Starting phenix.real_space_refine on Mon Jul 6 05:14:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ww6_37882/07_2026/8ww6_37882.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ww6_37882/07_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_37882/07_2026/8ww6_37882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ww6_37882/07_2026/8ww6_37882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ww6_37882/07_2026/8ww6_37882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ww6_37882/07_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-dev-6108/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: 6.78, per 1000 atoms: 0.21 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 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: 0.88 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: 6.65 Time building geometry restraints manager: 3.79 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: 5.400 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.330 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.800 ------------------------------------------------------------------------------- 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= 0.405 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 0.72067 / 0.41 (46003) hydrogen bonds : bond 0.19080 / 17.82 ( 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 : 1.226 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: 0.1948 time to fit residues: 82.7312 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 : 0.949 ------------------------------------------------------------------------------- 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 396 GLN D 869 ASN ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.080250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.060225 restraints weight = 236061.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.060281 restraints weight = 144440.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.060728 restraints weight = 109122.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.060936 restraints weight = 95787.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.061055 restraints weight = 90255.049| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33826 Z= 0.138 Angle : 0.671 16.099 46003 Z= 0.342 Chirality : 0.044 0.234 4814 Planarity : 0.005 0.064 5717 Dihedral : 13.948 168.426 4813 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.68 % Favored : 91.08 % Rotamer: Outliers : 0.89 % Allowed : 7.78 % Favored : 91.33 % 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: 0.44 (0.12), residues: 1739 sheet: -0.23 (0.29), residues: 325 loop : -1.43 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 301 TYR 0.041 0.002 TYR D 302 PHE 0.015 0.001 PHE F 616 TRP 0.038 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 0.67089 / 0.34 (46003) hydrogen bonds : bond 0.05232 / 4.81 ( 1282) hydrogen bonds : angle 6.22715 / 5.22 ( 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 210 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 708 MET cc_start: 0.9566 (mmp) cc_final: 0.9362 (mmp) REVERT: A 452 MET cc_start: 0.7804 (pmm) cc_final: 0.7326 (pmm) REVERT: A 615 MET cc_start: 0.9305 (tpp) cc_final: 0.9030 (tpp) REVERT: A 892 TYR cc_start: 0.7411 (p90) cc_final: 0.7180 (p90) REVERT: C 294 MET cc_start: 0.8665 (mmp) cc_final: 0.8450 (mmp) REVERT: C 452 MET cc_start: 0.8540 (pmm) cc_final: 0.8310 (pmm) REVERT: C 681 MET cc_start: 0.9154 (mmp) cc_final: 0.8939 (mmp) REVERT: D 341 TRP cc_start: 0.9206 (t60) cc_final: 0.8684 (t60) REVERT: D 412 MET cc_start: 0.8556 (mpp) cc_final: 0.8131 (mpp) REVERT: D 646 MET cc_start: 0.9369 (mpp) cc_final: 0.8944 (mpp) REVERT: E 341 TRP cc_start: 0.9314 (t60) cc_final: 0.9109 (t60) REVERT: E 426 MET cc_start: 0.8427 (tmm) cc_final: 0.8178 (ttt) REVERT: E 482 ASP cc_start: 0.8537 (m-30) cc_final: 0.8195 (m-30) REVERT: E 728 MET cc_start: 0.7378 (pmm) cc_final: 0.6873 (pmm) REVERT: F 335 TYR cc_start: 0.9547 (m-80) cc_final: 0.9043 (m-10) REVERT: F 666 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8973 (tm) REVERT: F 696 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7640 (ptpp) outliers start: 31 outliers final: 17 residues processed: 202 average time/residue: 0.1944 time to fit residues: 65.6370 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 : 1.147 ------------------------------------------------------------------------------- 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 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 696 LYS 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: 8.9990 chunk 100 optimal weight: 0.9980 chunk 377 optimal weight: 5.9990 chunk 362 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 296 HIS ** 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** A 640 ASN ** E 470 HIS ** 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 = 0.3693 r_free = 0.3693 target = 0.072345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052809 restraints weight = 211852.