and resid 251 through 257 Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 297 through 309 removed outlier: 3.732A pdb=" N ARG E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 330 Processing helix chain 'E' and resid 335 through 343 Processing helix chain 'E' and resid 356 through 367 removed outlier: 3.952A pdb=" N HIS E 367 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 386 removed outlier: 3.976A pdb=" N TYR E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 409 Processing helix chain 'E' and resid 414 through 427 removed outlier: 3.573A pdb=" N ILE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 494 removed outlier: 4.161A pdb=" N PHE E 477 " --> pdb=" O ILE E 473 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER E 478 " --> pdb=" O SER E 474 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN E 494 " --> pdb=" O TYR E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 516 removed outlier: 4.143A pdb=" N ASN E 502 " --> pdb=" O SER E 498 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR E 504 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS E 505 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER E 516 " --> pdb=" O GLU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 519 No H-bonds generated for 'chain 'E' and resid 517 through 519' Processing helix chain 'E' and resid 520 through 535 removed outlier: 3.892A pdb=" N PHE E 533 " --> pdb=" O ARG E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 605 removed outlier: 3.595A pdb=" N ILE E 605 " --> pdb=" O LEU E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 620 removed outlier: 3.814A pdb=" N THR E 620 " --> pdb=" O PHE E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 623 No H-bonds generated for 'chain 'E' and resid 621 through 623' Processing helix chain 'E' and resid 641 through 654 removed outlier: 3.519A pdb=" N GLY E 654 " --> pdb=" O ALA E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 666 Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.525A pdb=" N MET E 681 " --> pdb=" O SER E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 710 Processing helix chain 'E' and resid 746 through 752 removed outlier: 3.768A pdb=" N ARG E 752 " --> pdb=" O GLY E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 783 removed outlier: 3.823A pdb=" N ILE E 781 " --> pdb=" O ASP E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 810 removed outlier: 3.557A pdb=" N GLN E 791 " --> pdb=" O ASP E 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 831 Processing helix chain 'E' and resid 833 through 843 removed outlier: 3.542A pdb=" N ARG E 837 " --> pdb=" O ASP E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 854 through 870 removed outlier: 3.847A pdb=" N VAL E 858 " --> pdb=" O ASN E 854 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR E 868 " --> pdb=" O GLU E 864 " (cutoff:3.500A) Processing helix chain 'E' and resid 876 through 886 removed outlier: 3.703A pdb=" N LEU E 884 " --> pdb=" O LEU E 880 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU E 885 " --> pdb=" O SER E 881 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN E 886 " --> pdb=" O GLN E 882 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 893 removed outlier: 4.061A pdb=" N LYS E 891 " --> pdb=" O VAL E 888 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR E 892 " --> pdb=" O LEU E 889 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 removed outlier: 3.901A pdb=" N HIS F 296 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 310 removed outlier: 3.808A pdb=" N ARG F 301 " --> pdb=" O ASP F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 317 Processing helix chain 'F' and resid 317 through 330 Processing helix chain 'F' and resid 335 through 345 Processing helix chain 'F' and resid 356 through 366 Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.566A pdb=" N TYR F 380 " --> pdb=" O ARG F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 409 removed outlier: 3.662A pdb=" N GLU F 392 " --> pdb=" O GLN F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.609A pdb=" N ILE F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 476 removed outlier: 4.014A pdb=" N SER F 474 " --> pdb=" O HIS F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 494 removed outlier: 3.880A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 516 removed outlier: 3.623A pdb=" N ASN F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR F 504 " --> pdb=" O ILE F 500 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS F 505 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER F 516 " --> pdb=" O GLU F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 519 No H-bonds generated for 'chain 'F' and resid 517 through 519' Processing helix chain 'F' and resid 520 through 535 removed outlier: 4.333A pdb=" N PHE F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU F 534 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 605 Processing helix chain 'F' and resid 607 through 620 removed outlier: 3.635A pdb=" N THR F 620 " --> pdb=" O PHE F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 654 removed outlier: 3.760A pdb=" N LEU F 645 " --> pdb=" O GLY F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 710 Processing helix chain 'F' and resid 748 through 751 Processing helix chain 'F' and resid 787 through 810 Processing helix chain 'F' and resid 823 through 831 Processing helix chain 'F' and resid 833 through 843 removed outlier: 3.897A pdb=" N ARG F 837 " --> pdb=" O ASP F 833 " (cutoff:3.500A) Processing helix chain 'F' and resid 855 through 870 Processing helix chain 'F' and resid 877 through 884 removed outlier: 4.364A pdb=" N GLN F 882 " --> pdb=" O LEU F 878 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU F 884 " --> pdb=" O LEU F 880 " (cutoff:3.500A) Processing helix chain 'F' and resid 888 through 893 removed outlier: 3.640A pdb=" N LYS F 891 " --> pdb=" O VAL F 888 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR F 892 " --> pdb=" O LEU F 889 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 893 " --> pdb=" O GLU F 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 888 through 893' Processing sheet with id=AA1, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.724A pdb=" N TRP A 442 