Starting phenix.real_space_refine on Sun Aug 9 11:49:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvz_37880/08_2026/8wvz_37880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvz_37880/08_2026/8wvz_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wvz_37880/08_2026/8wvz_37880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvz_37880/08_2026/8wvz_37880.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wvz_37880/08_2026/8wvz_37880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvz_37880/08_2026/8wvz_37880.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 8.34, per 1000 atoms: 0.24 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: 3.55 Conformation dependent library (CDL) restraints added in 1.7 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: 1.07 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: 7.45 Time building geometry restraints manager: 4.75 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=" C3' DT H 4 " pdb=" C2' DT H 4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+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 ... (remaining 35655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 47281 1.93 - 3.86: 998 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: 3651 0.040 - 0.081: 1106 0.081 - 0.121: 325 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 1002)) selection = (chain 'B' and (resid 289 through 918 or resid 937 through 1002)) selection = (chain 'C' and (resid 289 through 918 or resid 937 through 1002)) selection = chain 'D' selection = (chain 'F' and (resid 289 through 918 or resid 937 through 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.210 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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= 0.187 Angle : 0.656 9.641 48479 Z= 0.379 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 : 12.94 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.016 0.000 ARG D 752 TYR 0.043 0.001 TYR F 302 PHE 0.026 0.001 PHE E 623 TRP 0.054 0.001 TRP C 381 HIS 0.007 0.001 HIS D 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.19 (35660) covalent geometry : angle 0.65582 / 0.38 (48479) hydrogen bonds : bond 0.16633 / 10.95 ( 1343) hydrogen bonds : angle 6.70819 / 4.83 ( 3921) *********************** 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 : 1.322 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: 0.8450 (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: 0.8583 (mt0) outliers start: 56 outliers final: 11 residues processed: 296 average time/residue: 0.2057 time to fit residues: 100.8217 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 : 1.166 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 HIS A 578 GLN A 640 ASN A 710 ASN A 737 ASN ** B 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 GLN B 869 ASN C 491 HIS C 494 GLN ** 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** D 453 ASN D 710 ASN D 886 ASN ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 HIS F 494 GLN F 640 ASN ** F 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.108015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070554 restraints weight = 151482.732| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 5.80 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35660 Z= 0.216 Angle : 0.673 10.336 48479 Z= 0.345 Chirality : 0.044 0.227 5109 Planarity : 0.005 0.059 6035 Dihedral : 12.560 178.878 4880 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.13 % Favored : 91.60 % Rotamer: Outliers : 1.11 % Allowed : 7.62 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 4072 helix: 0.68 (0.12), residues: 1864 sheet: -0.61 (0.28), residues: 366 loop : -1.47 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 301 TYR 0.031 0.002 TYR B 866 PHE 0.021 0.001 PHE D 342 TRP 0.043 0.002 TRP C 381 HIS 0.011 0.001 HIS C 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (35660) covalent geometry : angle 0.67300 / 0.34 (48479) hydrogen bonds : bond 0.04818 / 3.21 ( 1343) hydrogen bonds : angle 5.47963 / 3.98 ( 3921) *********************** 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 248 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.9030 (ppp) cc_final: 0.8082 (ppp) REVERT: A 482 ASP cc_start: 0.9059 (m-30) cc_final: 0.8633 (m-30) REVERT: A 789 ASP cc_start: 0.5830 (OUTLIER) cc_final: 0.5239 (p0) REVERT: B 482 ASP cc_start: 0.8895 (m-30) cc_final: 0.8490 (m-30) REVERT: B 695 ASN cc_start: 0.8375 (p0) cc_final: 0.7775 (m-40) REVERT: B 696 LYS cc_start: 0.9325 (tptt) cc_final: 0.8890 (tptt) REVERT: C 378 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8774 (mm) REVERT: C 381 TRP cc_start: 0.8341 (m-90) cc_final: 0.8032 (m-90) REVERT: C 631 MET