Starting phenix.real_space_refine on Sat Jun 28 12:10:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ww6_37882/06_2025/8ww6_37882.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ww6_37882/06_2025/8ww6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ww6_37882/06_2025/8ww6_37882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ww6_37882/06_2025/8ww6_37882.map" model { file = "/net/cci-nas-00/data/ceres_data/8ww6_37882/06_2025/8ww6_37882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ww6_37882/06_2025/8ww6_37882.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.038 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): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.15, per 1000 atoms: 0.61 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: 8.10 Conformation dependent library (CDL) restraints added in 4.1 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: 3.21 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: 12.20 Time building geometry restraints manager: 9.69 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=" C4 AGS C1001 " pdb=" C5 AGS C1001 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.94e+01 bond pdb=" C4 AGS D1001 " pdb=" C5 AGS D1001 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 AGS B1001 " pdb=" C5 AGS B1001 " ideal model delta sigma weight residual 1.386 1.468 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C5 AGS D1001 " pdb=" C6 AGS D1001 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C5 AGS B1001 " pdb=" C6 AGS B1001 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.74e+01 ... (remaining 33821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 44863 1.97 - 3.93: 997 3.93 - 5.90: 95 5.90 - 7.86: 36 7.86 - 9.83: 12 Bond angle restraints: 46003 Sorted by residual: angle pdb=" C5 AGS C1001 " pdb=" C4 AGS C1001 " pdb=" N3 AGS C1001 " ideal model delta sigma weight residual 126.80 118.87 7.93 7.41e-01 1.82e+00 1.14e+02 angle pdb=" C5 AGS D1001 " pdb=" C4 AGS D1001 " pdb=" N3 AGS D1001 " ideal model delta sigma weight residual 126.80 118.93 7.87 7.41e-01 1.82e+00 1.13e+02 angle pdb=" C5 AGS B1001 " pdb=" C4 AGS B1001 " pdb=" N3 AGS B1001 " ideal model delta sigma weight residual 126.80 119.01 7.79 7.41e-01 1.82e+00 1.11e+02 angle pdb=" C4 AGS D1001 " pdb=" C5 AGS D1001 " pdb=" N7 AGS D1001 " ideal model delta sigma weight residual 110.73 106.79 3.94 4.52e-01 4.89e+00 7.59e+01 angle pdb=" C4 AGS C1001 " pdb=" C5 AGS C1001 " pdb=" N7 AGS C1001 " ideal model delta sigma weight residual 110.73 106.81 3.92 4.52e-01 4.89e+00 7.52e+01 ... (remaining 45998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 19417 34.62 - 69.24: 573 69.24 - 103.86: 46 103.86 - 138.48: 2 138.48 - 173.10: 5 Dihedral angle restraints: 20043 sinusoidal: 8542 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=" O1B AGS B1001 " pdb=" O3B AGS B1001 " pdb=" PB AGS B1001 " pdb=" PG AGS B1001 " ideal model delta sinusoidal sigma weight residual 68.91 -119.47 -171.62 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1B AGS E1001 " pdb=" O3B AGS E1001 " pdb=" PB AGS E1001 " pdb=" PG AGS E1001 " ideal model delta sinusoidal sigma weight residual 68.91 -127.58 -163.51 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 20040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4365 0.071 - 0.142: 444 0.142 - 0.212: 13 0.212 - 0.283: 3 0.283 - 0.354: 1 Chirality restraints: 4826 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=" CB ILE E 605 " pdb=" CA ILE E 605 " pdb=" CG1 ILE E 605 " pdb=" CG2 ILE E 605 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE C 605 " pdb=" CA ILE C 605 " pdb=" CG1 ILE C 605 " pdb=" CG2 ILE C 605 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 4823 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 950 or resid 1001 thr \ ough 1002)) selection = (chain 'B' and (resid 289 through 916 or resid 937 through 950 or resid 1001 thr \ ough 1002)) selection = (chain 'C' and (resid 289 through 916 or resid 937 through 950 or resid 1001 thr \ ough 1002)) selection = (chain 'D' and (resid 289 through 916 or resid 937 through 950 or resid 1001 thr \ ough 1002)) selection = (chain 'E' and (resid 289 through 916 or resid 937 through 950 or resid 1001 thr \ ough 1002)) selection = (chain 'F' and (resid 289 through 916 or resid 937 through 950 or resid 1001 thr \ ough 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.370 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 74.100 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.180 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: 0.040 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 0.125 33826 Z= 0.221 Angle : 0.672 9.826 46003 Z= 0.406 Chirality : 0.042 0.354 4826 Planarity : 0.004 0.060 5717 Dihedral : 16.453 173.103 12611 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 16.