Starting phenix.real_space_refine on Sun Aug 9 05:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ww6_37882/08_2026/8ww6_37882.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ww6_37882/08_2026/8ww6_37882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ww6_37882/08_2026/8ww6_37882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ww6_37882/08_2026/8ww6_37882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ww6_37882/08_2026/8ww6_37882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ww6_37882/08_2026/8ww6_37882.map" } resolution = 3.73 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= 0.038 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 47 5.49 5 Mg 6 5.21 5 S 161 5.16 5 C 21022 2.51 5 N 5549 2.21 5 O 6040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s 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: 32825 Number of models: 1 Model: "" Number of chains: 14 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: "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: "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: "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: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5328 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, '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: "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: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.04, per 1000 atoms: 0.18 Number of scatterers: 32825 At special positions: 0 Unit cell: (143.445, 153.3, 148.92, 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 161 16.00 P 47 15.00 Mg 6 11.99 O 6040 8.00 N 5549 7.00 C 21022 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: 2.16 Conformation dependent library (CDL) restraints added in 1.3 seconds 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 29 sheets defined 51.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'B' and resid 289 through 297 Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 311 through 317 removed outlier: 3.859A pdb=" N TYR B 315 " --> pdb=" O PRO B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 removed outlier: 3.561A pdb=" N THR B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 377 through 386 removed outlier: 3.566A 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 427 Processing helix chain 'B' and resid 466 through 494 removed outlier: 3.520A pdb=" N SER B 474 " --> pdb=" O HIS B 470 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE B 477 " --> pdb=" O ILE B 473 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 479 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 484 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.859A pdb=" N ASN B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 516 removed outlier: 3.908A 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: 4.542A pdb=" N PHE B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 4.028A 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: 3.709A pdb=" N THR B 620 " --> pdb=" O PHE B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 654 removed outlier: 3.608A pdb=" N LEU B 645 " --> pdb=" O GLY B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 668 removed outlier: 4.037A pdb=" N LEU B 666 " --> pdb=" O ASN B 662 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.644A pdb=" N VAL B 709 " --> pdb=" O LEU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 751 removed outlier: 3.679A 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 777 through 783 removed outlier: 4.153A pdb=" N ILE B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 808 removed outlier: 3.580A pdb=" N GLN B 791 " --> pdb=" O ASP B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.641A pdb=" N GLU B 826 " --> pdb=" O GLU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 843 removed outlier: 3.708A pdb=" N VAL B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 870 removed outlier: 3.790A pdb=" N VAL B 858 " --> pdb=" O ASN B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 878 No H-bonds generated for 'chain 'B' and resid 876 through 878' Processing helix chain 'B' and resid 879 through 887 removed outlier: 5.174A pdb=" N GLU B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 892 removed outlier: 4.079A pdb=" N LYS B 891 " --> pdb=" O VAL B 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 4.113A pdb=" N HIS A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.721A pdb=" N ILE A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.287A 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 345 No H-bonds generated for 'chain 'A' and resid 344 through 345' Processing helix chain 'A' and resid 346 through 350 removed outlier: 4.336A pdb=" N LYS A 349 " --> pdb=" O CYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.869A pdb=" N ILE A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 409 Processing helix chain 'A' and resid 414 through 427 Processing helix chain 'A' and resid 466 through 494 removed outlier: 4.225A pdb=" N PHE A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 removed outlier: 3.806A pdb=" N ASN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.929A 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: 3.521A pdb=" N LYS A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 4.072A 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 Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 641 through 654 removed outlier: 3.787A pdb=" N LEU A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 removed outlier: 4.389A pdb=" N LEU A 666 " --> pdb=" O ASN A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 708 removed outlier: 4.151A pdb=" N LYS A 706 " --> pdb=" O THR A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 777 through 783 removed outlier: 4.284A pdb=" N ILE A 781 " --> pdb=" O ASP A 777 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 810 removed outlier: 3.705A pdb=" N GLN A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 833 through 843 removed outlier: 3.625A pdb=" N THR A 840 " --> pdb=" O HIS A 836 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 841 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 842 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 870 removed outlier: 3.827A pdb=" N VAL A 858 " --> pdb=" O ASN A 854 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 866 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 868 " --> pdb=" O GLU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 882 removed outlier: 4.118A pdb=" N GLN A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.149A pdb=" N LYS A 891 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 892 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 893 " --> pdb=" O GLU A 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 888 through 893' Processing helix chain 'C' and resid 290 through 297 removed outlier: 4.175A pdb=" N ASP C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 308 Processing helix chain 'C' and resid 311 through 317 removed outlier: 3.845A pdb=" N TYR C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 331 removed outlier: 3.703A pdb=" N TRP C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 354 through 367 Processing helix chain 'C' and resid 377 through 386 Processing helix chain 'C' and resid 388 through 409 removed outlier: 3.668A pdb=" N GLU C 392 " --> pdb=" O GLN C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 425 Processing helix chain 'C' and resid 466 through 494 removed outlier: 4.166A pdb=" N PHE C 477 " --> pdb=" O ILE C 473 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG C 479 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 516 removed outlier: 4.136A pdb=" N ASN C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LYS C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 4.083A 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: 5.293A pdb=" N PHE C 533 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 605 Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.799A pdb=" N THR C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 654 removed outlier: 3.959A pdb=" N LEU C 645 " --> pdb=" O GLY C 641 