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053923 restraints weight = 125453.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.054619 restraints weight = 92304.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055013 restraints weight = 76923.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.055184 restraints weight = 69455.472| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1410 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= 0.206 Angle : 0.659 14.135 46003 Z= 0.342 Chirality : 0.043 0.238 4814 Planarity : 0.004 0.057 5717 Dihedral : 12.984 169.444 4777 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.97 % Favored : 90.82 % Rotamer: Outliers : 1.01 % Allowed : 11.03 % Favored : 87.97 % 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: 0.50 (0.12), residues: 1754 sheet: -0.52 (0.29), residues: 332 loop : -1.48 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 670 TYR 0.027 0.002 TYR D 302 PHE 0.016 0.001 PHE D 838 TRP 0.044 0.002 TRP E 945 HIS 0.008 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (33826) covalent geometry : angle 0.65868 / 0.34 (46003) hydrogen bonds : bond 0.04673 / 4.24 ( 1282) hydrogen bonds : angle 6.02454 / 5.06 ( 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 202 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 708 MET cc_start: 0.9567 (mmp) cc_final: 0.9341 (mmp) REVERT: B 853 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6079 (t80) REVERT: A 452 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7482 (pmm) REVERT: A 615 MET cc_start: 0.9463 (tpp) cc_final: 0.9200 (tpp) REVERT: C 452 MET cc_start: 0.8715 (pmm) cc_final: 0.8491 (pmm) REVERT: C 878 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8736 (tp) REVERT: D 341 TRP cc_start: 0.9206 (t60) cc_final: 0.8823 (t60) REVERT: D 412 MET cc_start: 0.8709 (mpp) cc_final: 0.8163 (mpp) REVERT: D 646 MET cc_start: 0.9375 (mpp) cc_final: 0.8765 (mpp) REVERT: E 341 TRP cc_start: 0.9336 (t60) cc_final: 0.9106 (t60) REVERT: E 482 ASP cc_start: 0.8763 (m-30) cc_final: 0.8428 (m-30) REVERT: E 728 MET cc_start: 0.7582 (pmm) cc_final: 0.7053 (pmm) REVERT: F 335 TYR cc_start: 0.9515 (m-80) cc_final: 0.9129 (m-80) REVERT: F 341 TRP cc_start: 0.8143 (m100) cc_final: 0.7418 (m100) REVERT: F 666 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9045 (tm) REVERT: F 696 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7648 (ptpp) outliers start: 35 outliers final: 18 residues processed: 190 average time/residue: 0.2005 time to fit residues: 64.7712 Evaluate side-chains 181 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 452 MET 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 410 ASN Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 820 THR Chi-restraints excluded: chain E residue 821 ILE 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: 0.9980 chunk 268 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 317 optimal weight: 1.9990 chunk 199 optimal weight: 0.4980 chunk 227 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 349 optimal weight: 0.0970 chunk 81 optimal weight: 7.9990 chunk 352 optimal weight: 10.0000 chunk 10 optimal weight: 0.0060 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN C 496 HIS C 695 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.079700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.059921 restraints weight = 234208.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.059846 restraints weight = 143290.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.060266 restraints weight = 108401.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.060497 restraints weight = 94883.