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.640A pdb=" N GLY A 556 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 660 removed outlier: 3.964A pdb=" N TYR A 690 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 632 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 714 through 716 Processing sheet with id=AA5, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.685A pdb=" N TRP B 442 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 550 through 553 Processing sheet with id=AA7, first strand: chain 'B' and resid 658 through 660 removed outlier: 3.707A pdb=" N TYR B 690 " --> pdb=" O SER B 659 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N MET B 631 " --> pdb=" O ARG B 754 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N TYR B 756 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 633 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 713 through 716 removed outlier: 3.532A pdb=" N GLU B 724 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 761 through 762 removed outlier: 7.155A pdb=" N LYS B 761 " --> pdb=" O LYS B 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 431 through 434 removed outlier: 3.761A pdb=" N TRP C 442 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 550 through 553 Processing sheet with id=AB3, first strand: chain 'C' and resid 658 through 660 removed outlier: 3.574A pdb=" N TYR C 690 " --> pdb=" O SER C 659 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY C 689 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ALA C 735 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE C 691 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 632 " --> pdb=" O MET C 732 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER C 736 " --> pdb=" O TRP C 634 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET C 631 " --> pdb=" O ARG C 754 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYR C 756 " --> pdb=" O MET C 631 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU C 633 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 714 through 716 removed outlier: 3.583A pdb=" N GLU C 724 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 761 through 762 removed outlier: 6.626A pdb=" N LYS C 761 " --> pdb=" O LYS C 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 893 through 895 Processing sheet with id=AB7, first strand: chain 'D' and resid 430 through 434 removed outlier: 3.614A pdb=" N TRP D 442 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 550 through 553 Processing sheet with id=AB9, first strand: chain 'D' and resid 659 through 660 removed outlier: 3.873A pdb=" N TYR D 690 " --> pdb=" O SER D 659 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU D 632 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET D 631 " --> pdb=" O ARG D 754 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N TYR D 756 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU D 633 " --> pdb=" O TYR D 756 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 56 through 58 Processing sheet with id=AC2, first strand: chain 'E' and resid 94 through 95 removed outlier: 3.664A pdb=" N HIS E 157 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR E 144 " --> pdb=" O HIS E 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE E 142 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 143 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR E 225 " --> pdb=" O PHE E 143 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU E 145 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU E 223 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 430 through 434 removed outlier: 3.525A pdb=" N TRP E 442 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 550 through 553 removed outlier: 3.549A pdb=" N VAL E 557 " --> pdb=" O ILE E 568 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 658 through 660 removed outlier: 3.942A pdb=" N TYR E 690 " --> pdb=" O SER E 659 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU E 632 " --> pdb=" O ALA E 734 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU E 633 " --> pdb=" O TYR E 756 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER E 758 " --> pdb=" O LEU E 633 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 635 " --> pdb=" O SER E 758 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 713 through 714 removed outlier: 3.557A pdb=" N VAL E 714 " --> pdb=" O PHE E 726 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE E 726 " --> pdb=" O VAL E 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 430 through 434 removed outlier: 3.662A pdb=" N TRP F 442 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 550 through 553 Processing sheet with id=AC9, first strand: chain 'F' and resid 658 through 660 removed outlier: 3.655A pdb=" N SER F 659 " --> pdb=" O TYR F 688 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR F 690 " --> pdb=" O SER F 659 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU F 632 " --> pdb=" O ALA F 734 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 698 through 699 removed outlier: 6.598A pdb=" N GLU F 698 " --> pdb=" O ILE F 741 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 714 through 717 1343 hydrogen bonds defined for protein. 3921 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: 11.39 Time building geometry restraints manager: 9.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8892 1.33 - 1.45: 7563 1.45 - 1.58: 18868 1.58 - 1.70: 74 1.70 - 1.82: 263 Bond restraints: 35660 Sorted by residual: bond pdb=" CA ARG E 752 " pdb=" C ARG E 752 " ideal model delta sigma weight residual 1.530 1.474 0.056 1.11e-02 8.12e+03 2.51e+01 bond pdb=" CA ARG E 751 " pdb=" C ARG E 751 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.29e-02 6.01e+03 1.38e+01 bond pdb=" CA CYS F 790 " pdb=" C CYS F 790 " ideal model delta sigma weight residual 1.524 1.482 0.043 1.28e-02 6.10e+03 1.10e+01 bond pdb=" CA LYS F 775 " pdb=" C LYS F 775 " ideal model delta sigma weight residual 1.526 1.479 0.046 1.42e-02 4.96e+03 1.06e+01 bond pdb=" N ARG A 751 " pdb=" CA ARG A 751 " ideal model delta sigma weight residual 1.458 1.423 0.036 1.26e-02 6.30e+03 7.98e+00 ... (remaining 35655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 47363 1.93 - 3.86: 916 3.86 - 5.78: 162 5.78 - 7.71: 33 7.71 - 9.64: 5 Bond angle restraints: 