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C 646 " --> pdb=" O LYS C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 4.152A pdb=" N LEU C 666 " --> pdb=" O ASN C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 682 removed outlier: 3.864A pdb=" N PHE C 680 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 681 " --> pdb=" O SER C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 710 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.516A pdb=" N ARG C 752 " --> pdb=" O GLY C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 783 removed outlier: 4.266A pdb=" N ILE C 781 " --> pdb=" O ASP C 777 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS C 782 " --> pdb=" O PRO C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 808 removed outlier: 3.505A pdb=" N GLN C 791 " --> pdb=" O ASP C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 831 removed outlier: 3.538A pdb=" N GLU C 826 " --> pdb=" O GLU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 843 Processing helix chain 'C' and resid 855 through 870 removed outlier: 3.853A pdb=" N THR C 860 " --> pdb=" O SER C 856 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR C 868 " --> pdb=" O GLU C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 876 through 881 removed outlier: 3.936A pdb=" N LEU C 880 " --> pdb=" O ILE C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 891 removed outlier: 3.651A 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 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.591A pdb=" N ARG D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 317 removed outlier: 3.995A pdb=" N TYR D 315 " --> pdb=" O PRO D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 331 removed outlier: 3.740A pdb=" N THR D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.713A pdb=" N GLN D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 removed outlier: 3.753A pdb=" N TRP D 350 " --> pdb=" O PRO D 347 " (cutoff:3.500A) removed outlier: 4.436A 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 366 removed outlier: 3.936A pdb=" N LYS D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 388 through 409 removed outlier: 3.615A pdb=" N TYR D 409 " --> pdb=" O TYR D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 427 Processing helix chain 'D' and resid 466 through 476 Processing helix chain 'D' and resid 476 through 494 removed outlier: 4.314A pdb=" N VAL D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN D 494 " --> pdb=" O TYR D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 removed outlier: 4.013A pdb=" N LEU D 501 " --> pdb=" O GLU D 497 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LYS D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 4.388A 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: 4.970A pdb=" N PHE D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 605 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.600A pdb=" N THR D 620 " --> pdb=" O PHE D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 623 No H-bonds generated for 'chain 'D' and resid 621 through 623' Processing helix chain 'D' and resid 641 through 654 removed outlier: 3.697A pdb=" N LEU D 645 " --> pdb=" O GLY D 641 " (cutoff:3.500A) removed outlier: 3.842A 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 679 through 683 removed outlier: 3.691A pdb=" N LEU D 683 " --> pdb=" O PHE D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 710 Processing helix chain 'D' and resid 746 through 752 removed outlier: 3.679A pdb=" N TRP D 750 " --> pdb=" O ASP D 746 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG D 752 " --> pdb=" O GLY D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 783 removed outlier: 3.520A pdb=" N ILE D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 810 removed outlier: 3.573A pdb=" N GLN D 791 " --> pdb=" O ASP D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 831 removed outlier: 3.702A pdb=" N SER D 823 " --> pdb=" O PRO D 819 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N THR D 825 " --> pdb=" O ILE D 821 " (cutoff:3.500A) removed outlier: 3.614A 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: 4.265A pdb=" N VAL D 858 " --> pdb=" O ASN D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 887 removed outlier: 4.015A pdb=" N GLN D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 893 removed outlier: 3.948A pdb=" N LYS D 891 " --> pdb=" O VAL D 888 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 893 " --> pdb=" O GLU D 890 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 297 through 310 removed outlier: 3.937A pdb=" N ARG E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 317 Processing helix chain 'E' and resid 317 through 331 removed outlier: 3.567A pdb=" N THR E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 343 Processing helix chain 'E' and resid 353 through 366 removed outlier: 4.280A pdb=" N GLU E 359 " --> pdb=" O LYS E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 386 Processing helix chain 'E' and resid 388 through 409 Processing helix chain 'E' and resid 414 through 427 removed outlier: 3.674A pdb=" N ILE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 476 removed outlier: 3.623A pdb=" N SER E 474 " --> pdb=" O HIS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 494 removed outlier: 3.834A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 516 removed outlier: 3.961A pdb=" N ASN E 502 " --> pdb=" O SER E 498 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR E 504 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LYS E 505 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 4.308A 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: 3.869A pdb=" N PHE E 533 " --> pdb=" O ARG E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 605 Processing helix chain 'E' and resid 607 through 620 removed outlier: 3.547A 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 Processing helix chain 'E' and resid 662 through 666 Processing helix chain 'E' and resid 678 through 682 Processing helix chain 'E' and resid 705 through 710 Processing helix chain 'E' and resid 746 through 752 Processing helix chain 'E' and resid 777 through 783 removed outlier: 4.123A pdb=" N ILE E 781 " --> pdb=" O ASP E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 810 removed outlier: 3.747A pdb=" N GLN E 791 " --> pdb=" O ASP E 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 816 removed outlier: 3.502A pdb=" N VAL E 816 " --> pdb=" O ILE E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 819 through 831 removed outlier: 3.918A pdb=" N SER E 823 " --> pdb=" O PRO E 819 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N THR E 825 " --> pdb=" O ILE E 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 843 removed outlier: 3.729A pdb=" N ARG E 837 " --> pdb=" O ASP E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 854 through 870 removed outlier: 3.783A pdb=" N VAL E 858 " --> pdb=" O ASN E 854 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR E 868 " --> pdb=" O GLU E 864 " (cutoff:3.500A) Processing helix chain 'E' and resid 876 through 886 removed outlier: 3.702A pdb=" N LEU E 880 " --> pdb=" O ILE E 876 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN E 882 " --> pdb=" O LEU E 878 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 883 " --> pdb=" O GLU E 879 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU E 885 " --> pdb=" O SER E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 893 removed outlier: 3.728A pdb=" N LYS E 891 " --> pdb=" O VAL E 888 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR E 892 " --> pdb=" O LEU E 889 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 893 " --> pdb=" O GLU E 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 888 through 893' Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 297 through 310 removed outlier: 3.831A pdb=" N ARG F 301 " --> pdb=" O ASP F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 317 removed outlier: 4.236A pdb=" N TYR F 315 " --> pdb=" O PRO F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 330 Processing helix chain 'F' and resid 335 through 344 Processing helix chain 'F' and resid 358 through 367 