cc_start: 0.8773 (tpt) cc_final: 0.8422 (tpp) REVERT: C 875 HIS cc_start: 0.7371 (m-70) cc_final: 0.6994 (m-70) REVERT: E 417 MET cc_start: 0.9049 (mtt) cc_final: 0.8773 (mtm) outliers start: 41 outliers final: 25 residues processed: 235 average time/residue: 0.1984 time to fit residues: 79.3641 Evaluate side-chains 215 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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 B residue 341 TRP Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 853 TYR 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 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 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 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 236 optimal weight: 4.9990 chunk 351 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 chunk 386 optimal weight: 3.9990 chunk 402 optimal weight: 0.8980 chunk 372 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 496 HIS ** 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** D 747 HIS F 491 HIS F 782 HIS ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.108188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.069916 restraints weight = 150693.944| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 6.19 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35660 Z= 0.151 Angle : 0.626 9.094 48479 Z= 0.316 Chirality : 0.043 0.244 5109 Planarity : 0.004 0.059 6035 Dihedral : 12.308 177.713 4863 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.06 % Favored : 91.70 % Rotamer: Outliers : 1.25 % Allowed : 10.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 4072 helix: 0.82 (0.12), residues: 1843 sheet: -0.57 (0.29), residues: 346 loop : -1.45 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 874 TYR 0.031 0.001 TYR F 756 PHE 0.017 0.001 PHE E 623 TRP 0.023 0.001 TRP D 634 HIS 0.008 0.001 HIS C 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (35660) covalent geometry : angle 0.62649 / 0.32 (48479) hydrogen bonds : bond 0.04250 / 2.84 ( 1343) hydrogen bonds : angle 5.18336 / 3.78 ( 3921) *********************** 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 251 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.9042 (ppp) cc_final: 0.8266 (ppp) REVERT: A 482 ASP cc_start: 0.9017 (m-30) cc_final: 0.8572 (m-30) REVERT: A 789 ASP cc_start: 0.5841 (OUTLIER) cc_final: 0.5366 (p0) REVERT: A 791 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: B 482 ASP cc_start: 0.8850 (m-30) cc_final: 0.8447 (m-30) REVERT: B 695 ASN cc_start: 0.8356 (p0) cc_final: 0.7798 (m-40) REVERT: C 378 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8816 (mp) REVERT: C 381 TRP cc_start: 0.8243 (m-10) cc_final: 0.7983 (m-90) REVERT: C 681 MET cc_start: 0.9223 (mmp) cc_final: 0.8988 (mmp) REVERT: C 875 HIS cc_start: 0.7346 (m-70) cc_final: 0.6958 (m-70) REVERT: E 417 MET cc_start: 0.9021 (mtt) cc_final: 0.8703 (mtm) REVERT: F 642 LYS cc_start: 0.5711 (OUTLIER) cc_final: 0.5423 (mtmt) REVERT: F 822 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8097 (pp20) outliers start: 46 outliers final: 28 residues processed: 235 average time/residue: 0.2101 time to fit residues: 83.5688 Evaluate side-chains 222 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 776 GLU 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 853 TYR 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 C residue 868 THR Chi-restraints excluded: chain D residue 488 ILE 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 378 ILE Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 631 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 36 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 333 optimal weight: 4.9990 chunk 346 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 289 optimal weight: 0.8980 chunk 310 optimal weight: 0.9990 chunk 358 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 334 ASN ** 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 = 0.4047 r_free = 0.4047 target = 0.109670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.075869 restraints weight = 128724.056| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.81 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35660 Z= 0.160 Angle : 0.624 10.099 48479 Z= 0.313 Chirality : 0.042 0.239 5109 Planarity : 0.004 0.060 6035 Dihedral : 12.161 172.438 4863 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.96 % Favored : 91.80 % Rotamer: Outliers : 1.38 % Allowed : 11.98 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 4072 helix: 0.85 (0.12), residues: 1855 sheet: -0.72 (0.28), residues: 359 loop : -1.44 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 301 TYR 0.029 0.001 TYR D 398 PHE 0.013 0.001 PHE C 801 TRP 