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.060649 restraints weight = 88963.694| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33826 Z= 0.119 Angle : 0.626 13.363 46003 Z= 0.319 Chirality : 0.042 0.237 4814 Planarity : 0.004 0.053 5717 Dihedral : 12.426 168.652 4771 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.16 % Favored : 91.60 % Rotamer: Outliers : 0.98 % Allowed : 12.81 % Favored : 86.21 % 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: -0.65 (0.14), residues: 3847 helix: 0.59 (0.12), residues: 1740 sheet: -0.61 (0.28), residues: 335 loop : -1.42 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 301 TYR 0.022 0.001 TYR D 398 PHE 0.023 0.001 PHE A 912 TRP 0.044 0.001 TRP E 945 HIS 0.009 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (33826) covalent geometry : angle 0.62623 / 0.32 (46003) hydrogen bonds : bond 0.04159 / 3.78 ( 1282) hydrogen bonds : angle 5.67866 / 4.76 ( 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 201 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8855 (tpp) cc_final: 0.8631 (tpp) REVERT: B 708 MET cc_start: 0.9565 (mmp) cc_final: 0.9353 (mmp) REVERT: B 853 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6848 (t80) REVERT: A 452 MET cc_start: 0.7848 (pmm) cc_final: 0.7526 (pmm) REVERT: A 615 MET cc_start: 0.9359 (tpp) cc_final: 0.9088 (tpp) REVERT: A 653 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9064 (tt) REVERT: C 681 MET cc_start: 0.9131 (mmp) cc_final: 0.8789 (mmp) REVERT: C 878 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8740 (tp) REVERT: D 314 TYR cc_start: 0.7107 (m-10) cc_final: 0.6904 (m-80) REVERT: D 341 TRP cc_start: 0.9179 (t60) cc_final: 0.8660 (t60) REVERT: D 412 MET cc_start: 0.8740 (mpp) cc_final: 0.8164 (mpp) REVERT: D 646 MET cc_start: 0.9393 (mpp) cc_final: 0.8783 (mpp) REVERT: E 341 TRP cc_start: 0.9303 (t60) cc_final: 0.8930 (t60) REVERT: E 482 ASP cc_start: 0.8551 (m-30) cc_final: 0.8221 (m-30) REVERT: E 728 MET cc_start: 0.7393 (pmm) cc_final: 0.6807 (pmm) REVERT: E 753 LEU cc_start: 0.9498 (mt) cc_final: 0.8985 (mt) REVERT: F 335 TYR cc_start: 0.9522 (m-80) cc_final: 0.9234 (m-80) REVERT: F 341 TRP cc_start: 0.7984 (m100) cc_final: 0.7304 (m100) REVERT: F 666 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9062 (tm) REVERT: F 696 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7671 (ptpp) outliers start: 34 outliers final: 18 residues processed: 190 average time/residue: 0.1932 time to fit residues: 63.1800 Evaluate side-chains 180 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 653 LEU 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 405 TYR Chi-restraints excluded: chain D residue 417 MET 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: 4.9990 chunk 199 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 29 optimal weight: 0.0270 chunk 334 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 371 optimal weight: 9.9990 chunk 375 optimal weight: 0.3980 overall best weight: 3.2844 ------------------------------------------------------------------------------- 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** C 662 ASN D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 792 ASN ** 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 = 0.3682 r_free = 0.3682 target = 0.071863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.052383 restraints weight = 213831.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.053516 restraints weight = 126663.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.054223 restraints weight = 92887.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.054602 restraints weight = 77625.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.054791 restraints weight = 70268.823| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 33826 Z= 0.214 Angle : 0.659 14.339 46003 Z= 0.339 Chirality : 0.042 0.243 4814 Planarity : 0.004 0.054 5717 Dihedral : 11.975 169.628 4765 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.10 % Favored : 90.69 % Rotamer: Outliers : 1.38 % Allowed : 14.01 % Favored : 84.61 % 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: -0.67 (0.14), residues: 3847 helix: 0.62 (0.13), residues: 1749 sheet: -0.69 (0.29), residues: 323 loop : -1.49 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 717 TYR 0.026 0.002 TYR D 416 PHE 0.026 0.001 PHE A 912 TRP 0.024 0.001 TRP B 321 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (33826) covalent geometry : angle 0.65871 / 0.34 (46003) hydrogen bonds : bond 0.04153 / 3.73 ( 1282) hydrogen bonds : angle 5.74634 / 4.82 ( 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 205 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8908 (tpp) cc_final: 0.8696 (tpp) REVERT: B 666 LEU cc_start: 0.9046 (mm) cc_final: 0.8494 (pp) REVERT: B 853 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6620 (t80) REVERT: A 452 