Processing helix chain 'F' and resid 377 through 384 Processing helix chain 'F' and resid 388 through 409 removed outlier: 3.782A pdb=" N GLU F 392 " --> pdb=" O GLN F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.560A pdb=" N ILE F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 494 removed outlier: 3.617A pdb=" N SER F 474 " --> pdb=" O HIS F 470 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE F 477 " --> pdb=" O ILE F 473 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER F 478 " --> pdb=" O SER F 474 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG F 479 " --> pdb=" O GLU F 475 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.843A pdb=" N LEU F 501 " --> pdb=" O GLU F 497 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR F 504 " --> pdb=" O ILE F 500 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS F 505 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 4.052A 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: 4.343A pdb=" N PHE F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) removed outlier: 4.085A 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: 3.531A pdb=" N THR F 620 " --> pdb=" O PHE F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 654 Processing helix chain 'F' and resid 662 through 668 removed outlier: 4.086A pdb=" N LEU F 666 " --> pdb=" O ASN F 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 677 through 682 removed outlier: 3.616A pdb=" N MET F 681 " --> pdb=" O ASN F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 704 through 710 removed outlier: 3.707A pdb=" N MET F 708 " --> pdb=" O ARG F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 751 Processing helix chain 'F' and resid 778 through 783 removed outlier: 3.906A pdb=" N HIS F 782 " --> pdb=" O PRO F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 810 removed outlier: 3.558A pdb=" N GLN F 791 " --> pdb=" O ASP F 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 812 through 816 Processing helix chain 'F' and resid 822 through 831 Processing helix chain 'F' and resid 833 through 843 Processing helix chain 'F' and resid 855 through 870 removed outlier: 3.512A pdb=" N THR F 868 " --> pdb=" O GLU F 864 " (cutoff:3.500A) Processing helix chain 'F' and resid 876 through 884 removed outlier: 4.369A pdb=" N LEU F 880 " --> pdb=" O ILE F 876 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN F 882 " --> pdb=" O LEU F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 888 through 893 removed outlier: 3.737A pdb=" N LYS F 891 " --> pdb=" O VAL F 888 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR F 892 " --> pdb=" O LEU F 889 " (cutoff:3.500A) removed outlier: 3.961A 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 'B' and resid 430 through 434 removed outlier: 3.717A pdb=" N TRP B 442 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 550 through 553 Processing sheet with id=AA3, first strand: chain 'B' and resid 631 through 635 Processing sheet with id=AA4, first strand: chain 'B' and resid 658 through 660 removed outlier: 3.571A pdb=" N SER B 659 " --> pdb=" O TYR B 688 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 690 " --> pdb=" O SER B 659 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY B 689 " --> pdb=" O VAL B 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 698 through 699 removed outlier: 6.706A pdb=" N GLU B 698 " --> pdb=" O ILE B 741 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 713 through 716 removed outlier: 3.618A pdb=" N VAL B 714 " --> pdb=" O PHE B 726 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 761 through 762 removed outlier: 7.077A pdb=" N LYS B 761 " --> pdb=" O LYS B 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.801A pdb=" N TRP A 442 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 550 through 553 Processing sheet with id=AB1, first strand: chain 'A' and resid 658 through 660 removed outlier: 4.102A pdb=" N TYR A 690 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 689 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA A 735 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 691 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 632 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 714 through 718 removed outlier: 3.783A pdb=" N VAL A 714 " --> pdb=" O PHE A 726 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 718 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 431 through 434 removed outlier: 3.793A pdb=" N TRP C 442 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 550 through 553 Processing sheet with id=AB5, first strand: chain 'C' and resid 632 through 635 Processing sheet with id=AB6, first strand: chain 'C' and resid 658 through 661 removed outlier: 3.921A pdb=" N TYR C 690 " --> pdb=" O SER C 659 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 713 through 716 removed outlier: 3.502A pdb=" N GLU C 724 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 893 through 895 Processing sheet with id=AB9, first strand: chain 'D' and resid 430 through 434 removed outlier: 3.644A pdb=" N TRP D 442 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 550 through 553 removed outlier: 3.597A pdb=" N GLY D 556 " --> pdb=" O VAL D 553 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 658 through 660 removed outlier: 3.708A pdb=" N TYR D 690 " --> pdb=" O SER D 659 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 733 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 735 " --> pdb=" O PHE D 691 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU D 632 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N MET D 631 " --> pdb=" O ARG D 754 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR D 756 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU D 633 " --> pdb=" O TYR D 756 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 714 through 716 removed outlier: 3.930A pdb=" N VAL D 714 " --> pdb=" O PHE D 726 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE D 726 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA D 716 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU D 724 " --> pdb=" O ALA D 716 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 430 through 434 removed outlier: 3.772A pdb=" N TRP E 442 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 550 through 553 Processing sheet with id=AC6, first strand: chain 'E' and resid 658 through 660 removed outlier: 3.924A pdb=" N TYR E 690 " --> pdb=" O SER E 659 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU E 632 " --> pdb=" O ALA E 734 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 430 through 434 removed outlier: 3.931A 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: 3.816A pdb=" N TYR F 690 " --> pdb=" O SER F 659 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA F 735 " --> pdb=" O PHE F 691 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU F 632 " --> pdb=" O ALA F 734 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N SER F 736 " --> pdb=" O LEU F 632 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TRP F 634 " --> pdb=" O SER F 736 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 698 through 699 removed outlier: 6.514A 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 1282 hydrogen bonds defined for protein. 