0.024 0.001 TRP B 321 HIS 0.006 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (35660) covalent geometry : angle 0.62423 / 0.31 (48479) hydrogen bonds : bond 0.04039 / 2.70 ( 1343) hydrogen bonds : angle 5.04262 / 3.68 ( 3921) *********************** 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 251 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 1.397 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 452 MET cc_start: 0.9069 (ppp) cc_final: 0.8303 (ppp) REVERT: A 482 ASP cc_start: 0.9045 (m-30) cc_final: 0.8615 (m-30) REVERT: A 789 ASP cc_start: 0.6336 (OUTLIER) cc_final: 0.5765 (p0) REVERT: B 482 ASP cc_start: 0.8912 (m-30) cc_final: 0.8506 (m-30) REVERT: B 695 ASN cc_start: 0.8313 (p0) cc_final: 0.7833 (m110) REVERT: C 378 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.8757 (mp) REVERT: C 381 TRP cc_start: 0.8557 (m-10) cc_final: 0.8017 (m-90) REVERT: C 631 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8535 (tpt) REVERT: D 708 MET cc_start: 0.8667 (mmm) cc_final: 0.8336 (tpp) REVERT: E 304 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8447 (p-80) REVERT: E 344 GLN cc_start: 0.9121 (pm20) cc_final: 0.8719 (mp10) REVERT: F 583 CYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8176 (p) REVERT: F 822 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8181 (pp20) outliers start: 51 outliers final: 28 residues processed: 235 average time/residue: 0.2008 time to fit residues: 80.2255 Evaluate side-chains 224 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 426 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 834 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 560 ILE 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 467 ASP Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 892 TYR Chi-restraints excluded: chain F residue 583 CYS Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 779 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 0.0980 chunk 134 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 323 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 128 optimal weight: 30.0000 chunk 273 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 578 GLN ** 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 E 450 GLN ** 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 = 0.4026 r_free = 0.4026 target = 0.107244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.072191 restraints weight = 149639.678| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 6.50 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35660 Z= 0.161 Angle : 0.628 10.046 48479 Z= 0.313 Chirality : 0.042 0.370 5109 Planarity : 0.004 0.061 6035 Dihedral : 11.995 171.564 4855 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.83 % Favored : 91.92 % Rotamer: Outliers : 1.57 % Allowed : 13.39 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 4072 helix: 0.89 (0.12), residues: 1854 sheet: -0.78 (0.28), residues: 369 loop : -1.46 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 301 TYR 0.021 0.001 TYR B 398 PHE 0.021 0.001 PHE E 726 TRP 0.047 0.001 TRP B 321 HIS 0.007 0.001 HIS E 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (35660) covalent geometry : angle 0.62841 / 0.31 (48479) hydrogen bonds : bond 0.03967 / 2.65 ( 1343) hydrogen bonds : angle 4.98590 / 3.64 ( 3921) *********************** 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 253 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 1.371 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 452 MET cc_start: 0.9097 (ppp) cc_final: 0.8279 (ppp) REVERT: A 482 ASP cc_start: 0.9030 (m-30) cc_final: 0.8615 (m-30) REVERT: A 789 ASP cc_start: 0.6405 (OUTLIER) cc_final: 0.5848 (p0) REVERT: B 482 ASP cc_start: 0.8878 (m-30) cc_final: 0.8462 (m-30) REVERT: C 378 ILE cc_start: 0.9228 (mp) cc_final: 0.8881 (mp) REVERT: C 381 TRP cc_start: 0.8438 (m-10) cc_final: 0.8016 (m-90) REVERT: C 681 MET cc_start: 0.9083 (mmp) cc_final: 0.8844 (mmp) REVERT: C 791 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: E 304 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8415 (p-80) REVERT: E 344 GLN cc_start: 0.9302 (pm20) cc_final: 0.8882 (mp10) REVERT: F 583 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8196 (p) REVERT: F 822 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8224 (pp20) outliers start: 58 outliers final: 37 residues processed: 237 average time/residue: 0.1990 time to fit residues: 80.3287 Evaluate side-chains 229 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 426 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 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 834 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 700 LEU 