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7692 (pmm) REVERT: A 615 MET cc_start: 0.9450 (tpp) cc_final: 0.9182 (tpp) REVERT: C 452 MET cc_start: 0.8838 (pmm) cc_final: 0.8540 (pmm) REVERT: C 681 MET cc_start: 0.8857 (mmp) cc_final: 0.8582 (mmp) REVERT: D 341 TRP cc_start: 0.9185 (t60) cc_final: 0.8733 (t60) REVERT: D 412 MET cc_start: 0.8751 (mpp) cc_final: 0.8180 (mpp) REVERT: D 646 MET cc_start: 0.9396 (mpp) cc_final: 0.8791 (mpp) REVERT: D 869 ASN cc_start: 0.9401 (OUTLIER) cc_final: 0.9077 (p0) REVERT: E 341 TRP cc_start: 0.9303 (t60) cc_final: 0.8929 (t60) REVERT: E 417 MET cc_start: 0.8987 (pmm) cc_final: 0.8658 (pmm) REVERT: E 482 ASP cc_start: 0.8708 (m-30) cc_final: 0.8388 (m-30) REVERT: E 728 MET cc_start: 0.7704 (pmm) cc_final: 0.7053 (pmm) REVERT: E 753 LEU cc_start: 0.9504 (mt) cc_final: 0.8988 (mt) REVERT: F 335 TYR cc_start: 0.9515 (m-80) cc_final: 0.9190 (m-80) REVERT: F 341 TRP cc_start: 0.8129 (m100) cc_final: 0.7333 (m100) REVERT: F 435 ASP cc_start: 0.8836 (p0) cc_final: 0.8526 (p0) REVERT: F 651 MET cc_start: 0.9055 (tpp) cc_final: 0.8728 (tpp) REVERT: F 666 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9079 (tm) REVERT: F 696 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7801 (ptpp) outliers start: 48 outliers final: 29 residues processed: 195 average time/residue: 0.1857 time to fit residues: 62.1085 Evaluate side-chains 188 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 618 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 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 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 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 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 945 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 214 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 337 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 297 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 361 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 662 ASN D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 695 ASN ** 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 = 0.3691 r_free = 0.3691 target = 0.072301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.052603 restraints weight = 208370.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.053706 restraints weight = 125282.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.054381 restraints weight = 92732.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054695 restraints weight = 77792.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.055006 restraints weight = 71040.122| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33826 Z= 0.167 Angle : 0.637 12.499 46003 Z= 0.325 Chirality : 0.042 0.240 4814 Planarity : 0.004 0.053 5717 Dihedral : 11.799 169.285 4765 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.68 % Favored : 91.11 % Rotamer: Outliers : 1.61 % Allowed : 14.73 % Favored : 83.66 % 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: 0.67 (0.13), residues: 1741 sheet: -0.69 (0.29), residues: 312 loop : -1.49 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 842 TYR 0.019 0.002 TYR D 398 PHE 0.037 0.001 PHE D 838 TRP 0.025 0.001 TRP B 321 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (33826) covalent geometry : angle 0.63673 / 0.33 (46003) hydrogen bonds : bond 0.04007 / 3.59 ( 1282) hydrogen bonds : angle 5.63091 / 4.71 ( 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 214 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8939 (tpp) cc_final: 0.8720 (tpp) REVERT: B 666 LEU cc_start: 0.8998 (mm) cc_final: 0.8569 (pp) REVERT: B 708 MET cc_start: 0.9525 (mmp) cc_final: 0.9298 (mmp) REVERT: B 853 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6690 (t80) REVERT: A 452 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7688 (pmm) REVERT: A 615 MET cc_start: 0.9463 (tpp) cc_final: 0.9196 (tpp) REVERT: C 700 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8712 (pp) REVERT: D 341 TRP cc_start: 0.9168 (t60) cc_final: 0.8690 (t60) REVERT: D 412 MET cc_start: 0.8764 (mpp) cc_final: 0.8161 (mpp) REVERT: D 646 MET cc_start: 0.9400 (mpp) cc_final: 0.8827 (mpp) REVERT: D 869 ASN cc_start: 0.9359 (OUTLIER) cc_final: 0.9015 (m110) REVERT: E 417 MET cc_start: 0.9001 (pmm) cc_final: 0.8628 (pmm) REVERT: E 482 ASP cc_start: 0.8718 (m-30) cc_final: 0.8390 (m-30) REVERT: E 728 MET cc_start: 0.7675 (pmm) cc_final: 0.6952 (pmm) REVERT: E 753 LEU cc_start: 0.9483 (mt) cc_final: 0.8976 (mt) REVERT: F 335 TYR cc_start: 0.9513 (m-80) cc_final: 0.9166 (m-80) REVERT: F 341 TRP cc_start: 0.8142 (m100) cc_final: 0.7350 (m100) REVERT: F 651 MET cc_start: 0.9092 (tpp) cc_final: 0.8760 (tpp) REVERT: F 666 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9093 (tm) REVERT: F 696 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7768 (ptpp) outliers start: 56 outliers final: 31 residues processed: 202 average time/residue: 0.1874 time to fit residues: 64.6471 Evaluate side-chains 191 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 425 MET 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 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 699 VAL Chi-restraints excluded: chain C residue 700 LEU 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 310 LEU 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 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 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: 7.9990 chunk 253 optimal weight: 8.9990 chunk 378 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 346 optimal weight: 4.9990 chunk 370 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 360 optimal weight: 20.0000 chunk 289 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 GLN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 792 ASN B 812 GLN ** 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** D 869 ASN ** E 330 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.077112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.056947 restraints weight = 236864.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.056765 restraints weight = 145555.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.057185 restraints weight = 110982.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.057334 restraints weight = 96900.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.057334 restraints weight = 90578.135| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33826 Z= 0.234 Angle : 0.676 12.328 46003 Z= 0.347 Chirality : 0.043 0.242 4814 Planarity : 0.004 0.053 5717 Dihedral : 11.681 169.655 4765 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.25 % Favored : 90.51 % Rotamer: Outliers : 1.41 % Allowed : 15.57 % Favored : 83.03 % 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: -0.70 (0.14), residues: 3847 helix: 0.62 (0.13), residues: 1742 sheet: -0.71 (0.29), residues: 322 loop : -1.52 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 529 TYR 0.019 0.002 TYR F 416 PHE 0.029 0.001 PHE D 838 TRP 0.030 0.002 TRP E 945 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (33826) covalent geometry : angle 0.67616 / 0.35 (46003) hydrogen bonds : bond 0.04098 / 3.67 ( 1282) hydrogen bonds : angle 5.73493 / 4.80 ( 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 204 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 631 MET cc_start: 0.8152 (tpt) cc_final: 0.7800 (tpp) REVERT: B 853 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.7080 (t80) REVERT: A 452 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7721 (pmm) REVERT: A 615 MET cc_start: 0.9419 (tpp) cc_final: 0.9141 (tpp) REVERT: C 681 MET cc_start: 0.9109 (mmp) cc_final: 0.8861 (mmp) REVERT: D 341 TRP cc_start: 0.9125 (t60) cc_final: 0.8621 (t60) REVERT: D 412 MET cc_start: 0.8884 (mpp) cc_final: 0.8245 (mpp) REVERT: D 646 MET cc_start: 0.9379 (mpp) cc_final: 0.8798 (mpp) REVERT: D 869 ASN cc_start: 0.9407 (OUTLIER) cc_final: 0.9077 (m-40) REVERT: E 341 TRP cc_start: 0.9149 (t60) cc_final: 0.8908 (t60) REVERT: E 482 ASP cc_start: 0.8658 (m-30) cc_final: 0.8371 (m-30) REVERT: E 728 MET cc_start: 0.7534 (pmm) cc_final: 0.6740 (pmm) REVERT: F 335 TYR cc_start: 0.9505 (m-80) cc_final: 0.9199 (m-10) REVERT: F 341 TRP cc_start: 0.8075 (m100) cc_final: 0.7387 (m100) REVERT: F 435 ASP cc_start: 0.8845 (p0) cc_final: 0.8524 (p0) REVERT: F 651 MET cc_start: 0.9127 (tpp) cc_final: 0.8806 (tpp) REVERT: F 666 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9208 (tm) REVERT: F 696 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7661 (ptpp) outliers start: 49 outliers final: 38 residues processed: 192 average time/residue: 0.1778 time to fit residues: 58.8157 Evaluate side-chains 192 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 425 MET 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 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 452 MET 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 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 310 LEU 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 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 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 871 ASN 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: 0.8980 chunk 248 optimal weight: 0.9990 chunk 325 optimal weight: 7.9990 chunk 337 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 254 optimal weight: 0.7980 chunk 368 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 581 HIS ** 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 = 0.3806 r_free = 0.3806 target = 0.078656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.058729 restraints weight = 235171.