3756 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: 5.15 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 13812 1.39 - 1.56: 19663 1.56 - 1.73: 88 1.73 - 1.90: 257 1.90 - 2.07: 6 Bond restraints: 33826 Sorted by residual: bond pdb=" PG AGS B1001 " pdb=" S1G AGS B1001 " ideal model delta sigma weight residual 1.936 2.074 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" PG AGS C1001 " pdb=" S1G AGS C1001 " ideal model delta sigma weight residual 1.936 2.074 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" PG AGS D1001 " pdb=" S1G AGS D1001 " ideal model delta sigma weight residual 1.936 2.074 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" O3B AGS A1001 " pdb=" PB AGS A1001 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" O3B AGS E1001 " pdb=" PB AGS E1001 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 33821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 44686 1.97 - 3.93: 1122 3.93 - 5.90: 125 5.90 - 7.86: 43 7.86 - 9.83: 27 Bond angle restraints: 46003 Sorted by residual: angle pdb=" C ARG F 670 " pdb=" CA ARG F 670 " pdb=" CB ARG F 670 " ideal model delta sigma weight residual 116.54 110.46 6.08 1.15e+00 7.56e-01 2.80e+01 angle pdb=" N ILE D 373 " pdb=" CA ILE D 373 " pdb=" C ILE D 373 " ideal model delta sigma weight residual 113.71 108.72 4.99 9.50e-01 1.11e+00 2.76e+01 angle pdb=" N ILE B 785 " pdb=" CA ILE B 785 " pdb=" C ILE B 785 " ideal model delta sigma weight residual 113.39 106.28 7.11 1.47e+00 4.63e-01 2.34e+01 angle pdb=" O4' DT H 8 " pdb=" C1' DT H 8 " pdb=" N1 DT H 8 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.24e+01 angle pdb=" C TYR D 853 " pdb=" N ASN D 854 " pdb=" CA ASN D 854 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 ... (remaining 45998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 19464 34.62 - 69.24: 597 69.24 - 103.86: 88 103.86 - 138.48: 0 138.48 - 173.10: 2 Dihedral angle restraints: 20151 sinusoidal: 8650 harmonic: 11501 Sorted by residual: dihedral pdb=" CA ILE B 876 " pdb=" C ILE B 876 " pdb=" N ALA B 877 " pdb=" CA ALA B 877 " ideal model delta harmonic sigma weight residual 180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" C4' DT H 12 " pdb=" C3' DT H 12 " pdb=" O3' DT H 12 " pdb=" P DT H 13 " ideal model delta sinusoidal sigma weight residual -140.00 33.10 -173.10 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT H 3 " pdb=" C3' DT H 3 " pdb=" O3' DT H 3 " pdb=" P DT H 4 " ideal model delta sinusoidal sigma weight residual -140.00 29.48 -169.48 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 20148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4337 0.071 - 0.142: 454 0.142 - 0.212: 16 0.212 - 0.283: 6 0.283 - 0.354: 1 Chirality restraints: 4814 Sorted by residual: chirality pdb=" CB ILE A 605 " pdb=" CA ILE A 605 " pdb=" CG1 ILE A 605 " pdb=" CG2 ILE A 605 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C3' AGS E1001 " pdb=" C2' AGS E1001 " pdb=" C4' AGS E1001 " pdb=" O3' AGS E1001 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' AGS A1001 " pdb=" C2' AGS A1001 " pdb=" C4' AGS A1001 " pdb=" O3' AGS A1001 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4811 not shown) Planarity restraints: 5717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 822 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLU D 822 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU D 822 " 0.021 2.00e-02 2.50e+03 pdb=" N SER D 823 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 381 " -0.016 2.00e-02 2.50e+03 1.66e-02 6.87e+00 pdb=" CG TRP C 381 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 381 " -0.021 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 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 381 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 381 " -0.001 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=" C PRO C 311 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.77e+00 pdb=" N PRO C 312 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 312 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 312 " -0.033 5.00e-02 4.00e+02 ... (remaining 5714 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 159 2.38 - 3.01: 19553 3.01 - 3.64: 55051 3.64 - 4.27: 77716 4.27 - 4.90: 121256 Nonbonded interactions: 273735 Sorted by model distance: nonbonded pdb=" CG2 THR C 643 " pdb="MG MG C1002 " model vdw 1.746 2.590 nonbonded pdb=" O3G AGS C1001 " pdb="MG MG C1002 " model vdw 1.752 2.170 nonbonded pdb=" O3G AGS E1001 " pdb="MG MG E1002 " model vdw 1.948 2.170 nonbonded pdb=" O3G AGS B1001 " pdb="MG MG B1002 " model vdw 1.954 2.170 nonbonded pdb=" O1A AGS E1001 " pdb="MG MG E1002 " model vdw 1.969 2.170 ... (remaining 273730 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 916 or resid 937 through 1002)) selection = (chain 'B' and (resid 289 through 916 or resid 937 through 1002)) selection = (chain 'C' and (resid 289 through 916 or resid 937 through 1002)) selection = (chain 'D' and (resid 289 through 916 or resid 937 through 1002)) selection = (chain 'E' and (resid 289 through 916 or resid 937 through 1002)) selection = (chain 'F' and (resid 289 through 916 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.710 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 33826 Z= 0.230 Angle : 0.721 9.826 46003 Z= 0.406 Chirality : 0.043 0.354 4814 Planarity : 0.004 0.060 5717 Dihedral : 16.932 173.103 12719 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.25 % Favored : 90.51 % Rotamer: Outliers : 1.46 % Allowed : 1.09 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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: -0.69 (0.14), residues: 3847 helix: 0.56 (0.13), residues: 1693 sheet: -0.29 (0.30), residues: 327 loop : -1.48 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 717 TYR 0.023 0.001 TYR A 892 PHE 0.023 0.001 PHE D 477 TRP 0.045 0.001 TRP C 381 HIS 0.008 0.001 HIS E 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.23 (33826) covalent geometry : angle 0.72098 / 0.41 (46003) hydrogen bonds : bond 0.19080 / 17.88 ( 1282) hydrogen bonds : angle 7.81330 / 6.78 ( 3756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 1.155 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: symmetry clash revert: symmetry clash REVERT: A 379 MET cc_start: 0.7814 (tmm) cc_final: 0.7535 (tmm) REVERT: A 892 TYR cc_start: 0.7606 (p90) cc_final: 0.7323 (p90) REVERT: C 294 MET cc_start: 0.7875 (mmp) cc_final: 0.7561 (mmm) REVERT: C 452 MET cc_start: 0.8465 (pmm) cc_final: 0.8181 (pmm) REVERT: D 341 TRP cc_start: 0.9159 (t60) cc_final: 0.8795 (t60) REVERT: E 482 ASP cc_start: 0.8586 (m-30) cc_final: 0.8275 (m-30) REVERT: E 728 MET cc_start: 0.7348 (pmm) cc_final: 0.6912 (pmm) REVERT: F 335 TYR cc_start: 0.9435 (m-80) cc_final: 0.8828 (m-80) REVERT: F 362 TRP cc_start: 0.7370 (t-100) cc_final: 0.7118 (t-100) REVERT: F 417 MET cc_start: 0.7874 (mtm) cc_final: 0.7440 (mtm) REVERT: F 426 MET cc_start: 0.8389 (tmm) cc_final: 0.8183 (tmm) outliers start: 51 outliers final: 20 residues processed: 259 average time/residue: 0.2031 time to fit residues: 87.0067 Evaluate side-chains 179 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 874 ARG Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 829 ARG Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 671 GLU Chi-restraints excluded: chain F residue 698 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 308 ASN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS B 491 HIS ** B 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 ASN B 871 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN C 491 HIS C 494 GLN ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 869 ASN ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 ASN ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.080276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.060343 restraints weight = 235963.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.060346 restraints weight = 144890.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.060872 restraints weight = 109700.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.061125 restraints weight = 94571.