48479 Sorted by residual: angle pdb=" N ILE C 785 " pdb=" CA ILE C 785 " pdb=" C ILE C 785 " ideal model delta sigma weight residual 112.96 107.87 5.09 1.00e+00 1.00e+00 2.59e+01 angle pdb=" C TYR D 853 " pdb=" N ASN D 854 " pdb=" CA ASN D 854 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C LYS A 899 " pdb=" CA LYS A 899 " pdb=" CB LYS A 899 " ideal model delta sigma weight residual 117.23 110.52 6.71 1.36e+00 5.41e-01 2.44e+01 angle pdb=" C LYS F 899 " pdb=" CA LYS F 899 " pdb=" CB LYS F 899 " ideal model delta sigma weight residual 117.23 110.67 6.56 1.36e+00 5.41e-01 2.33e+01 angle pdb=" C GLU E 23 " pdb=" N VAL E 24 " pdb=" CA VAL E 24 " ideal model delta sigma weight residual 121.97 130.52 -8.55 1.80e+00 3.09e-01 2.26e+01 ... (remaining 48474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 20478 34.88 - 69.76: 588 69.76 - 104.64: 43 104.64 - 139.52: 5 139.52 - 174.39: 6 Dihedral angle restraints: 21120 sinusoidal: 8946 harmonic: 12174 Sorted by residual: dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 113.44 -173.44 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 104.57 -164.58 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O2A ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PA ADP F1001 " pdb=" PB ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 92.84 -152.84 1 2.00e+01 2.50e-03 4.54e+01 ... (remaining 21117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3682 0.040 - 0.081: 1083 0.081 - 0.121: 317 0.121 - 0.162: 23 0.162 - 0.202: 4 Chirality restraints: 5109 Sorted by residual: chirality pdb=" CB ILE B 605 " pdb=" CA ILE B 605 " pdb=" CG1 ILE B 605 " pdb=" CG2 ILE B 605 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ARG A 301 " pdb=" N ARG A 301 " pdb=" C ARG A 301 " pdb=" CB ARG A 301 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CB ILE D 560 " pdb=" CA ILE D 560 " pdb=" CG1 ILE D 560 " pdb=" CG2 ILE D 560 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 5106 not shown) Planarity restraints: 6035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 822 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C GLU B 822 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU B 822 " -0.021 2.00e-02 2.50e+03 pdb=" N SER B 823 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 381 " -0.019 2.00e-02 2.50e+03 1.98e-02 9.77e+00 pdb=" CG TRP C 381 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 381 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 381 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 381 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 381 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 381 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 381 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 381 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 822 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C GLU D 822 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU D 822 " 0.019 2.00e-02 2.50e+03 pdb=" N SER D 823 " 0.018 2.00e-02 2.50e+03 ... (remaining 6032 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 87 2.35 - 2.99: 18513 2.99 - 3.63: 55850 3.63 - 4.26: 79391 4.26 - 4.90: 128250 Nonbonded interactions: 282091 Sorted by model distance: nonbonded pdb=" OG1 THR F 643 " pdb="MG MG F1002 " model vdw 1.715 2.170 nonbonded pdb=" OG1 THR E 643 " pdb="MG MG E1002 " model vdw 1.715 2.170 nonbonded pdb=" O1B ADP B1001 " pdb="MG MG B1002 " model vdw 1.727 2.170 nonbonded pdb=" O3A ADP D1001 " pdb="MG MG D1002 " model vdw 1.755 2.170 nonbonded pdb=" O1B ADP D1001 " pdb="MG MG D1002 " model vdw 1.783 2.170 ... (remaining 282086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 289 through 918 or resid 937 through 950 or resid 1001 thr \ ough 1002)) selection = (chain 'B' and (resid 289 through 918 or resid 937 through 950 or resid 1001 thr \ ough 1002)) selection = (chain 'C' and (resid 289 through 918 or resid 937 through 950 or resid 1001 thr \ ough 1002)) selection = chain 'D' selection = (chain 'F' and (resid 289 through 918 or resid 937 through 950 or resid 1001 thr \ ough 1002)) } 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: 3.730 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: 1.280 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 71.420 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.003 0.056 35660 Z= 0.164 Angle : 0.645 9.641 48479 Z= 0.348 Chirality : 0.041 0.202 5109 Planarity : 0.004 0.059 6035 Dihedral : 16.374 174.394 13252 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.20 % Favored : 91.45 % Rotamer: Outliers : 1.52 % Allowed : 0.98 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 4072 helix: 0.75 (0.13), residues: 1815 sheet: -0.42 (0.29), residues: 348 loop : -1.39 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP C 381 HIS 0.007 0.001 HIS D 383 PHE 0.026 0.001 PHE E 623 TYR 0.043 0.001 TYR F 302 ARG 0.016 0.000 ARG D 752 Details of bonding type rmsd hydrogen bonds : bond 0.16633 ( 1343) hydrogen bonds : angle 6.70819 ( 3921) covalent geometry : bond 0.00293 (35660) covalent geometry : angle 0.64537 (48479) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 3.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8964 (tpp) cc_final: 0.8681 (tpp) REVERT: A 452 MET cc_start: 0.8938 (ppp) cc_final: 0.8445 (ppp) REVERT: A 482 ASP cc_start: 0.8886 (m-30) cc_final: 0.8438 (m-30) REVERT: A 789 ASP cc_start: 0.5477 (OUTLIER) cc_final: 0.5078 (p0) REVERT: B 482 ASP cc_start: 0.8675 (m-30) cc_final: 0.8409 (m-30) REVERT: C 294 MET cc_start: 0.8926 (mpp) cc_final: 0.8707 (mpp) REVERT: C 378 ILE cc_start: 0.9457 (mp) cc_final: 0.8677 (mp) REVERT: C 912 PHE cc_start: 0.7263 (m-80) cc_final: 0.6976 (t80) REVERT: D 749 THR cc_start: 0.8017 (m) cc_final: 0.7513 (p) REVERT: E 728 MET cc_start: 0.8982 (ppp) cc_final: 0.8654 (ppp) REVERT: F 642 LYS cc_start: 0.5460 (OUTLIER) cc_final: 0.4899 (mttt) REVERT: F 776 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: F 791 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8582 (mt0) outliers start: 56 outliers final: 11 residues processed: 296 average time/residue: 0.4680 time to fit residues: 227.7621 Evaluate side-chains 207 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 3.