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.058663 restraints weight = 143848.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.059104 restraints weight = 108207.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.059302 restraints weight = 94278.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.059432 restraints weight = 88711.181| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33826 Z= 0.122 Angle : 0.643 12.377 46003 Z= 0.324 Chirality : 0.042 0.237 4814 Planarity : 0.004 0.053 5717 Dihedral : 11.557 169.033 4765 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.34 % Favored : 91.42 % Rotamer: Outliers : 1.49 % Allowed : 15.88 % Favored : 82.62 % 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: -0.54 (0.14), residues: 3847 helix: 0.72 (0.13), residues: 1729 sheet: -0.60 (0.29), residues: 309 loop : -1.39 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 529 TYR 0.020 0.001 TYR B 866 PHE 0.026 0.001 PHE D 838 TRP 0.027 0.001 TRP B 321 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (33826) covalent geometry : angle 0.64256 / 0.32 (46003) hydrogen bonds : bond 0.03844 / 3.47 ( 1282) hydrogen bonds : angle 5.48895 / 4.58 ( 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 216 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 631 MET cc_start: 0.8282 (tpt) cc_final: 0.7808 (tpp) REVERT: B 745 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9374 (p) REVERT: B 853 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.7105 (t80) REVERT: A 452 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7675 (pmm) REVERT: A 615 MET cc_start: 0.9408 (tpp) cc_final: 0.9127 (tpp) REVERT: C 681 MET cc_start: 0.9041 (mmp) cc_final: 0.8658 (mmp) REVERT: C 728 MET cc_start: 0.8514 (ppp) cc_final: 0.8222 (ppp) REVERT: D 341 TRP cc_start: 0.9105 (t60) cc_final: 0.8746 (t60) REVERT: D 412 MET cc_start: 0.8843 (mpp) cc_final: 0.8187 (mpp) REVERT: D 477 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: D 646 MET cc_start: 0.9365 (mpp) cc_final: 0.9054 (mpp) REVERT: E 341 TRP cc_start: 0.9148 (t60) cc_final: 0.8842 (t60) REVERT: E 417 MET cc_start: 0.8900 (pmm) cc_final: 0.8471 (pmm) REVERT: E 482 ASP cc_start: 0.8591 (m-30) cc_final: 0.8262 (m-30) REVERT: E 581 HIS cc_start: 0.8524 (OUTLIER) cc_final: 0.8280 (p-80) REVERT: E 728 MET cc_start: 0.7493 (pmm) cc_final: 0.6754 (pmm) REVERT: E 753 LEU cc_start: 0.9503 (mt) cc_final: 0.9028 (mt) REVERT: F 335 TYR cc_start: 0.9513 (m-80) cc_final: 0.9188 (m-10) REVERT: F 341 TRP cc_start: 0.8006 (m100) cc_final: 0.7347 (m100) REVERT: F 435 ASP cc_start: 0.8821 (p0) cc_final: 0.8513 (p0) REVERT: F 651 MET cc_start: 0.9126 (tpp) cc_final: 0.8756 (tpp) REVERT: F 666 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9168 (tm) REVERT: F 696 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7716 (ptpp) outliers start: 52 outliers final: 34 residues processed: 203 average time/residue: 0.1703 time to fit residues: 59.1793 Evaluate side-chains 194 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 425 MET 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 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 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 781 ILE 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 308 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 236 optimal weight: 9.9990 chunk 352 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 248 optimal weight: 0.1980 chunk 289 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 304 HIS ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 581 HIS ** 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 = 0.3727 r_free = 0.3727 target = 0.078060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.058120 restraints weight = 181202.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.059125 restraints weight = 119718.