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.061186 restraints weight = 88738.802| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33826 Z= 0.138 Angle : 0.677 16.068 46003 Z= 0.344 Chirality : 0.044 0.253 4814 Planarity : 0.005 0.055 5717 Dihedral : 13.922 169.503 4813 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.66 % Favored : 91.11 % Rotamer: Outliers : 0.89 % Allowed : 7.87 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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: -0.71 (0.14), residues: 3847 helix: 0.43 (0.12), residues: 1737 sheet: -0.24 (0.29), residues: 325 loop : -1.42 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 301 TYR 0.039 0.002 TYR D 302 PHE 0.015 0.001 PHE F 616 TRP 0.037 0.001 TRP C 381 HIS 0.011 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (33826) covalent geometry : angle 0.67705 / 0.34 (46003) hydrogen bonds : bond 0.05107 / 4.68 ( 1282) hydrogen bonds : angle 6.21075 / 5.20 ( 3756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 708 MET cc_start: 0.9565 (mmp) cc_final: 0.9362 (mmp) REVERT: A 452 MET cc_start: 0.7813 (pmm) cc_final: 0.7329 (pmm) REVERT: A 615 MET cc_start: 0.9289 (tpp) cc_final: 0.9006 (tpp) REVERT: A 892 TYR cc_start: 0.7413 (p90) cc_final: 0.7183 (p90) REVERT: C 294 MET cc_start: 0.8664 (mmp) cc_final: 0.8454 (mmp) REVERT: C 452 MET cc_start: 0.8543 (pmm) cc_final: 0.8341 (pmm) REVERT: D 341 TRP cc_start: 0.9200 (t60) cc_final: 0.8670 (t60) REVERT: D 412 MET cc_start: 0.8541 (mpp) cc_final: 0.8136 (mpp) REVERT: D 426 MET cc_start: 0.8155 (tmm) cc_final: 0.7866 (tmm) REVERT: D 646 MET cc_start: 0.9380 (mpp) cc_final: 0.8969 (mpp) REVERT: E 341 TRP cc_start: 0.9314 (t60) cc_final: 0.9110 (t60) REVERT: E 482 ASP cc_start: 0.8517 (m-30) cc_final: 0.8179 (m-30) REVERT: E 728 MET cc_start: 0.7390 (pmm) cc_final: 0.6890 (pmm) REVERT: F 335 TYR cc_start: 0.9539 (m-80) cc_final: 0.9036 (m-10) REVERT: F 651 MET cc_start: 0.9212 (tpp) cc_final: 0.8979 (tpp) REVERT: F 666 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8978 (tm) outliers start: 31 outliers final: 18 residues processed: 202 average time/residue: 0.1828 time to fit residues: 61.8737 Evaluate side-chains 180 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 892 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 366 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 377 optimal weight: 6.9990 chunk 362 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 301 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.079992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.060239 restraints weight = 236134.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.060238 restraints weight = 143983.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.060662 restraints weight = 107973.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.060895 restraints weight = 94080.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.061061 restraints weight = 88475.830| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33826 Z= 0.125 Angle : 0.625 14.169 46003 Z= 0.319 Chirality : 0.042 0.259 4814 Planarity : 0.004 0.056 5717 Dihedral : 12.867 169.400 4777 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.14 % Favored : 91.63 % Rotamer: Outliers : 0.86 % Allowed : 10.88 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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: -0.66 (0.14), residues: 3847 helix: 0.54 (0.12), residues: 1744 sheet: -0.41 (0.29), residues: 320 loop : -1.43 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 670 TYR 0.028 0.001 TYR D 302 PHE 0.016 0.001 PHE F 616 TRP 0.045 0.001 TRP E 945 HIS 0.009 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (33826) covalent geometry : angle 0.62468 / 0.32 (46003) hydrogen bonds : bond 0.04452 / 4.08 ( 1282) hydrogen bonds : angle 5.84638 / 4.91 ( 3756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 708 MET cc_start: 0.9577 (mmp) cc_final: 0.9369 (mmp) REVERT: B 853 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6429 (t80) REVERT: A 452 MET cc_start: 0.7910 (pmm) cc_final: 0.7431 (pmm) REVERT: A 615 MET cc_start: 0.9346 (tpp) cc_final: 0.9079 (tpp) REVERT: A 681 MET cc_start: 0.8753 (ttm) cc_final: 0.8443 (mtt) REVERT: A 892 TYR cc_start: 0.7521 (p90) cc_final: 0.7255 (p90) REVERT: C 452 MET cc_start: 0.8584 (pmm) cc_final: 0.8384 (pmm) REVERT: C 631 MET cc_start: 0.8430 (tpp) cc_final: 0.7779 (tpp) REVERT: C 878 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8680 (tp) REVERT: D 341 TRP cc_start: 0.9203 (t60) cc_final: 0.8799 (t60) REVERT: D 412 MET cc_start: 0.8602 (mpp) cc_final: 0.8120 (mpp) REVERT: D 426 MET cc_start: 0.8156 (tmm) cc_final: 0.7771 (tmm) REVERT: D 646 MET cc_start: 0.9382 (mpp) cc_final: 0.8707 (mpp) REVERT: D 708 MET cc_start: 0.8929 (mmp) cc_final: 0.8725 (mmp) REVERT: E 341 TRP cc_start: 0.9309 (t60) cc_final: 0.8999 (t60) REVERT: E 482 ASP cc_start: 0.8522 (m-30) cc_final: 0.8183 (m-30) REVERT: E 728 MET cc_start: 0.7410 (pmm) cc_final: 0.6932 (pmm) REVERT: E 753 LEU cc_start: 0.9479 (mt) cc_final: 0.8914 (mt) REVERT: F 335 TYR cc_start: 0.9519 (m-80) cc_final: 0.9181 (m-80) REVERT: F 341 TRP cc_start: 0.8026 (m100) cc_final: 0.7374 (m100) REVERT: F 426 MET cc_start: 0.8293 (tmm) cc_final: 0.8087 (tmm) REVERT: F 651 MET cc_start: 0.9229 (tpp) cc_final: 0.8993 (tpp) REVERT: F 666 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8966 (tm) REVERT: F 696 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7577 (ptpp) outliers start: 30 outliers final: 17 residues processed: 191 average time/residue: 0.1948 time to fit residues: 63.3045 Evaluate side-chains 179 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 820 THR Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 696 LYS Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 237 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 317 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 chunk 349 optimal weight: 0.0030 chunk 81 optimal weight: 5.9990 chunk 352 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 HIS ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.072901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.053238 restraints weight = 209840.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.054370 restraints weight = 124314.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.055076 restraints weight = 91371.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.055509 restraints weight = 76361.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.055661 restraints weight = 68721.645| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33826 Z= 0.176 Angle : 0.630 13.249 46003 Z= 0.323 Chirality : 0.042 0.262 4814 Planarity : 0.004 0.053 5717 Dihedral : 12.344 169.881 4767 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.68 % Favored : 91.08 % Rotamer: Outliers : 1.09 % Allowed : 12.44 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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: -0.61 (0.14), residues: 3847 helix: 0.63 (0.13), residues: 1745 sheet: -0.58 (0.29), residues: 319 loop : -1.42 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 301 TYR 0.022 0.002 TYR D 398 PHE 0.025 0.001 PHE A 912 TRP 0.038 0.001 TRP E 945 HIS 0.008 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (33826) covalent geometry : angle 0.63039 / 0.32 (46003) hydrogen bonds : bond 0.04164 / 3.79 ( 1282) hydrogen bonds : angle 5.73976 / 4.81 ( 3756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8897 (tpp) cc_final: 0.8668 (tpp) REVERT: B 853 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6556 (t80) REVERT: A 452 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7531 (pmm) REVERT: A 615 MET cc_start: 0.9469 (tpp) cc_final: 0.9212 (tpp) REVERT: A 653 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9127 (tt) REVERT: C 452 MET cc_start: 0.8673 (pmm) cc_final: 0.8459 (pmm) REVERT: C 681 MET cc_start: 0.8863 (mmp) cc_final: 0.8653 (mmp) REVERT: C 878 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8708 (tp) REVERT: D 341 TRP cc_start: 0.9223 (t60) cc_final: 0.8758 (t60) REVERT: D 412 MET cc_start: 0.8739 (mpp) cc_final: 0.8185 (mpp) REVERT: D 426 MET cc_start: 0.8317 (tmm) cc_final: 0.7933 (tmm) REVERT: D 646 MET cc_start: 0.9400 (mpp) cc_final: 0.8760 (mpp) REVERT: D 869 ASN cc_start: 0.9352 (OUTLIER) cc_final: 0.9043 (p0) REVERT: E 335 TYR cc_start: 0.8778 (m-80) cc_final: 0.8553 (m-80) REVERT: E 341 TRP cc_start: 0.9298 (t60) cc_final: 0.8950 (t60) REVERT: E 482 ASP cc_start: 0.8709 (m-30) cc_final: 0.8369 (m-30) REVERT: E 728 MET cc_start: 0.7586 (pmm) cc_final: 0.7028 (pmm) REVERT: E 753 LEU cc_start: 0.9501 (mt) cc_final: 0.9002 (mt) REVERT: F 335 TYR cc_start: 0.9514 (m-80) cc_final: 0.9169 (m-80) REVERT: F 341 TRP cc_start: 0.8075 (m100) cc_final: 0.7328 (m100) REVERT: F 426 MET cc_start: 0.8253 (tmm) cc_final: 0.7969 (tmm) REVERT: F 651 MET cc_start: 0.9258 (tpp) cc_final: 0.9025 (tpp) REVERT: F 666 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9041 (tm) REVERT: F 696 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7626 (ptpp) outliers start: 38 outliers final: 19 residues processed: 193 average time/residue: 0.1740 time to fit residues: 57.3203 Evaluate side-chains 182 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 820 THR Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 696 LYS Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 235 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 371 optimal weight: 4.9990 chunk 375 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 764 HIS B 765 ASN B 812 GLN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 792 ASN E 916 GLN ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.076285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.055850 restraints weight = 237463.