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 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 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 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 E residue 892 TYR Chi-restraints excluded: chain F residue 583 CYS Chi-restraints excluded: chain F residue 779 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 100 optimal weight: 0.9980 chunk 357 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 212 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 727 GLN ** 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 = 0.4027 r_free = 0.4027 target = 0.107089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068770 restraints weight = 149358.802| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 6.08 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35660 Z= 0.157 Angle : 0.628 12.360 48479 Z= 0.312 Chirality : 0.042 0.242 5109 Planarity : 0.004 0.061 6035 Dihedral : 11.900 171.741 4855 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.13 % Favored : 91.63 % Rotamer: Outliers : 1.84 % Allowed : 14.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 4072 helix: 0.94 (0.12), residues: 1846 sheet: -0.78 (0.29), residues: 356 loop : -1.43 (0.15), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 376 TYR 0.022 0.001 TYR D 398 PHE 0.025 0.001 PHE E 726 TRP 0.030 0.001 TRP B 321 HIS 0.007 0.001 HIS E 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (35660) covalent geometry : angle 0.62820 / 0.31 (48479) hydrogen bonds : bond 0.03901 / 2.61 ( 1343) hydrogen bonds : angle 4.92279 / 3.60 ( 3921) *********************** 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 259 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 191 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: A 452 MET cc_start: 0.9126 (ppp) cc_final: 0.8300 (ppp) REVERT: A 482 ASP cc_start: 0.9020 (m-30) cc_final: 0.8616 (m-30) REVERT: A 789 ASP cc_start: 0.6538 (OUTLIER) cc_final: 0.5963 (p0) REVERT: B 482 ASP cc_start: 0.8858 (m-30) cc_final: 0.8465 (m-30) REVERT: B 791 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8357 (mp10) REVERT: C 378 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8687 (mp) REVERT: C 381 TRP cc_start: 0.8477 (m-10) cc_final: 0.8050 (m-90) REVERT: C 631 MET cc_start: 0.8829 (tpt) cc_final: 0.8621 (tpp) REVERT: C 681 MET cc_start: 0.9135 (mmp) cc_final: 0.8807 (mmp) REVERT: C 791 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: D 302 TYR cc_start: 0.8837 (m-80) cc_final: 0.8137 (m-80) REVERT: E 304 HIS cc_start: 0.8991 (OUTLIER) cc_final: 0.8494 (p-80) REVERT: E 344 GLN cc_start: 0.9284 (pm20) cc_final: 0.9024 (pm20) REVERT: F 583 CYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8245 (p) REVERT: F 822 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8209 (pp20) outliers start: 68 outliers final: 41 residues processed: 239 average time/residue: 0.1865 time to fit residues: 75.9510 Evaluate side-chains 237 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 405 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 745 THR 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 791 GLN Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 700 LEU 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 C residue 868 THR Chi-restraints excluded: chain D residue 425 MET 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 653 LEU Chi-restraints excluded: chain D residue 699 VAL 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 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 583 CYS Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 779 ARG 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 900 THR 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 112 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 275 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 245 optimal weight: 2.9990 chunk 373 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 374 optimal weight: 0.0770 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 ASN A 549 HIS B 389 GLN B 727 GLN ** 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** D 470 HIS ** 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 = 0.4033 r_free = 0.4033 target = 0.110606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.076633 restraints weight = 129158.408| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.85 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35660 Z= 0.116 Angle : 0.627 14.574 48479 Z= 0.306 Chirality : 0.042 0.246 5109 Planarity : 0.004 0.061 6035 Dihedral : 11.782 171.482 4855 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.76 % Favored : 91.99 % Rotamer: Outliers : 1.46 % Allowed : 14.80 