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain D residue 751 ARG Chi-restraints excluded: chain E residue 871 ASN Chi-restraints excluded: chain F residue 642 LYS Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 791 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 345 optimal weight: 9.9990 chunk 310 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 chunk 165 optimal weight: 0.4980 chunk 320 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 0.9990 chunk 371 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 640 ASN A 710 ASN A 737 ASN B 415 HIS ** B 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 GLN B 869 ASN C 491 HIS C 494 GLN ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN D 710 ASN D 886 ASN E 747 HIS F 491 HIS F 494 GLN F 640 ASN F 782 HIS ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.108310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.070318 restraints weight = 149448.688| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 5.92 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35660 Z= 0.177 Angle : 0.652 10.850 48479 Z= 0.331 Chirality : 0.043 0.182 5109 Planarity : 0.004 0.058 6035 Dihedral : 12.435 179.964 4880 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.06 % Favored : 91.67 % Rotamer: Outliers : 1.17 % Allowed : 7.64 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 4072 helix: 0.76 (0.12), residues: 1845 sheet: -0.53 (0.28), residues: 363 loop : -1.41 (0.15), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP C 381 HIS 0.010 0.001 HIS C 875 PHE 0.020 0.001 PHE D 342 TYR 0.032 0.001 TYR B 866 ARG 0.005 0.001 ARG F 301 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 1343) hydrogen bonds : angle 5.30439 ( 3921) covalent geometry : bond 0.00399 (35660) covalent geometry : angle 0.65170 (48479) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.9168 (tpp) cc_final: 0.8948 (tpp) REVERT: A 452 MET cc_start: 0.9047 (ppp) cc_final: 0.8099 (ppp) REVERT: A 482 ASP cc_start: 0.9017 (m-30) cc_final: 0.8575 (m-30) REVERT: A 789 ASP cc_start: 0.5682 (OUTLIER) cc_final: 0.5111 (p0) REVERT: B 482 ASP cc_start: 0.8870 (m-30) cc_final: 0.8480 (m-30) REVERT: B 695 ASN cc_start: 0.8397 (p0) cc_final: 0.7834 (m-40) REVERT: B 696 LYS cc_start: 0.9309 (tptt) cc_final: 0.8900 (tptt) REVERT: C 378 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8936 (mp) REVERT: C 631 MET cc_start: 0.8703 (tpt) cc_final: 0.8355 (tpp) REVERT: C 681 MET cc_start: 0.9115 (mmp) cc_final: 0.8878 (mmp) REVERT: C 875 HIS cc_start: 0.7280 (m-70) cc_final: 0.6743 (m-70) REVERT: E 417 MET cc_start: 0.9018 (mtt) cc_final: 0.8785 (mtm) REVERT: E 680 PHE cc_start: 0.5855 (m-80) cc_final: 0.5652 (m-10) REVERT: F 642 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.4872 (mtmt) REVERT: F 945 TRP cc_start: 0.6703 (t60) cc_final: 0.6480 (t60) outliers start: 43 outliers final: 28 residues processed: 238 average time/residue: 0.4312 time to fit residues: 173.9529 Evaluate side-chains 225 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 866 TYR Chi-restraints excluded: chain A residue 945 TRP Chi-restraints excluded: chain B residue 341 TRP Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 945 TRP Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 892 TYR Chi-restraints excluded: chain F residue 642 LYS Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 822 GLU Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 866 TYR Chi-restraints excluded: chain F residue 895 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 252 optimal weight: 0.2980 chunk 135 optimal weight: 5.9990 chunk 397 optimal weight: 0.5980 chunk 332 optimal weight: 0.0170 chunk 140 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 342 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 496 HIS ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.112316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.079080 restraints weight = 131555.420| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.84 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35660 Z= 0.111 Angle : 0.603 10.376 48479 Z= 0.301 Chirality : 0.041 0.210 5109 Planarity : 0.004 0.059 6035 Dihedral : 12.114 175.171 4863 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.39 % Favored : 92.39 % Rotamer: Outliers : 1.19 % Allowed : 10.46 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 4072 helix: 0.88 (0.12), residues: 1837 sheet: -0.61 (0.28), residues: 384 loop : -1.41 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP C 381 HIS 0.006 0.001 HIS C 367 PHE 0.017 0.001 PHE E 623 TYR 0.023 0.001 TYR B 398 ARG 0.005 0.000 ARG F 301 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1343) hydrogen bonds : angle 5.00549 ( 3921) covalent geometry : bond 0.00237 (35660) covalent geometry : angle 0.60255 (48479) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.9216 (t80) cc_final: 0.8868 (m-80) REVERT: A 452 MET cc_start: 0.9044 (ppp) cc_final: 0.8222 (ppp) REVERT: A 482 ASP cc_start: 0.9040 (m-30) cc_final: 0.8573 (m-30) REVERT: A 789 ASP cc_start: 0.5861 (OUTLIER) cc_final: 0.5221 (p0) REVERT: B 482 ASP cc_start: 0.8910 (m-30) cc_final: 0.8502 (m-30) REVERT: B 695 ASN cc_start: 0.8296 (p0) cc_final: 0.7866 (m110) REVERT: C 378 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9243 (mp) REVERT: C 381 TRP cc_start: 0.8664 (m-90) cc_final: 0.8456 (m-90) REVERT: C 631 MET cc_start: 0.8590 (tpt) cc_final: 0.8289 (tpp) REVERT: C 875 HIS cc_start: 0.7168 (m-70) cc_final: 0.6657 (m-70) REVERT: D 708 MET cc_start: 0.8584 (mmm) cc_final: 0.8371 (tpp) REVERT: E 304 HIS cc_start: 0.8842 (OUTLIER) cc_final: 0.8180 (p-80) REVERT: E 344 GLN cc_start: 0.9163 (pm20) cc_final: 0.8712 (mp10) REVERT: E 417 MET cc_start: 0.9007 (mtt) cc_final: 0.8746 (mtm) REVERT: E 680 PHE cc_start: 0.5757 (m-80) cc_final: 0.5393 (m-10) REVERT: F 776 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6878 (mp0) outliers start: 44 outliers final: 23 residues processed: 248 average time/residue: 0.4255 time to fit residues: 178.0827 Evaluate side-chains 225 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 866 TYR Chi-restraints excluded: chain A residue 945 TRP Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 945 TRP Chi-restraints excluded: chain E residue 304 HIS Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 779 ARG Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 