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.055660 restraints weight = 148415.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.056053 restraints weight = 113816.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.056269 restraints weight = 99983.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.056325 restraints weight = 94056.150| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 33826 Z= 0.315 Angle : 0.742 14.176 46003 Z= 0.385 Chirality : 0.044 0.276 4814 Planarity : 0.005 0.052 5717 Dihedral : 12.087 171.020 4765 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.51 % Favored : 90.28 % Rotamer: Outliers : 1.58 % Allowed : 13.99 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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: -0.90 (0.14), residues: 3847 helix: 0.41 (0.12), residues: 1754 sheet: -0.83 (0.28), residues: 345 loop : -1.58 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 670 TYR 0.028 0.002 TYR A 892 PHE 0.027 0.002 PHE A 912 TRP 0.024 0.002 TRP D 634 HIS 0.010 0.002 HIS D 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.31 (33826) covalent geometry : angle 0.74211 / 0.38 (46003) hydrogen bonds : bond 0.04575 / 4.09 ( 1282) hydrogen bonds : angle 6.04347 / 5.07 ( 3756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 631 MET cc_start: 0.8490 (tpp) cc_final: 0.8196 (tpt) REVERT: B 666 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8598 (pp) REVERT: B 708 MET cc_start: 0.9549 (mmp) cc_final: 0.9323 (mmp) REVERT: B 853 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.6940 (t80) REVERT: A 452 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7753 (pmm) REVERT: A 615 MET cc_start: 0.9418 (tpp) cc_final: 0.9154 (tpp) REVERT: C 452 MET cc_start: 0.8841 (pmm) cc_final: 0.8570 (pmm) REVERT: C 681 MET cc_start: 0.9173 (mmp) cc_final: 0.8857 (mmp) REVERT: D 341 TRP cc_start: 0.9177 (t60) cc_final: 0.8686 (t60) REVERT: D 412 MET cc_start: 0.8870 (mpp) cc_final: 0.8251 (mpp) REVERT: D 646 MET cc_start: 0.9391 (mpp) cc_final: 0.8785 (mpp) REVERT: E 335 TYR cc_start: 0.8750 (m-80) cc_final: 0.8481 (m-80) REVERT: E 482 ASP cc_start: 0.8676 (m-30) cc_final: 0.8386 (m-30) REVERT: E 728 MET cc_start: 0.7460 (pmm) cc_final: 0.6559 (pmm) REVERT: F 335 TYR cc_start: 0.9519 (m-80) cc_final: 0.9275 (m-80) REVERT: F 341 TRP cc_start: 0.8059 (m100) cc_final: 0.7343 (m100) REVERT: F 426 MET cc_start: 0.8212 (tmm) cc_final: 0.7719 (tmm) REVERT: F 666 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9194 (tm) REVERT: F 696 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7518 (ptpp) outliers start: 55 outliers final: 31 residues processed: 202 average time/residue: 0.1873 time to fit residues: 65.3676 Evaluate side-chains 189 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 892 TYR Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 662 ASN Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 669 CYS Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 696 LYS Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 214 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 337 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 361 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 GLN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 ASN ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 ASN E 695 ASN E 916 GLN ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.077936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.057687 restraints weight = 235362.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.057755 restraints weight = 144954.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.058208 restraints weight = 109764.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.058434 restraints weight = 96001.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.058585 restraints weight = 89698.287| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33826 Z= 0.153 Angle : 0.645 12.536 46003 Z= 0.330 Chirality : 0.043 0.266 4814 Planarity : 0.004 0.051 5717 Dihedral : 11.826 169.937 4765 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.55 % Favored : 91.24 % Rotamer: Outliers : 1.58 % Allowed : 15.22 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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: -0.72 (0.14), residues: 3847 helix: 0.59 (0.13), residues: 1745 sheet: -0.75 (0.29), residues: 323 loop : -1.51 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 670 TYR 0.019 0.002 TYR F 302 PHE 0.037 0.001 PHE D 838 TRP 0.026 0.001 TRP B 321 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (33826) covalent geometry : angle 0.64506 / 0.33 (46003) hydrogen bonds : bond 0.04127 / 3.71 ( 1282) hydrogen bonds : angle 5.66104 / 4.74 ( 3756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 631 MET cc_start: 0.8180 (tpp) cc_final: 0.6750 (tmm) REVERT: B 666 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8581 (pp) REVERT: B 853 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.7002 (t80) REVERT: A 452 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7711 (pmm) REVERT: A 615 MET cc_start: 0.9393 (tpp) cc_final: 0.9108 (tpp) REVERT: A 653 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9124 (tt) REVERT: C 452 MET cc_start: 0.8774 (pmm) cc_final: 0.8567 (pmm) REVERT: C 681 MET cc_start: 0.9026 (mmp) cc_final: 0.8718 (mmp) REVERT: D 341 TRP cc_start: 0.9142 (t60) cc_final: 0.8650 (t60) REVERT: D 412 MET cc_start: 0.8847 (mpp) cc_final: 0.8228 (mpp) REVERT: D 646 MET cc_start: 0.9362 (mpp) cc_final: 0.8794 (mpp) REVERT: D 869 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.9052 (m110) REVERT: E 335 TYR cc_start: 0.8694 (m-80) cc_final: 0.8419 (m-80) REVERT: E 341 TRP cc_start: 0.9273 (t60) cc_final: 0.9029 (t60) REVERT: E 417 MET cc_start: 0.8950 (pmm) cc_final: 0.8562 (pmm) REVERT: E 482 ASP cc_start: 0.8601 (m-30) cc_final: 0.8295 (m-30) REVERT: E 728 MET cc_start: 0.7444 (pmm) cc_final: 0.6669 (pmm) REVERT: E 753 LEU cc_start: 0.9471 (mt) cc_final: 0.8960 (mt) REVERT: F 335 TYR cc_start: 0.9502 (m-80) cc_final: 0.9247 (m-80) REVERT: F 341 TRP cc_start: 0.8034 (m100) cc_final: 0.7327 (m100) REVERT: F 426 MET cc_start: 0.8172 (tmm) cc_final: 0.7604 (tmm) REVERT: F 452 MET cc_start: 0.7808 (ptm) cc_final: 0.7602 (ptm) REVERT: F 666 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9163 (tm) REVERT: F 696 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7661 (ptpp) outliers start: 55 outliers final: 32 residues processed: 205 average time/residue: 0.1921 time to fit residues: 67.7490 Evaluate side-chains 197 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 662 ASN Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 696 LYS Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR 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: 386 random chunks: chunk 93 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 378 optimal weight: 0.0770 chunk 314 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 346 optimal weight: 4.9990 chunk 370 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 360 optimal weight: 6.9990 chunk 289 optimal weight: 0.0870 overall best weight: 1.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 ASN D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 916 GLN ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.078264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.058241 restraints weight = 235054.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058077 restraints weight = 144765.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.058452 restraints weight = 109910.