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 4072 helix: 0.96 (0.12), residues: 1850 sheet: -0.85 (0.27), residues: 395 loop : -1.43 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 301 TYR 0.023 0.001 TYR D 398 PHE 0.018 0.001 PHE E 726 TRP 0.029 0.001 TRP B 321 HIS 0.012 0.001 HIS E 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (35660) covalent geometry : angle 0.62669 / 0.31 (48479) hydrogen bonds : bond 0.03591 / 2.41 ( 1343) hydrogen bonds : angle 4.81424 / 3.52 ( 3921) *********************** 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 253 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 1.304 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 404 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8634 (pm20) REVERT: A 452 MET cc_start: 0.9127 (ppp) cc_final: 0.8271 (ppp) REVERT: A 482 ASP cc_start: 0.9005 (m-30) cc_final: 0.8580 (m-30) REVERT: A 789 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6065 (p0) REVERT: B 482 ASP cc_start: 0.8886 (m-30) cc_final: 0.8478 (m-30) REVERT: B 791 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8365 (mp10) REVERT: C 378 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8542 (mp) REVERT: C 381 TRP cc_start: 0.8729 (m-10) cc_final: 0.8105 (m-90) REVERT: C 681 MET cc_start: 0.8878 (mmp) cc_final: 0.8628 (mmp) REVERT: C 791 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: E 303 LEU cc_start: 0.9680 (mt) cc_final: 0.9362 (pp) REVERT: E 304 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8330 (p-80) REVERT: E 335 TYR cc_start: 0.8645 (m-80) cc_final: 0.8317 (m-80) REVERT: E 344 GLN cc_start: 0.9146 (pm20) cc_final: 0.8675 (mp10) REVERT: F 822 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8187 (pp20) outliers start: 54 outliers final: 35 residues processed: 235 average time/residue: 0.1926 time to fit residues: 77.1453 Evaluate side-chains 235 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 405 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 745 THR 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 791 GLN 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 791 GLN Chi-restraints excluded: chain C residue 817 PHE 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 699 VAL 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 E residue 866 TYR Chi-restraints excluded: chain F residue 779 ARG 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 6 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 351 optimal weight: 3.9990 chunk 398 optimal weight: 0.3980 chunk 218 optimal weight: 0.0270 chunk 344 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 369 optimal weight: 7.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.110046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.075379 restraints weight = 126254.514| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.97 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35660 Z= 0.142 Angle : 0.645 15.897 48479 Z= 0.312 Chirality : 0.042 0.322 5109 Planarity : 0.004 0.062 6035 Dihedral : 11.692 171.849 4855 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.78 % Favored : 91.97 % Rotamer: Outliers : 1.49 % Allowed : 15.45 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 4072 helix: 0.99 (0.12), residues: 1847 sheet: -0.75 (0.28), residues: 373 loop : -1.42 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 301 TYR 0.021 0.001 TYR B 398 PHE 0.018 0.001 PHE E 726 TRP 0.027 0.001 TRP B 321 HIS 0.006 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (35660) covalent geometry : angle 0.64453 / 0.31 (48479) hydrogen bonds : bond 0.03682 / 2.47 ( 1343) hydrogen bonds : angle 4.82326 / 3.53 ( 3921) *********************** 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 248 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8645 (pm20) REVERT: A 452 MET cc_start: 0.9117 (ppp) cc_final: 0.8243 (ppp) REVERT: A 482 ASP cc_start: 0.9062 (m-30) cc_final: 0.8652 (m-30) REVERT: A 789 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.6101 (p0) REVERT: B 482 ASP cc_start: 0.8907 (m-30) cc_final: 0.8506 (m-30) REVERT: B 651 MET cc_start: 0.8890 (mmm) cc_final: 0.8638 (mmm) REVERT: B 791 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8322 (mp10) REVERT: C 681 MET cc_start: 0.8835 (mmp) cc_final: 0.8581 (mmp) REVERT: C 791 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: D 302 TYR cc_start: 0.8856 (m-80) cc_final: 0.8095 (m-80) REVERT: E 303 LEU cc_start: 0.9683 (mt) cc_final: 0.9357 (pp) REVERT: E 304 HIS cc_start: 0.9013 (OUTLIER) cc_final: 0.8344 (p-80) REVERT: E 335 TYR cc_start: 0.8613 (m-80) cc_final: 0.8255 (m-80) REVERT: E 344 GLN cc_start: 0.9132 (pm20) cc_final: 0.8819 (pm20) REVERT: E 417 MET cc_start: 0.9058 (mtt) cc_final: 