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.059799 restraints weight = 93590.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060024 restraints weight = 81541.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.060279 restraints weight = 76787.749| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2263 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= 0.121 Angle : 0.646 15.321 46003 Z= 0.324 Chirality : 0.042 0.246 4814 Planarity : 0.004 0.053 5717 Dihedral : 11.429 169.018 4765 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.47 % 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 : 0.00 % 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: -0.51 (0.14), residues: 3847 helix: 0.75 (0.13), residues: 1733 sheet: -0.54 (0.29), residues: 314 loop : -1.38 (0.15), residues: 1800 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 B 740 TRP 0.026 0.001 TRP B 321 HIS 0.038 0.001 HIS E 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (33826) covalent geometry : angle 0.64565 / 0.32 (46003) hydrogen bonds : bond 0.03730 / 3.38 ( 1282) hydrogen bonds : angle 5.39667 / 4.51 ( 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 205 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 631 MET cc_start: 0.8249 (tpt) cc_final: 0.7634 (tpp) REVERT: B 745 THR cc_start: 0.9569 (OUTLIER) cc_final: 0.9348 (p) REVERT: B 853 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7066 (t80) REVERT: A 452 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7581 (pmm) REVERT: A 615 MET cc_start: 0.9556 (tpp) cc_final: 0.9329 (tpp) REVERT: C 475 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8205 (mm-30) REVERT: C 681 MET cc_start: 0.8864 (mmp) cc_final: 0.8533 (mmp) REVERT: C 728 MET cc_start: 0.8395 (ppp) cc_final: 0.8156 (ppp) REVERT: D 341 TRP cc_start: 0.8913 (t60) cc_final: 0.8557 (t60) REVERT: D 412 MET cc_start: 0.8724 (mpp) cc_final: 0.8153 (mpp) REVERT: D 477 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8621 (m-80) REVERT: D 646 MET cc_start: 0.9323 (mpp) cc_final: 0.8743 (mpp) REVERT: E 341 TRP cc_start: 0.9136 (t60) cc_final: 0.8762 (t60) REVERT: E 417 MET cc_start: 0.8924 (pmm) cc_final: 0.8491 (pmm) REVERT: E 482 ASP cc_start: 0.8602 (m-30) cc_final: 0.8268 (m-30) REVERT: E 728 MET cc_start: 0.7883 (pmm) cc_final: 0.7296 (pmm) REVERT: E 732 MET cc_start: 0.8860 (mmm) cc_final: 0.8608 (mmm) REVERT: E 753 LEU cc_start: 0.9514 (mt) cc_final: 0.9051 (mt) REVERT: F 335 TYR cc_start: 0.9515 (m-80) cc_final: 0.9110 (m-10) REVERT: F 341 TRP cc_start: 0.8114 (m100) cc_final: 0.7435 (m100) REVERT: F 435 ASP cc_start: 0.8813 (p0) cc_final: 0.8458 (p0) REVERT: F 651 MET cc_start: 0.9120 (tpp) cc_final: 0.8783 (tpp) REVERT: F 666 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9042 (tm) REVERT: F 696 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7809 (ptpp) outliers start: 45 outliers final: 33 residues processed: 194 average time/residue: 0.1752 time to fit residues: 58.4109 Evaluate side-chains 196 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 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 631 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 477 PHE 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 477 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 51 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 50 optimal weight: 0.0170 chunk 118 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 276 optimal weight: 0.0000 chunk 358 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 overall best weight: 1.6028 ------------------------------------------------------------------------------- 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 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.071577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054121 restraints weight = 222966.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.055356 restraints weight = 127165.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056168 restraints weight = 89770.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.056716 restraints weight = 72452.