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.058705 restraints weight = 96392.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.058859 restraints weight = 89702.637| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33826 Z= 0.137 Angle : 0.643 12.313 46003 Z= 0.325 Chirality : 0.042 0.261 4814 Planarity : 0.004 0.049 5717 Dihedral : 11.632 169.884 4765 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.66 % Favored : 91.11 % Rotamer: Outliers : 1.58 % Allowed : 15.77 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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: -0.64 (0.14), residues: 3847 helix: 0.66 (0.13), residues: 1739 sheet: -0.81 (0.28), residues: 343 loop : -1.44 (0.16), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 717 TYR 0.019 0.001 TYR B 866 PHE 0.031 0.001 PHE D 838 TRP 0.031 0.001 TRP E 945 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (33826) covalent geometry : angle 0.64277 / 0.33 (46003) hydrogen bonds : bond 0.03978 / 3.59 ( 1282) hydrogen bonds : angle 5.54907 / 4.64 ( 3756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 631 MET cc_start: 0.8319 (tpp) cc_final: 0.6846 (tmm) REVERT: B 666 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8670 (pp) REVERT: B 853 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.7086 (t80) REVERT: A 452 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7697 (pmm) REVERT: A 615 MET cc_start: 0.9395 (tpp) cc_final: 0.9139 (tpp) REVERT: A 653 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9094 (tt) REVERT: C 452 MET cc_start: 0.8791 (pmm) cc_final: 0.8559 (pmm) REVERT: C 681 MET cc_start: 0.9018 (mmp) cc_final: 0.8811 (mmp) REVERT: C 728 MET cc_start: 0.8505 (ppp) cc_final: 0.8246 (ppp) REVERT: D 341 TRP cc_start: 0.9136 (t60) cc_final: 0.8649 (t60) REVERT: D 412 MET cc_start: 0.8830 (mpp) cc_final: 0.8191 (mpp) REVERT: D 416 TYR cc_start: 0.8673 (t80) cc_final: 0.8186 (t80) REVERT: D 477 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: D 646 MET cc_start: 0.9373 (mpp) cc_final: 0.8805 (mpp) REVERT: D 869 ASN cc_start: 0.9421 (OUTLIER) cc_final: 0.9018 (m110) REVERT: E 335 TYR cc_start: 0.8709 (m-80) cc_final: 0.8427 (m-80) REVERT: E 341 TRP cc_start: 0.9259 (t60) cc_final: 0.8978 (t60) REVERT: E 417 MET cc_start: 0.8949 (pmm) cc_final: 0.8546 (pmm) REVERT: E 482 ASP cc_start: 0.8605 (m-30) cc_final: 0.8298 (m-30) REVERT: E 728 MET cc_start: 0.7523 (pmm) cc_final: 0.6755 (pmm) REVERT: E 753 LEU cc_start: 0.9478 (mt) cc_final: 0.8968 (mt) REVERT: F 335 TYR cc_start: 0.9503 (m-80) cc_final: 0.9233 (m-80) REVERT: F 341 TRP cc_start: 0.8053 (m100) cc_final: 0.7353 (m100) REVERT: F 435 ASP cc_start: 0.8776 (p0) cc_final: 0.8435 (p0) REVERT: F 666 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9154 (tm) outliers start: 55 outliers final: 34 residues processed: 205 average time/residue: 0.1947 time to fit residues: 69.2286 Evaluate side-chains 196 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 477 PHE Chi-restraints excluded: chain D residue 745 THR Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain D residue 900 THR Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 662 ASN Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 900 THR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 243 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 chunk 337 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 368 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 581 HIS E 916 GLN ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.078045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.058077 restraints weight = 235277.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.058013 restraints weight = 143831.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.058500 restraints weight = 109046.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.058660 restraints weight = 94571.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.058724 restraints weight = 89349.303| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33826 Z= 0.153 Angle : 0.649 14.768 46003 Z= 0.328 Chirality : 0.042 0.260 4814 Planarity : 0.004 0.050 5717 Dihedral : 11.534 170.017 4765 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.68 % Favored : 91.08 % Rotamer: Outliers : 1.49 % Allowed : 16.14 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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: 3847 helix: 0.70 (0.13), residues: 1740 sheet: -0.81 (0.28), residues: 335 loop : -1.42 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 529 TYR 0.019 0.001 TYR B 866 PHE 0.027 0.001 PHE D 838 TRP 0.027 0.001 TRP E 945 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (33826) covalent geometry : angle 0.64890 / 0.33 (46003) hydrogen bonds : bond 0.03888 / 3.53 ( 1282) hydrogen bonds : angle 5.51166 / 4.62 ( 3756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 631 MET cc_start: 0.8414 (tpp) cc_final: 0.7002 (tmm) REVERT: B 666 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8732 (pp) REVERT: B 745 THR cc_start: 0.9573 (OUTLIER) cc_final: 0.9344 (p) REVERT: B 853 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.7120 (t80) REVERT: A 452 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7707 (pmm) REVERT: A 615 MET cc_start: 0.9401 (tpp) cc_final: 0.9140 (tpp) REVERT: A 631 MET cc_start: 0.8815 (tpp) cc_final: 0.8344 (tpp) REVERT: A 653 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9094 (tt) REVERT: C 452 MET cc_start: 0.8805 (pmm) cc_final: 0.8576 (pmm) REVERT: C 728 MET cc_start: 0.8507 (ppp) cc_final: 0.8225 (ppp) REVERT: D 341 TRP cc_start: 0.9124 (t60) cc_final: 0.8640 (t60) REVERT: D 412 MET cc_start: 0.8838 (mpp) cc_final: 0.8222 (mpp) REVERT: D 477 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8564 (m-80) REVERT: D 646 MET cc_start: 0.9364 (mpp) cc_final: 0.8780 (mpp) REVERT: D 869 ASN cc_start: 0.9454 (OUTLIER) cc_final: 0.9063 (m110) REVERT: E 335 TYR cc_start: 0.8750 (m-80) cc_final: 0.8440 (m-80) REVERT: E 341 TRP cc_start: 0.9218 (t60) cc_final: 0.8839 (t60) REVERT: E 482 ASP cc_start: 0.8612 (m-30) cc_final: 0.8310 (m-30) REVERT: E 581 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.8266 (p-80) REVERT: E 728 MET cc_start: 0.7498 (pmm) cc_final: 0.6768 (pmm) REVERT: E 732 MET cc_start: 0.8881 (mmm) cc_final: 0.8675 (mmm) REVERT: E 753 LEU cc_start: 0.9478 (mt) cc_final: 0.8965 (mt) REVERT: F 335 TYR cc_start: 0.9511 (m-80) cc_final: 0.9188 (m-10) REVERT: F 341 TRP cc_start: 0.8021 (m100) cc_final: 0.7362 (m100) REVERT: F 426 MET cc_start: 0.8218 (tmm) cc_final: 0.7944 (tmm) REVERT: F 435 ASP cc_start: 0.8807 (p0) cc_final: 0.8497 (p0) REVERT: F 666 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9166 (tm) outliers start: 52 outliers final: 34 residues processed: 202 average time/residue: 0.1945 time to fit residues: 68.1258 Evaluate side-chains 198 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 477 PHE Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain D residue 900 THR Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 581 HIS Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 662 ASN Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR 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: 386 random chunks: chunk 308 optimal weight: 0.9990 chunk 166 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 236 optimal weight: 3.9990 chunk 352 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 248 optimal weight: 0.3980 chunk 289 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 ASN D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 581 HIS ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.077986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.058099 restraints weight = 179863.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059093 restraints weight = 119238.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.059749 restraints weight = 93264.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.060105 restraints weight = 81302.