0.8462 (mtm) REVERT: F 302 TYR cc_start: 0.8194 (p90) cc_final: 0.7831 (p90) REVERT: F 822 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8263 (pp20) outliers start: 55 outliers final: 38 residues processed: 231 average time/residue: 0.1850 time to fit residues: 73.0863 Evaluate side-chains 234 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 632 LEU 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 425 MET 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 699 VAL 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 E residue 844 VAL Chi-restraints excluded: chain E residue 866 TYR Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 779 ARG 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 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 315 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 8 optimal weight: 0.0030 chunk 382 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.7570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 HIS ** 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 = 0.4034 r_free = 0.4034 target = 0.110164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.075788 restraints weight = 127043.566| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 4.89 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35660 Z= 0.115 Angle : 0.649 14.609 48479 Z= 0.312 Chirality : 0.042 0.245 5109 Planarity : 0.004 0.061 6035 Dihedral : 11.585 171.645 4851 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.59 % Favored : 92.17 % Rotamer: Outliers : 1.41 % Allowed : 15.83 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 4072 helix: 0.98 (0.12), residues: 1851 sheet: -0.73 (0.28), residues: 379 loop : -1.43 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 301 TYR 0.035 0.001 TYR D 398 PHE 0.015 0.001 PHE E 726 TRP 0.026 0.001 TRP B 321 HIS 0.006 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (35660) covalent geometry : angle 0.64857 / 0.31 (48479) hydrogen bonds : bond 0.03504 / 2.35 ( 1343) hydrogen bonds : angle 4.76159 / 3.49 ( 3921) *********************** 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 247 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 1.359 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 404 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8740 (pm20) REVERT: A 452 MET cc_start: 0.9118 (ppp) cc_final: 0.8197 (ppp) REVERT: A 482 ASP cc_start: 0.9059 (m-30) cc_final: 0.8629 (m-30) REVERT: A 789 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6210 (p0) REVERT: B 482 ASP cc_start: 0.8983 (m-30) cc_final: 0.8659 (m-30) REVERT: B 651 MET cc_start: 0.8985 (mmm) cc_final: 0.8704 (mmm) REVERT: B 695 ASN cc_start: 0.8489 (p0) cc_final: 0.7909 (m-40) REVERT: B 728 MET cc_start: 0.8850 (ptp) cc_final: 0.8647 (ptt) REVERT: B 791 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8348 (mp10) REVERT: B 899 LYS cc_start: 0.8678 (tppt) cc_final: 0.7909 (ptmt) REVERT: C 681 MET cc_start: 0.8882 (mmp) cc_final: 0.8624 (mmp) REVERT: C 791 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: C 912 PHE cc_start: 0.7772 (m-80) cc_final: 0.7476 (t80) REVERT: D 302 TYR cc_start: 0.8826 (m-80) cc_final: 0.7966 (m-80) REVERT: E 303 LEU cc_start: 0.9681 (mt) cc_final: 0.9345 (pp) REVERT: E 304 HIS cc_start: 0.9022 (OUTLIER) cc_final: 0.8345 (p-80) REVERT: E 335 TYR cc_start: 0.8646 (m-80) cc_final: 0.8276 (m-80) REVERT: E 344 GLN cc_start: 0.9129 (pm20) cc_final: 0.8654 (mp10) REVERT: E 417 MET cc_start: 0.9022 (mtt) cc_final: 0.8442 (mtm) REVERT: E 786 MET cc_start: 0.8579 (mmp) cc_final: 0.8365 (pmm) REVERT: F 302 TYR cc_start: 0.8220 (p90) cc_final: 0.7865 (p90) REVERT: F 583 CYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8108 (p) REVERT: F 822 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8327 (pp20) outliers start: 52 outliers final: 38 residues processed: 229 average time/residue: 0.1905 time to fit residues: 74.3938 Evaluate side-chains 236 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 632 LEU 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 452 MET Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 491 HIS 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 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 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 583 CYS Chi-restraints excluded: chain F residue 779 ARG 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 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 148 optimal weight: 0.9990 chunk 322 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 157 optimal weight: 0.0040 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 177 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.109864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076424 