822 GLU Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 866 TYR Chi-restraints excluded: chain F residue 895 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 358 optimal weight: 0.6980 chunk 242 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 203 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 348 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 782 HIS ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 ASN F 491 HIS F 727 GLN ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.110758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.078016 restraints weight = 130970.931| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 4.70 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35660 Z= 0.148 Angle : 0.611 10.606 48479 Z= 0.304 Chirality : 0.041 0.171 5109 Planarity : 0.004 0.060 6035 Dihedral : 11.898 174.713 4853 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.66 % Favored : 92.09 % Rotamer: Outliers : 1.44 % Allowed : 12.03 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 4072 helix: 0.98 (0.13), residues: 1837 sheet: -0.77 (0.27), residues: 389 loop : -1.40 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 321 HIS 0.010 0.001 HIS A 782 PHE 0.016 0.001 PHE E 726 TYR 0.030 0.001 TYR D 398 ARG 0.009 0.000 ARG F 779 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 1343) hydrogen bonds : angle 4.92064 ( 3921) covalent geometry : bond 0.00336 (35660) covalent geometry : angle 0.61091 (48479) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 3.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.9152 (t80) cc_final: 0.8750 (m-80) REVERT: A 452 MET cc_start: 0.9078 (ppp) cc_final: 0.8250 (ppp) REVERT: A 482 ASP cc_start: 0.9036 (m-30) cc_final: 0.8598 (m-30) REVERT: A 789 ASP cc_start: 0.6316 (OUTLIER) cc_final: 0.5789 (p0) REVERT: A 791 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: B 482 ASP cc_start: 0.8971 (m-30) cc_final: 0.8646 (m-30) REVERT: B 695 ASN cc_start: 0.8406 (p0) cc_final: 0.7966 (m110) REVERT: B 906 CYS cc_start: 0.7488 (m) cc_final: 0.7251 (m) REVERT: C 378 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.8795 (mp) REVERT: C 381 TRP cc_start: 0.8613 (m-90) cc_final: 0.8116 (m-90) REVERT: C 875 HIS cc_start: 0.7234 (m-70) cc_final: 0.7021 (m-70) REVERT: D 302 TYR cc_start: 0.8833 (m-80) cc_final: 0.8450 (m-80) REVERT: E 82 MET cc_start: 0.6907 (tpp) cc_final: 0.6015 (tpt) REVERT: E 304 HIS cc_start: 0.8917 (OUTLIER) cc_final: 0.8407 (p-80) REVERT: E 344 GLN cc_start: 0.9031 (pm20) cc_final: 0.8647 (pm20) REVERT: E 417 MET cc_start: 0.8999 (mtt) cc_final: 0.8698 (mtm) REVERT: E 708 MET cc_start: 0.8836 (mtt) cc_final: 0.8606 (mtp) REVERT: E 728 MET cc_start: 0.9103 (ppp) cc_final: 0.8811 (ppp) REVERT: F 776 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6909 (mp0) outliers start: 53 outliers final: 29 residues processed: 237 average time/residue: 0.4405 time to fit residues: 179.5692 Evaluate side-chains 234 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 866 TYR Chi-restraints excluded: chain A residue 945 TRP Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 945 TRP Chi-restraints excluded: chain E residue 304 HIS Chi-restraints excluded: chain E residue 341 TRP Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 779 ARG Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 866 TYR Chi-restraints excluded: chain F residue 895 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 206 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 312 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 48 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 HIS A 782 HIS ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.108408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.070174 restraints weight = 149463.772| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 6.22 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35660 Z= 0.116 Angle : 0.601 11.317 48479 Z= 0.297 Chirality : 0.041 0.220 5109 Planarity : 0.004 0.060 6035 Dihedral : 11.763 174.451 4853 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.56 % Favored : 92.19 % Rotamer: Outliers : 1.54 % Allowed : 12.98 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 4072 helix: 1.01 (0.13), residues: 1843 sheet: -0.68 (0.27), residues: 410 loop : -1.40 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 321 HIS 0.010 0.001 HIS A 782 PHE 0.010 0.001 PHE E 623 TYR 0.023 0.001 TYR D 398 ARG 0.006 0.000 ARG F 301 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 1343) hydrogen bonds : angle 4.77276 ( 3921) covalent geometry : bond 0.00261 (35660) covalent geometry : angle 0.60102 (48479) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.9097 (ppp) cc_final: 0.8261 (ppp) REVERT: A 482 ASP cc_start: 0.8940 (m-30) cc_final: 0.8514 (m-30) REVERT: A 631 MET cc_start: 0.8902 (tpt) cc_final: 0.8615 (tpp) REVERT: A 789 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.6056 (p0) REVERT: A 791 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: B 482 ASP cc_start: 0.8851 (m-30) cc_final: 0.8565 (m-30) REVERT: B 695 ASN cc_start: 0.8457 (p0) cc_final: 0.7963 (m-40) REVERT: C 378 ILE cc_start: 0.9125 (mp) cc_final: 0.8764 (mp) REVERT: C 381 TRP cc_start: 0.8483 (m-10) cc_final: 0.8132 (m-90) REVERT: C 791 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8310 (mp10) REVERT: E 303 LEU cc_start: 0.9637 (mt) cc_final: 0.9270 (pp) REVERT: E 304 HIS cc_start: 0.8938 (OUTLIER) cc_final: 0.8208 (p-80) REVERT: E 344 GLN cc_start: 0.9268 (pm20) cc_final: 0.8978 (pm20) REVERT: E 417 MET cc_start: 0.8889 (mtt) cc_final: 0.8644 (mtm) REVERT: F 776 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: F 822 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8022 (pp20) outliers start: 57 outliers final: 32 residues processed: 252 average time/residue: 0.4586 time to fit residues: 198.6322 Evaluate side-chains 236 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 866 TYR Chi-restraints excluded: chain A residue 945 TRP Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 945 TRP Chi-restraints excluded: chain E residue 304 HIS Chi-restraints excluded: chain E residue 341 TRP Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 835 LEU Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 779 