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (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 TRP 0.045 0.001 TRP C 381 HIS 0.008 0.001 HIS E 875 PHE 0.023 0.001 PHE D 477 TYR 0.023 0.001 TYR A 892 ARG 0.006 0.000 ARG B 717 Details of bonding type rmsd hydrogen bonds : bond 0.19080 ( 1282) hydrogen bonds : angle 7.81330 ( 3756) covalent geometry : bond 0.00375 (33826) covalent geometry : angle 0.67234 (46003) *********************** 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 : 3.832 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: B 912 PHE cc_start: 0.5063 (t80) cc_final: 0.4635 (t80) 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: 0.4610 time to fit residues: 194.7752 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 : 4.239 ------------------------------------------------------------------------------- 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 325 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 302 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 350 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 308 ASN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS ** B 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 ASN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.072693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.053129 restraints weight = 212280.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.054284 restraints weight = 126006.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054990 restraints weight = 92420.306| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33826 Z= 0.206 Angle : 0.666 9.295 46003 Z= 0.350 Chirality : 0.043 0.195 4826 Planarity : 0.005 0.059 5717 Dihedral : 13.576 173.640 4705 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.81 % Favored : 90.95 % Rotamer: Outliers : 0.92 % Allowed : 7.87 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3847 helix: 0.47 (0.12), residues: 1754 sheet: -0.44 (0.29), residues: 331 loop : -1.50 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 381 HIS 0.009 0.001 HIS A 383 PHE 0.016 0.001 PHE D 838 TYR 0.027 0.002 TYR D 398 ARG 0.008 0.001 ARG C 829 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 1282) hydrogen bonds : angle 6.29370 ( 3756) covalent geometry : bond 0.00439 (33826) covalent geometry : angle 0.66557 (46003) *********************** 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 206 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 7.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 708 MET cc_start: 0.9578 (mmp) cc_final: 0.9347 (mmp) REVERT: A 615 MET cc_start: 0.9391 (tpp) cc_final: 0.9140 (tpp) REVERT: A 728 MET cc_start: 0.6901 (ttm) cc_final: 0.6669 (ttm) REVERT: C 452 MET cc_start: 0.8688 (pmm) cc_final: 0.8258 (pmm) REVERT: C 681 MET cc_start: 0.8947 (mmp) cc_final: 0.8742 (mmp) REVERT: D 341 TRP cc_start: 0.9236 (t60) cc_final: 0.8692 (t60) REVERT: D 412 MET cc_start: 0.8675 (mpp) cc_final: 0.8232 (mpp) REVERT: D 416 TYR cc_start: 0.8717 (t80) cc_final: 0.8153 (t80) REVERT: D 426 MET cc_start: 0.8255 (tmm) cc_final: 0.8027 (tmm) REVERT: D 646 MET cc_start: 0.9396 (mpp) cc_final: 0.9032 (mpp) REVERT: E 426 MET cc_start: 0.8503 (tmm) cc_final: 0.8242 (ttt) REVERT: E 482 ASP cc_start: 0.8770 (m-30) cc_final: 0.8433 (m-30) REVERT: E 728 MET cc_start: 0.7502 (pmm) cc_final: 0.6973 (pmm) REVERT: F 335 TYR cc_start: 0.9538 (m-80) cc_final: 0.9028 (m-10) REVERT: F 666 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8963 (tm) REVERT: F 696 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7684 (ptpp) outliers start: 32 outliers final: 16 residues processed: 198 average time/residue: 0.6152 time to fit residues: 209.3630 Evaluate side-chains 178 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 4.092 ------------------------------------------------------------------------------- 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 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain C residue 295 LEU 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 E residue 467 ASP Chi-restraints excluded: chain E residue 820 THR Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 822 GLU 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 54 optimal weight: 6.9990 chunk 359 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 318 optimal weight: 8.9990 chunk 362 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 249 optimal weight: 0.5980 chunk 145 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 chunk 301 optimal weight: 0.3980 chunk 248 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS ** 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 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** 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 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 = 0.3700 r_free = 0.3700 target = 0.072545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.053037 restraints weight = 212931.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.054171 restraints weight = 126115.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.054884 restraints weight = 92760.629| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33826 Z= 0.160 Angle : 0.625 9.790 46003 Z= 0.325 Chirality : 0.042 0.168 4826 Planarity : 0.004 0.057 5717 Dihedral : 13.320 179.793 4667 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.60 % Favored : 91.16 % Rotamer: Outliers : 1.06 % Allowed : 11.32 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3847 helix: 0.51 (0.12), residues: 1759 sheet: -0.59 (0.28), residues: 341 loop : -1.51 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP E 945 HIS 0.008 0.001 HIS A 383 PHE 0.021 0.001 PHE B 691 TYR 0.028 0.002 TYR D 302 ARG 0.005 0.000 ARG F 670 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 1282) hydrogen bonds : angle 5.88320 ( 3756) covalent geometry : bond 0.00345 (33826) covalent geometry : angle 0.62454 (46003) *********************** 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 204 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8953 (tpp) cc_final: 0.8702 (tpp) REVERT: B 631 MET cc_start: 0.8749 (tpt) cc_final: 0.7753 (tpp) REVERT: B 853 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6382 (t80) REVERT: A 452 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7580 (pmm) REVERT: A 615 MET cc_start: 0.9410 (tpp) cc_final: 0.9137 (tpp) REVERT: C 452 MET cc_start: 0.8717 (pmm) cc_final: 0.8510 (pmm) REVERT: D 341 TRP cc_start: 0.9192 (t60) cc_final: 0.8721 (t60) REVERT: D 412 MET cc_start: 0.8756 (mpp) cc_final: 0.8199 (mpp) REVERT: D 416 TYR cc_start: 0.8615 (t80) cc_final: 0.8090 (t80) REVERT: D 426 MET cc_start: 0.8212 (tmm) cc_final: 0.7919 (tmm) REVERT: D 646 MET cc_start: 0.9403 (mpp) cc_final: 0.8885 (mpp) REVERT: E 341 TRP cc_start: 0.9204 (t60) cc_final: 0.8869 (t60) REVERT: E 482 ASP cc_start: 0.8729 (m-30) cc_final: 0.8407 (m-30) REVERT: E 728 MET cc_start: 0.7579 (pmm) cc_final: 0.6998 (pmm) REVERT: E 753 LEU cc_start: 0.9488 (mt) cc_final: 0.8966 (mt) REVERT: F 335 TYR cc_start: 0.9513 (m-80) cc_final: 0.9165 (m-80) REVERT: F 341 TRP cc_start: 0.8122 (m100) cc_final: 0.7389 (m100) REVERT: F 666 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9076 (tm) outliers start: 37 outliers final: 18 residues processed: 193 average time/residue: 0.4281 time to fit residues: 139.2711 Evaluate side-chains 180 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 3.777 ------------------------------------------------------------------------------- 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 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 945 TRP Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 351 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 156 optimal weight: 0.5980 chunk 223 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 710 ASN ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS C 323 ASN C 496 HIS C 662 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 695 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.072351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.052829 restraints weight = 212604.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.053960 restraints weight = 125612.