restraints weight = 132963.112| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.82 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35660 Z= 0.111 Angle : 0.655 16.953 48479 Z= 0.313 Chirality : 0.042 0.244 5109 Planarity : 0.004 0.062 6035 Dihedral : 11.515 171.685 4851 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.51 % Favored : 92.26 % Rotamer: Outliers : 1.41 % Allowed : 15.80 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 4072 helix: 0.99 (0.12), residues: 1846 sheet: -0.73 (0.28), residues: 379 loop : -1.43 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 301 TYR 0.033 0.001 TYR D 398 PHE 0.013 0.001 PHE E 726 TRP 0.028 0.001 TRP B 321 HIS 0.028 0.001 HIS D 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (35660) covalent geometry : angle 0.65518 / 0.31 (48479) hydrogen bonds : bond 0.03411 / 2.28 ( 1343) hydrogen bonds : angle 4.72942 / 3.47 ( 3921) ********************** 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 246 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: A 452 MET cc_start: 0.9109 (ppp) cc_final: 0.8164 (ppp) REVERT: A 482 ASP cc_start: 0.9033 (m-30) cc_final: 0.8597 (m-30) REVERT: A 789 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6256 (p0) REVERT: B 482 ASP cc_start: 0.8981 (m-30) cc_final: 0.8659 (m-30) REVERT: B 651 MET cc_start: 0.8927 (mmm) cc_final: 0.8644 (mmm) REVERT: B 695 ASN cc_start: 0.8517 (p0) cc_final: 0.8002 (m110) REVERT: B 708 MET cc_start: 0.8981 (tpp) cc_final: 0.8733 (tpp) REVERT: B 791 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8347 (mp10) REVERT: B 899 LYS cc_start: 0.8781 (tppt) cc_final: 0.8026 (ptmt) REVERT: C 681 MET cc_start: 0.8906 (mmp) cc_final: 0.8650 (mmp) REVERT: C 791 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: C 912 PHE cc_start: 0.7936 (m-80) cc_final: 0.7636 (t80) REVERT: D 302 TYR cc_start: 0.8835 (m-80) cc_final: 0.7941 (m-80) REVERT: E 165 LEU cc_start: 0.5090 (OUTLIER) cc_final: 0.4794 (mm) REVERT: E 303 LEU cc_start: 0.9695 (mt) cc_final: 0.9371 (pp) REVERT: E 304 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8350 (p-80) REVERT: E 310 LEU cc_start: 0.7830 (tp) cc_final: 0.7320 (tp) REVERT: E 335 TYR cc_start: 0.8680 (m-80) cc_final: 0.8315 (m-80) REVERT: E 344 GLN cc_start: 0.9145 (pm20) cc_final: 0.8848 (pm20) REVERT: E 728 MET cc_start: 0.9123 (ppp) cc_final: 0.8887 (ppp) REVERT: F 302 TYR cc_start: 0.8225 (p90) cc_final: 0.7851 (p90) REVERT: F 583 CYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8120 (p) REVERT: F 822 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8372 (pp20) outliers start: 52 outliers final: 36 residues processed: 228 average time/residue: 0.1876 time to fit residues: 73.0831 Evaluate side-chains 235 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 632 LEU 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 452 MET Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 557 VAL 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 165 LEU 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 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 583 CYS 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 303 optimal weight: 3.9990 chunk 255 optimal weight: 0.0870 chunk 274 optimal weight: 30.0000 chunk 292 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 188 optimal weight: 0.3980 chunk 209 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 233 optimal weight: 0.7980 chunk 263 optimal weight: 10.0000 chunk 214 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.110367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.076121 restraints weight = 126747.450| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.96 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2299 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= 0.108 Angle : 0.652 16.418 48479 Z= 0.311 Chirality : 0.042 0.243 5109 Planarity : 0.004 0.062 6035 Dihedral : 11.424 171.666 4849 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.29 % Favored : 92.49 % Rotamer: Outliers : 1.30 % Allowed : 15.93 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 4072 helix: 1.02 (0.12), residues: 1847 sheet: -0.60 (0.27), residues: 400 loop : -1.41 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 779 TYR 0.032 0.001 TYR D 398 PHE 0.010 0.001 PHE E 477 TRP 0.028 0.001 TRP B 321 HIS 0.006 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (35660) covalent geometry : angle 0.65248 / 0.31 (48479) hydrogen bonds : bond 0.03281 / 2.20 ( 1343) hydrogen bonds : angle 4.68498 / 3.44 ( 3921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8126.60 seconds wall clock time: 140 minutes 36.61 seconds (8436.61 seconds total)