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056882 restraints weight = 62991.939| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33826 Z= 0.133 Angle : 0.654 12.799 46003 Z= 0.327 Chirality : 0.042 0.235 4814 Planarity : 0.004 0.053 5717 Dihedral : 11.347 169.245 4765 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.53 % Favored : 91.27 % Rotamer: Outliers : 1.26 % Allowed : 16.34 % Favored : 82.40 % 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: -0.46 (0.14), residues: 3847 helix: 0.79 (0.13), residues: 1738 sheet: -0.48 (0.29), residues: 314 loop : -1.39 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 717 TYR 0.022 0.001 TYR D 416 PHE 0.029 0.001 PHE D 342 TRP 0.025 0.001 TRP B 321 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (33826) covalent geometry : angle 0.65424 / 0.33 (46003) hydrogen bonds : bond 0.03668 / 3.32 ( 1282) hydrogen bonds : angle 5.37754 / 4.51 ( 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 205 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 631 MET cc_start: 0.8385 (tpt) cc_final: 0.7853 (tpp) REVERT: B 745 THR cc_start: 0.9520 (OUTLIER) cc_final: 0.9285 (p) REVERT: B 853 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.7008 (t80) REVERT: A 452 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7588 (pmm) REVERT: A 615 MET cc_start: 0.9495 (tpp) cc_final: 0.9244 (tpp) REVERT: C 475 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8247 (mm-30) REVERT: C 681 MET cc_start: 0.8794 (mmp) cc_final: 0.8489 (mmp) REVERT: C 728 MET cc_start: 0.8381 (ppp) cc_final: 0.8135 (ppp) REVERT: D 341 TRP cc_start: 0.8909 (t60) cc_final: 0.8640 (t60) REVERT: D 412 MET cc_start: 0.8743 (mpp) cc_final: 0.8162 (mpp) REVERT: D 477 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8625 (m-80) REVERT: D 646 MET cc_start: 0.9356 (mpp) cc_final: 0.8788 (mpp) REVERT: E 341 TRP cc_start: 0.9026 (t60) cc_final: 0.8630 (t60) REVERT: E 477 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: E 482 ASP cc_start: 0.8573 (m-30) cc_final: 0.8252 (m-30) REVERT: E 728 MET cc_start: 0.7745 (pmm) cc_final: 0.7134 (pmm) REVERT: E 732 MET cc_start: 0.8773 (mmm) cc_final: 0.8555 (mmm) REVERT: E 753 LEU cc_start: 0.9504 (mt) cc_final: 0.9027 (mt) REVERT: F 335 TYR cc_start: 0.9464 (m-80) cc_final: 0.8959 (m-10) REVERT: F 341 TRP cc_start: 0.8196 (m100) cc_final: 0.7440 (m100) REVERT: F 435 ASP cc_start: 0.8798 (p0) cc_final: 0.8439 (p0) REVERT: F 651 MET cc_start: 0.9027 (tpp) cc_final: 0.8692 (tpp) REVERT: F 666 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9090 (tm) REVERT: F 696 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7855 (ptpp) outliers start: 44 outliers final: 32 residues processed: 194 average time/residue: 0.1810 time to fit residues: 60.3660 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 : 1.325 ------------------------------------------------------------------------------- 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 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 631 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 781 ILE 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 900 THR Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 477 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 244 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 chunk 54 optimal weight: 0.0970 chunk 173 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 373 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 292 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.077958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.057943 restraints weight = 182612.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.059007 restraints weight = 119932.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059666 restraints weight = 93342.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.060035 restraints weight = 81352.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060178 restraints weight = 75326.552| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33826 Z= 0.124 Angle : 0.653 14.978 46003 Z= 0.324 Chirality : 0.042 0.235 4814 Planarity : 0.004 0.053 5717 Dihedral : 11.254 169.193 4765 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.42 % Favored : 91.37 % Rotamer: Outliers : 1.29 % Allowed : 16.31 % Favored : 82.40 % 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: -0.44 (0.14), residues: 3847 helix: 0.82 (0.13), residues: 1741 sheet: -0.44 (0.29), residues: 314 loop : -1.40 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 529 TYR 0.022 0.001 TYR E 398 PHE 0.021 0.001 PHE A 912 TRP 0.030 0.001 TRP E 362 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33826) covalent geometry : angle 0.65274 / 0.32 (46003) hydrogen bonds : bond 0.03594 / 3.26 ( 1282) hydrogen bonds : angle 5.32614 / 4.47 ( 3756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5501.54 seconds wall clock time: 96 minutes 38.94 seconds (5798.94 seconds total)