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.054664 restraints weight = 92301.196| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33826 Z= 0.161 Angle : 0.616 9.447 46003 Z= 0.319 Chirality : 0.042 0.202 4826 Planarity : 0.004 0.060 5717 Dihedral : 13.281 179.760 4659 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.55 % Favored : 91.24 % Rotamer: Outliers : 1.12 % Allowed : 13.67 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3847 helix: 0.60 (0.13), residues: 1749 sheet: -0.65 (0.29), residues: 322 loop : -1.47 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP E 945 HIS 0.007 0.001 HIS C 367 PHE 0.025 0.001 PHE A 912 TYR 0.021 0.002 TYR D 398 ARG 0.004 0.000 ARG F 670 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 1282) hydrogen bonds : angle 5.69321 ( 3756) covalent geometry : bond 0.00349 (33826) covalent geometry : angle 0.61636 (46003) *********************** 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 202 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8985 (tpp) cc_final: 0.8734 (tpp) REVERT: B 631 MET cc_start: 0.8792 (tpt) cc_final: 0.7773 (tpp) REVERT: B 666 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8604 (pp) REVERT: B 853 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6643 (t80) REVERT: A 452 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7647 (pmm) REVERT: A 615 MET cc_start: 0.9454 (tpp) cc_final: 0.9179 (tpp) REVERT: C 452 MET cc_start: 0.8737 (pmm) cc_final: 0.8510 (pmm) REVERT: D 341 TRP cc_start: 0.9174 (t60) cc_final: 0.8694 (t60) REVERT: D 412 MET cc_start: 0.8798 (mpp) cc_final: 0.8184 (mpp) REVERT: D 416 TYR cc_start: 0.8682 (t80) cc_final: 0.8159 (t80) REVERT: D 426 MET cc_start: 0.8248 (tmm) cc_final: 0.7920 (tmm) REVERT: D 646 MET cc_start: 0.9401 (mpp) cc_final: 0.8793 (mpp) REVERT: E 335 TYR cc_start: 0.8774 (m-80) cc_final: 0.8544 (m-80) REVERT: E 341 TRP cc_start: 0.9158 (t60) cc_final: 0.8802 (t60) REVERT: E 417 MET cc_start: 0.9021 (pmm) cc_final: 0.8692 (pmm) REVERT: E 482 ASP cc_start: 0.8742 (m-30) cc_final: 0.8412 (m-30) REVERT: E 728 MET cc_start: 0.7603 (pmm) cc_final: 0.6945 (pmm) REVERT: E 753 LEU cc_start: 0.9517 (mt) cc_final: 0.8984 (mt) REVERT: F 335 TYR cc_start: 0.9519 (m-80) cc_final: 0.9197 (m-80) REVERT: F 341 TRP cc_start: 0.8110 (m100) cc_final: 0.7331 (m100) REVERT: F 666 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9077 (tm) outliers start: 39 outliers final: 21 residues processed: 190 average time/residue: 0.4677 time to fit residues: 150.0818 Evaluate side-chains 183 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 4.051 ------------------------------------------------------------------------------- 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 666 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 C residue 295 LEU Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 331 THR 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 821 ILE Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 662 ASN Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR 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 57 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 311 optimal weight: 0.4980 chunk 146 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 319 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.078572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058227 restraints weight = 176071.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059181 restraints weight = 120185.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.059817 restraints weight = 95637.517| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33826 Z= 0.149 Angle : 0.612 10.730 46003 Z= 0.315 Chirality : 0.042 0.214 4826 Planarity : 0.004 0.056 5717 Dihedral : 13.210 179.705 4659 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.58 % Favored : 91.21 % Rotamer: Outliers : 1.61 % Allowed : 14.45 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3847 helix: 0.67 (0.13), residues: 1755 sheet: -0.62 (0.29), residues: 321 loop : -1.49 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 945 HIS 0.007 0.001 HIS C 367 PHE 0.036 0.001 PHE D 838 TYR 0.019 0.001 TYR D 398 ARG 0.004 0.000 ARG F 670 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 1282) hydrogen bonds : angle 5.51660 ( 3756) covalent geometry : bond 0.00324 (33826) covalent geometry : angle 0.61155 (46003) *********************** 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 222 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8903 (tpp) cc_final: 0.8675 (tpp) REVERT: B 631 MET cc_start: 0.8773 (tpt) cc_final: 0.7796 (tpp) REVERT: B 666 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8589 (pp) REVERT: B 853 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6925 (t80) REVERT: A 452 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7608 (pmm) REVERT: A 615 MET cc_start: 0.9555 (tpp) cc_final: 0.9313 (tpp) REVERT: A 728 MET cc_start: 0.7997 (tpp) cc_final: 0.7724 (tpt) REVERT: C 452 MET cc_start: 0.8737 (pmm) cc_final: 0.8494 (pmm) REVERT: C 700 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8608 (pp) REVERT: D 290 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7350 (tp) REVERT: D 341 TRP cc_start: 0.9013 (t60) cc_final: 0.8421 (t60) REVERT: D 412 MET cc_start: 0.8682 (mpp) cc_final: 0.8198 (mpp) REVERT: D 416 TYR cc_start: 0.8497 (t80) cc_final: 0.8027 (t80) REVERT: D 426 MET cc_start: 0.8247 (tmm) cc_final: 0.7924 (tmm) REVERT: D 646 MET cc_start: 0.9349 (mpp) cc_final: 0.8769 (mpp) REVERT: E 335 TYR cc_start: 0.8773 (m-80) cc_final: 0.8419 (m-80) REVERT: E 417 MET cc_start: 0.8963 (pmm) cc_final: 0.8575 (pmm) REVERT: E 482 ASP cc_start: 0.8655 (m-30) cc_final: 0.8322 (m-30) REVERT: E 728 MET cc_start: 0.7922 (pmm) cc_final: 0.7251 (pmm) REVERT: E 753 LEU cc_start: 0.9506 (mt) cc_final: 0.9028 (mt) REVERT: F 335 TYR cc_start: 0.9504 (m-80) cc_final: 0.9181 (m-80) REVERT: F 341 TRP cc_start: 0.8108 (m100) cc_final: 0.7384 (m100) REVERT: F 666 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9078 (tm) outliers start: 56 outliers final: 33 residues processed: 209 average time/residue: 0.4594 time to fit residues: 162.1740 Evaluate side-chains 200 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 4.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 HIS 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 666 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 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 851 THR Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 290 LEU 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 413 LEU Chi-restraints excluded: chain D residue 703 SER 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 821 ILE Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain E residue 945 TRP Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 338 optimal weight: 9.9990 chunk 228 optimal weight: 0.3980 chunk 149 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 364 optimal weight: 8.9990 chunk 309 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 380 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 ASN C 695 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.077761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.057399 restraints weight = 235636.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.057409 restraints weight = 145658.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.057838 restraints weight = 111003.994| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33826 Z= 0.176 Angle : 0.638 11.754 46003 Z= 0.326 Chirality : 0.042 0.150 4826 Planarity : 0.004 0.072 5717 Dihedral : 13.174 178.080 4659 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.63 % Favored : 91.16 % Rotamer: Outliers : 1.52 % Allowed : 16.03 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3847 helix: 0.71 (0.13), residues: 1754 sheet: -0.60 (0.30), residues: 310 loop : -1.47 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 945 HIS 0.007 0.001 HIS C 367 PHE 0.026 0.001 PHE D 838 TYR 0.018 0.002 TYR D 398 ARG 0.004 0.000 ARG F 670 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1282) hydrogen bonds : angle 5.51061 ( 3756) covalent geometry : bond 0.00385 (33826) covalent geometry : angle 0.63768 (46003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 4.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8892 (tpp) cc_final: 0.8666 (tpp) REVERT: B 631 MET cc_start: 0.8783 (tpt) cc_final: 0.7576 (tpp) REVERT: B 666 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8694 (pp) REVERT: B 745 THR cc_start: 0.9589 (OUTLIER) cc_final: 0.9371 (p) REVERT: B 853 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.7188 (t80) REVERT: A 452 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7688 (pmm) REVERT: A 615 MET cc_start: 0.9366 (tpp) cc_final: 0.9065 (tpp) REVERT: A 728 MET cc_start: 0.8032 (tpp) cc_final: 0.7673 (tpt) REVERT: C 452 MET cc_start: 0.8810 (pmm) cc_final: 0.8577 (pmm) REVERT: D 341 TRP cc_start: 0.9112 (t60) cc_final: 0.8626 (t60) REVERT: D 412 MET cc_start: 0.8885 (mpp) cc_final: 0.8269 (mpp) REVERT: D 416 TYR cc_start: 0.8663 (t80) cc_final: 0.8230 (t80) REVERT: D 426 MET cc_start: 0.8079 (tmm) cc_final: 0.7864 (ttt) REVERT: D 477 