ARG Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 822 GLU Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 895 TRP Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 347 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 384 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 305 optimal weight: 0.4980 chunk 70 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 370 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 782 HIS ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.108159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.072910 restraints weight = 148804.340| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 6.41 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35660 Z= 0.123 Angle : 0.612 13.909 48479 Z= 0.301 Chirality : 0.041 0.178 5109 Planarity : 0.004 0.061 6035 Dihedral : 11.600 174.588 4851 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.47 % Favored : 92.31 % Rotamer: Outliers : 1.33 % Allowed : 14.58 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 4072 helix: 1.04 (0.13), residues: 1845 sheet: -0.65 (0.27), residues: 407 loop : -1.39 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 321 HIS 0.006 0.001 HIS C 367 PHE 0.014 0.001 PHE F 571 TYR 0.022 0.001 TYR D 398 ARG 0.007 0.000 ARG F 376 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 1343) hydrogen bonds : angle 4.74427 ( 3921) covalent geometry : bond 0.00277 (35660) covalent geometry : angle 0.61194 (48479) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 4.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8748 (pm20) REVERT: A 452 MET cc_start: 0.9117 (ppp) cc_final: 0.8211 (ppp) REVERT: A 482 ASP cc_start: 0.9006 (m-30) cc_final: 0.8569 (m-30) REVERT: A 789 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6252 (p0) REVERT: A 791 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: B 482 ASP cc_start: 0.8898 (m-30) cc_final: 0.8580 (m-30) REVERT: B 695 ASN cc_start: 0.8386 (p0) cc_final: 0.7859 (m-40) REVERT: B 791 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8399 (mp10) REVERT: C 378 ILE cc_start: 0.9236 (mp) cc_final: 0.8883 (mp) REVERT: C 381 TRP cc_start: 0.8548 (m-10) cc_final: 0.8142 (m-90) REVERT: C 791 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8278 (mp10) REVERT: E 304 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8387 (p-80) REVERT: F 376 ARG cc_start: 0.6153 (tmt170) cc_final: 0.5780 (ttp-170) REVERT: F 822 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8151 (pp20) outliers start: 49 outliers final: 30 residues processed: 233 average time/residue: 0.4328 time to fit residues: 173.3595 Evaluate side-chains 232 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 866 TYR Chi-restraints excluded: chain A residue 945 TRP Chi-restraints excluded: chain B residue 791 GLN Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 945 TRP Chi-restraints excluded: chain E residue 304 HIS Chi-restraints excluded: chain E residue 341 TRP Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 835 LEU Chi-restraints excluded: chain F residue 779 ARG Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 822 GLU Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 895 TRP Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 390 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 chunk 387 optimal weight: 0.2980 chunk 233 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 394 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 160 optimal weight: 0.1980 chunk 386 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.107633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.073426 restraints weight = 149372.798| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 5.68 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35660 Z= 0.133 Angle : 0.634 15.937 48479 Z= 0.308 Chirality : 0.041 0.192 5109 Planarity : 0.004 0.061 6035 Dihedral : 11.489 174.799 4851 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.54 % Favored : 92.26 % Rotamer: Outliers : 1.41 % Allowed : 15.01 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 4072 helix: 1.09 (0.13), residues: 1839 sheet: -0.67 (0.27), residues: 407 loop : -1.40 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 321 HIS 0.006 0.001 HIS E 875 PHE 0.013 0.001 PHE F 571 TYR 0.021 0.001 TYR B 398 ARG 0.015 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 1343) hydrogen bonds : angle 4.73183 ( 3921) covalent geometry : bond 0.00302 (35660) covalent geometry : angle 0.63365 (48479) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 ARG cc_start: 0.9442 (mtm110) cc_final: 0.9195 (mtm180) REVERT: A 404 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8740 (pm20) REVERT: A 452 MET cc_start: 0.9117 (ppp) cc_final: 0.8200 (ppp) REVERT: A 482 ASP cc_start: 0.9036 (m-30) cc_final: 0.8597 (m-30) REVERT: A 789 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6258 (p0) REVERT: A 791 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: B 482 ASP cc_start: 0.8960 (m-30) cc_final: 0.8647 (m-30) REVERT: B 695 ASN cc_start: 0.8542 (p0) cc_final: 0.7963 (m-40) REVERT: B 791 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8387 (mp10) REVERT: C 378 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8863 (mp) REVERT: C 381 TRP cc_start: 0.8622 (m-10) cc_final: 0.8163 (m-90) REVERT: C 631 MET cc_start: 0.8745 (tpt) cc_final: 0.8428 (tpp) REVERT: C 791 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: E 304 HIS cc_start: 0.8908 (OUTLIER) cc_final: 0.8504 (p-80) REVERT: E 335 TYR cc_start: 0.8717 (m-80) cc_final: 0.8379 (m-80) REVERT: E 344 GLN cc_start: 0.9305 (pm20) cc_final: 0.8937 (mp10) REVERT: E 417 MET cc_start: 0.9116 (mtt) cc_final: 0.8613 (mtm) REVERT: E 432 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8970 (t) REVERT: E 728 MET cc_start: 0.9050 (ppp) cc_final: 0.8847 (ppp) REVERT: F 822 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8334 (pp20) outliers start: 52 outliers final: 35 residues processed: 239 average time/residue: 0.4247 time to fit residues: 173.8664 Evaluate side-chains 241 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 866 TYR Chi-restraints excluded: chain A residue 945 TRP Chi-restraints excluded: chain B residue 791 GLN Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 945 TRP Chi-restraints excluded: chain E