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060276 restraints weight = 75601.344| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33826 Z= 0.118 Angle : 0.652 12.512 46003 Z= 0.325 Chirality : 0.042 0.258 4814 Planarity : 0.004 0.051 5717 Dihedral : 11.449 169.716 4765 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.47 % Favored : 91.29 % Rotamer: Outliers : 1.29 % Allowed : 16.46 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.54 (0.14), residues: 3847 helix: 0.72 (0.12), residues: 1740 sheet: -0.76 (0.27), residues: 358 loop : -1.37 (0.16), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 529 TYR 0.021 0.001 TYR B 866 PHE 0.026 0.001 PHE D 342 TRP 0.026 0.001 TRP B 321 HIS 0.026 0.001 HIS E 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (33826) covalent geometry : angle 0.65164 / 0.33 (46003) hydrogen bonds : bond 0.03751 / 3.41 ( 1282) hydrogen bonds : angle 5.39073 / 4.52 ( 3756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 631 MET cc_start: 0.8487 (tpp) cc_final: 0.8147 (tpt) REVERT: B 666 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8707 (pp) REVERT: B 745 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9374 (p) REVERT: B 853 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.7066 (t80) REVERT: A 452 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7581 (pmm) REVERT: A 615 MET cc_start: 0.9556 (tpp) cc_final: 0.9315 (tpp) REVERT: A 631 MET cc_start: 0.8870 (tpp) cc_final: 0.8387 (tpp) REVERT: C 452 MET cc_start: 0.8781 (pmm) cc_final: 0.8515 (pmm) REVERT: C 728 MET cc_start: 0.8407 (ppp) cc_final: 0.8158 (ppp) REVERT: D 341 TRP cc_start: 0.8991 (t60) cc_final: 0.8609 (t60) REVERT: D 412 MET cc_start: 0.8710 (mpp) cc_final: 0.8151 (mpp) REVERT: D 416 TYR cc_start: 0.8508 (t80) cc_final: 0.8092 (t80) REVERT: D 477 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: D 646 MET cc_start: 0.9316 (mpp) cc_final: 0.8736 (mpp) REVERT: D 869 ASN cc_start: 0.9296 (OUTLIER) cc_final: 0.9012 (m110) REVERT: E 335 TYR cc_start: 0.8792 (m-80) cc_final: 0.8429 (m-80) REVERT: E 341 TRP cc_start: 0.9206 (t60) cc_final: 0.8830 (t60) REVERT: E 417 MET cc_start: 0.8932 (pmm) cc_final: 0.8479 (pmm) REVERT: E 482 ASP cc_start: 0.8648 (m-30) cc_final: 0.8320 (m-30) REVERT: E 728 MET cc_start: 0.7816 (pmm) cc_final: 0.7185 (pmm) REVERT: E 753 LEU cc_start: 0.9512 (mt) cc_final: 0.9047 (mt) REVERT: F 335 TYR cc_start: 0.9512 (m-80) cc_final: 0.9094 (m-10) REVERT: F 341 TRP cc_start: 0.8093 (m100) cc_final: 0.7415 (m100) REVERT: F 426 MET cc_start: 0.8276 (tmm) cc_final: 0.7946 (tmm) REVERT: F 435 ASP cc_start: 0.8826 (p0) cc_final: 0.8482 (p0) REVERT: F 666 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9045 (tm) outliers start: 45 outliers final: 33 residues processed: 198 average time/residue: 0.1929 time to fit residues: 65.8934 Evaluate side-chains 199 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 477 PHE Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 662 ASN Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR 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: 386 random chunks: chunk 51 optimal weight: 1.9990 chunk 281 optimal weight: 0.0010 chunk 168 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 276 optimal weight: 0.4980 chunk 358 optimal weight: 4.9990 chunk 274 optimal weight: 0.5980 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 ASN D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.078218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.058299 restraints weight = 181647.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.059329 restraints weight = 119286.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.060013 restraints weight = 92892.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.060376 restraints weight = 80721.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.060585 restraints weight = 75079.206| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33826 Z= 0.117 Angle : 0.659 12.715 46003 Z= 0.327 Chirality : 0.042 0.257 4814 Planarity : 0.004 0.052 5717 Dihedral : 11.321 169.708 4765 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.53 % Favored : 91.27 % Rotamer: Outliers : 1.29 % Allowed : 16.34 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.52 (0.14), residues: 3847 helix: 0.73 (0.12), residues: 1752 sheet: -0.66 (0.28), residues: 340 loop : -1.40 (0.16), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 529 TYR 0.021 0.001 TYR B 866 PHE 0.023 0.001 PHE D 838 TRP 0.027 0.001 TRP B 381 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (33826) covalent geometry : angle 0.65870 / 0.33 (46003) hydrogen bonds : bond 0.03639 / 3.32 ( 1282) hydrogen bonds : angle 5.32937 / 4.46 ( 3756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 631 MET cc_start: 0.8543 (tpp) cc_final: 0.8301 (tpp) REVERT: B 666 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8702 (pp) REVERT: B 745 THR cc_start: 0.9540 (OUTLIER) cc_final: 0.9330 (p) REVERT: B 853 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7056 (t80) REVERT: A 452 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7522 (pmm) REVERT: A 615 MET cc_start: 0.9546 (tpp) cc_final: 0.9322 (tpp) REVERT: A 631 MET cc_start: 0.8895 (tpp) cc_final: 0.8463 (tpp) REVERT: C 452 MET cc_start: 0.8756 (pmm) cc_final: 0.8507 (pmm) REVERT: C 653 LEU cc_start: 0.9477 (tp) cc_final: 0.9275 (tp) REVERT: C 728 MET cc_start: 0.8371 (ppp) cc_final: 0.8110 (ppp) REVERT: D 341 TRP cc_start: 0.8990 (t60) cc_final: 0.8603 (t60) REVERT: D 412 MET cc_start: 0.8682 (mpp) cc_final: 0.8144 (mpp) REVERT: D 416 TYR cc_start: 0.8478 (t80) cc_final: 0.8076 (t80) REVERT: D 477 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: D 646 MET cc_start: 0.9323 (mpp) cc_final: 0.8746 (mpp) REVERT: D 869 ASN cc_start: 0.9340 (OUTLIER) cc_final: 0.9000 (p0) REVERT: E 335 TYR cc_start: 0.8791 (m-80) cc_final: 0.8411 (m-80) REVERT: E 482 ASP cc_start: 0.8599 (m-30) cc_final: 0.8268 (m-30) REVERT: E 728 MET cc_start: 0.7815 (pmm) cc_final: 0.7249 (pmm) REVERT: E 753 LEU cc_start: 0.9510 (mt) cc_final: 0.9041 (mt) REVERT: F 335 TYR cc_start: 0.9504 (m-80) cc_final: 0.9082 (m-10) REVERT: F 341 TRP cc_start: 0.8088 (m100) cc_final: 0.7413 (m100) REVERT: F 426 MET cc_start: 0.8302 (tmm) cc_final: 0.7989 (tmm) REVERT: F 435 ASP cc_start: 0.8792 (p0) cc_final: 0.8420 (p0) REVERT: F 666 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9005 (tm) outliers start: 45 outliers final: 32 residues processed: 199 average time/residue: 0.1959 time to fit residues: 67.6670 Evaluate side-chains 202 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 477 PHE Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain D residue 900 THR Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR 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: 386 random chunks: chunk 244 optimal weight: 0.9990 chunk 274 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 373 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.077879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057931 restraints weight = 182538.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.058962 restraints weight = 119996.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.059641 restraints weight = 93973.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.059995 restraints weight = 81594.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.060203 restraints weight = 75592.511| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33826 Z= 0.138 Angle : 0.656 13.736 46003 Z= 0.326 Chirality : 0.042 0.259 4814 Planarity : 0.004 0.052 5717 Dihedral : 11.256 169.988 4765 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.53 % Favored : 91.27 % Rotamer: Outliers : 1.26 % Allowed : 16.57 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 3847 helix: 0.79 (0.13), residues: 1752 sheet: -0.62 (0.28), residues: 330 loop : -1.39 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 682 TYR 0.020 0.001 TYR B 866 PHE 0.029 0.001 PHE D 342 TRP 0.027 0.001 TRP E 362 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (33826) covalent geometry : angle 0.65637 / 0.33 (46003) hydrogen bonds : bond 0.03613 / 3.28 ( 1282) hydrogen bonds : angle 5.33982 / 4.48 ( 3756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5948.73 seconds wall clock time: 104 minutes 16.24 seconds (6256.24 seconds total)