residue 304 HIS Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 835 LEU Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 866 TYR Chi-restraints excluded: chain F residue 779 ARG Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 822 GLU Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 866 TYR Chi-restraints excluded: chain F residue 895 TRP Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 73 optimal weight: 4.9990 chunk 331 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 286 optimal weight: 5.9990 chunk 131 optimal weight: 30.0000 chunk 388 optimal weight: 6.9990 chunk 43 optimal weight: 0.0770 chunk 359 optimal weight: 0.0980 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 ASN C 383 HIS ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 HIS ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.110061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.076896 restraints weight = 130388.559| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 4.75 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35660 Z= 0.158 Angle : 0.650 14.640 48479 Z= 0.315 Chirality : 0.042 0.163 5109 Planarity : 0.004 0.062 6035 Dihedral : 11.408 175.182 4851 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.83 % Favored : 91.97 % Rotamer: Outliers : 1.82 % Allowed : 15.04 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 4072 helix: 1.11 (0.13), residues: 1845 sheet: -0.72 (0.28), residues: 378 loop : -1.41 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 321 HIS 0.007 0.001 HIS E 875 PHE 0.012 0.001 PHE D 342 TYR 0.029 0.001 TYR D 398 ARG 0.006 0.000 ARG F 301 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 1343) hydrogen bonds : angle 4.75834 ( 3921) covalent geometry : bond 0.00360 (35660) covalent geometry : angle 0.64971 (48479) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8779 (pm20) REVERT: A 452 MET cc_start: 0.9109 (ppp) cc_final: 0.8150 (ppp) REVERT: A 482 ASP cc_start: 0.9084 (m-30) cc_final: 0.8657 (m-30) REVERT: A 713 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7856 (t0) REVERT: A 785 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7666 (pp) REVERT: A 789 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6224 (p0) REVERT: B 482 ASP cc_start: 0.8999 (m-30) cc_final: 0.8678 (m-30) REVERT: B 695 ASN cc_start: 0.8425 (p0) cc_final: 0.7947 (m-40) REVERT: B 708 MET cc_start: 0.8801 (mmm) cc_final: 0.8538 (tpp) REVERT: B 791 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8360 (mp10) REVERT: C 378 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8610 (mp) REVERT: C 381 TRP cc_start: 0.8823 (m-10) cc_final: 0.8182 (m-90) REVERT: C 791 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8481 (mp10) REVERT: D 302 TYR cc_start: 0.8851 (m-80) cc_final: 0.8038 (m-80) REVERT: E 82 MET cc_start: 0.6840 (tpp) cc_final: 0.5873 (tpp) REVERT: E 304 HIS cc_start: 0.9031 (OUTLIER) cc_final: 0.8596 (p-80) REVERT: E 335 TYR cc_start: 0.8681 (m-80) cc_final: 0.8246 (m-80) REVERT: E 344 GLN cc_start: 0.9235 (pm20) cc_final: 0.8817 (mp10) REVERT: E 417 MET cc_start: 0.9122 (mtt) cc_final: 0.8551 (mtm) REVERT: E 432 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.8991 (t) REVERT: E 728 MET cc_start: 0.9064 (ppp) cc_final: 0.8801 (ppp) outliers start: 67 outliers final: 43 residues processed: 237 average time/residue: 0.4107 time to fit residues: 166.5215 Evaluate side-chains 242 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 866 TYR Chi-restraints excluded: chain A residue 945 TRP Chi-restraints excluded: chain B residue 791 GLN Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 945 TRP Chi-restraints excluded: chain E residue 304 HIS Chi-restraints excluded: chain E residue 341 TRP Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 835 LEU Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 866 TYR Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 822 GLU Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 866 TYR Chi-restraints excluded: chain F residue 895 TRP Chi-restraints excluded: chain F residue 900 THR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 290 optimal weight: 0.8980 chunk 386 optimal weight: 5.9990 chunk 362 optimal weight: 0.7980 chunk 249 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 353 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 ASN ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.107609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.069783 restraints weight = 149094.835| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 5.78 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35660 Z= 0.116 Angle : 0.640 15.839 48479 Z= 0.308 Chirality : 0.041 0.164 5109 Planarity : 0.004 0.061 6035 Dihedral : 11.322 175.032 4851 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.56 % Favored : 92.24 % Rotamer: Outliers : 1.46 % Allowed : 15.39 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 4072 helix: 1.11 (0.13), residues: 1843 sheet: -0.74 (0.26), residues: 421 loop : -1.41 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP B 321 HIS 0.006 0.001 HIS C 367 PHE 0.010 0.001 PHE D 511 TYR 0.029 0.001 TYR D 398 ARG 0.005 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 1343) hydrogen bonds : angle 4.68346 ( 3921) covalent geometry : bond 0.00262 (35660) covalent geometry : angle 0.63955 (48479) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8741 (pm20) REVERT: A 452 MET cc_start: 0.9087 (ppp) cc_final: 0.8092 (ppp) REVERT: A 482 ASP cc_start: 0.9051 (m-30) cc_final: 0.8598 (m-30) REVERT: A 651 MET cc_start: 0.8900 (ttp) cc_final: 0.8343 (tmm) REVERT: A 713 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7851 (t0) REVERT: A 785 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7555 (pp) REVERT: A 789 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6376 (p0) REVERT: B 482 ASP cc_start: 0.8975 (m-30) cc_final: 0.8647 (m-30) REVERT: B 695 ASN cc_start: 0.8470 (p0) cc_final: 0.7866 (m110) REVERT: B 791 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8384 (mp10) REVERT: B 899 LYS cc_start: 0.8793 (tppt) cc_final: 0.8058 (ptmt) REVERT: C 378 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8773 (mp) REVERT: C 381 TRP cc_start: 0.8647 (m-10) cc_final: 0.8172 (m-90) REVERT: C 791 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: C 912 PHE cc_start: 0.8151 (t80) cc_final: 0.7937 (m-80) REVERT: D 302 TYR cc_start: 0.8852 (m-80) cc_final: 0.8095 (m-80) REVERT: D 379 MET cc_start: 0.9105 (tmm) cc_final: 0.8887 (tpt) REVERT: E 304 HIS cc_start: 0.9043 (OUTLIER) cc_final: 0.8588 (p-80) REVERT: E 335 TYR cc_start: 0.8770 (m-80) cc_final: 0.8383 (m-80) REVERT: E 405 TYR cc_start: 0.9229 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: E 432 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.9037 (t) REVERT: E 728 MET cc_start: 0.8988 (ppp) cc_final: 0.8782 (ppp) REVERT: F 822 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8299 (pp20) outliers start: 54 outliers final: 36 residues processed: 230 average time/residue: 0.4531 time to fit residues: 178.1902 Evaluate side-chains 238 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 866 TYR Chi-restraints excluded: chain A residue 945 TRP Chi-restraints excluded: chain B residue 791 GLN Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 945 TRP Chi-restraints excluded: chain E residue 304 HIS Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 405 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 835 LEU Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 866 TYR Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 822 GLU Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 866 TYR Chi-restraints excluded: chain F residue 895 TRP Chi-restraints excluded: chain F residue 900 THR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 362 optimal weight: 3.9990 chunk 310 optimal weight: 0.9990 chunk 323 optimal weight: 6.9990 chunk 296 optimal weight: 0.9980 chunk 356 optimal weight: 0.0060 chunk 277 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 HIS ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.107282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.072511 restraints weight = 148254.565| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 6.11 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35660 Z= 0.128 Angle : 0.644 16.154 48479 Z= 0.310 Chirality : 0.041 0.164 5109 Planarity : 0.004 0.061 6035 Dihedral : 11.261 175.161 4851 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.59 % Favored : 92.22 % Rotamer: Outliers : 1.33 % Allowed : 15.42 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 4072 helix: 1.12 (0.13), residues: 1845 sheet: -0.61 (0.27), residues: 406 loop : -1.39 (0.15), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP B 321 HIS 0.006 0.001 HIS C 367 PHE 0.010 0.001 PHE D 511 TYR 0.028 0.001 TYR D 398 ARG 0.004 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 1343) hydrogen bonds : angle 4.69681 ( 3921) covalent geometry : bond 0.00293 (35660) covalent geometry : angle 0.64442 (48479) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 3.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8717 (pm20) REVERT: A 452 MET cc_start: 0.9077 (ppp) cc_final: 0.8097 (ppp) REVERT: A 482 ASP cc_start: 0.9001 (m-30) cc_final: 0.8555 (m-30) REVERT: A 713 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7805 (t0) REVERT: A 789 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6454 (p0) REVERT: B 482 ASP cc_start: 0.8930 (m-30) cc_final: 0.8601 (m-30) REVERT: B 695 ASN cc_start: 0.8409 (p0) cc_final: 0.7881 (m110) REVERT: B 791 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8374 (mp10) REVERT: B 899 LYS cc_start: 0.9027 (tppt) cc_final: 0.8399 (ptmt) REVERT: C 791 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8512 (mp10) REVERT: C 912 PHE cc_start: 0.8587 (t80) cc_final: 0.8353 (m-80) REVERT: D 302 TYR cc_start: 0.8878 (m-80) cc_final: 0.8172 (m-80) REVERT: E 304 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.8576 (p-80) REVERT: E 310 LEU cc_start: 0.7928 (tp) cc_final: 0.7428 (tp) REVERT: E 335 TYR cc_start: 0.8720 (m-80) cc_final: 0.8423 (m-80) REVERT: E 344 GLN cc_start: 0.9325 (pm20) cc_final: 0.9041 (mp10) REVERT: E 405 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8890 (m-80) REVERT: E 432 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9020 (t) outliers start: 49 outliers final: 38 residues processed: 226 average time/residue: 0.4331 time to fit residues: 168.5327 Evaluate side-chains 238 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 866 TYR Chi-restraints excluded: chain A residue 945 TRP Chi-restraints excluded: chain B residue 791 GLN Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 945 TRP Chi-restraints excluded: chain E residue 304 HIS Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 405 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 835 LEU Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 866 TYR Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 822 GLU Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 866 TYR Chi-restraints excluded: chain F residue 895 TRP Chi-restraints excluded: chain F residue 900 THR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 293 optimal weight: 0.4980 chunk 150 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 396 optimal weight: 0.0570 chunk 321 optimal weight: 6.9990 chunk 374 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 HIS E 491 HIS ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.108156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.073413 restraints weight = 148759.880| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 6.20 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35660 Z= 0.107 Angle : 0.643 16.352 48479 Z= 0.307 Chirality : 0.041 0.263 5109 Planarity : 0.004 0.061 6035 Dihedral : 11.192 174.978 4851 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.39 % Favored : 92.41 % Rotamer: Outliers : 1.22 % Allowed : 15.80 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 4072 helix: 1.10 (0.13), residues: 1839 sheet: -0.49 (0.28), residues: 403 loop : -1.39 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP B 321 HIS 0.023 0.001 HIS E 491 PHE 0.009 0.001 PHE D 342 TYR 0.030 0.001 TYR D 398 ARG 0.006 0.000 ARG F 301 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 1343) hydrogen bonds : angle 4.64809 ( 3921) covalent geometry : bond 0.00235 (35660) covalent geometry : angle 0.64263 (48479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17788.35 seconds wall clock time: 305 minutes 26.17 seconds (18326.17 seconds total)