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8571 (m-80) REVERT: D 646 MET cc_start: 0.9391 (mpp) cc_final: 0.8820 (mpp) REVERT: E 335 TYR cc_start: 0.8717 (m-80) cc_final: 0.8462 (m-80) REVERT: E 482 ASP cc_start: 0.8604 (m-30) cc_final: 0.8272 (m-30) REVERT: E 728 MET cc_start: 0.7502 (pmm) cc_final: 0.6783 (pmm) REVERT: E 753 LEU cc_start: 0.9488 (mt) cc_final: 0.8983 (mt) REVERT: F 335 TYR cc_start: 0.9505 (m-80) cc_final: 0.9192 (m-10) REVERT: F 341 TRP cc_start: 0.8026 (m100) cc_final: 0.7363 (m100) REVERT: F 435 ASP cc_start: 0.8869 (p0) cc_final: 0.8556 (p0) REVERT: F 666 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9197 (tm) outliers start: 53 outliers final: 35 residues processed: 204 average time/residue: 0.5841 time to fit residues: 203.5469 Evaluate side-chains 202 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 5.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 HIS 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 666 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 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 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 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 413 LEU Chi-restraints excluded: chain D residue 477 PHE Chi-restraints excluded: chain D residue 703 SER 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 821 ILE Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain E residue 945 TRP 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 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 30 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 378 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 367 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 363 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.078082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058099 restraints weight = 182792.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.059138 restraints weight = 120339.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.059812 restraints weight = 93734.071| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 33826 Z= 0.114 Angle : 0.615 11.398 46003 Z= 0.311 Chirality : 0.041 0.145 4826 Planarity : 0.004 0.058 5717 Dihedral : 13.086 178.757 4659 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.11 % Favored : 91.66 % Rotamer: Outliers : 1.49 % Allowed : 16.28 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3847 helix: 0.79 (0.13), residues: 1746 sheet: -0.63 (0.28), residues: 334 loop : -1.36 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 945 HIS 0.007 0.001 HIS C 367 PHE 0.024 0.001 PHE A 912 TYR 0.021 0.001 TYR B 866 ARG 0.004 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 1282) hydrogen bonds : angle 5.27388 ( 3756) covalent geometry : bond 0.00251 (33826) covalent geometry : angle 0.61452 (46003) *********************** 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 224 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8894 (tpp) cc_final: 0.8635 (tpp) REVERT: B 481 MET cc_start: 0.9017 (mmt) cc_final: 0.8775 (mmt) REVERT: B 631 MET cc_start: 0.8762 (tpt) cc_final: 0.7648 (tpp) REVERT: B 666 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8641 (pp) REVERT: B 745 THR cc_start: 0.9580 (OUTLIER) cc_final: 0.9357 (p) REVERT: B 853 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.7085 (t80) REVERT: A 452 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7491 (pmm) REVERT: A 615 MET cc_start: 0.9546 (tpp) cc_final: 0.9288 (tpp) REVERT: A 728 MET cc_start: 0.8028 (tpp) cc_final: 0.7748 (tpt) REVERT: C 452 MET cc_start: 0.8758 (pmm) cc_final: 0.8486 (pmm) REVERT: D 290 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7542 (tp) REVERT: D 341 TRP cc_start: 0.9010 (t60) cc_final: 0.8415 (t60) REVERT: D 412 MET cc_start: 0.8760 (mpp) cc_final: 0.8200 (mpp) REVERT: D 416 TYR cc_start: 0.8487 (t80) cc_final: 0.7972 (t80) REVERT: D 426 MET cc_start: 0.8210 (tmm) cc_final: 0.7898 (tmm) REVERT: D 477 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: D 646 MET cc_start: 0.9330 (mpp) cc_final: 0.9008 (mpp) REVERT: E 335 TYR cc_start: 0.8789 (m-80) cc_final: 0.8403 (m-80) REVERT: E 482 ASP cc_start: 0.8583 (m-30) cc_final: 0.8230 (m-30) REVERT: E 728 MET cc_start: 0.7773 (pmm) cc_final: 0.7185 (pmm) REVERT: E 753 LEU cc_start: 0.9518 (mt) cc_final: 0.9045 (mt) REVERT: F 335 TYR cc_start: 0.9520 (m-80) cc_final: 0.9133 (m-10) REVERT: F 341 TRP cc_start: 0.8076 (m100) cc_final: 0.7405 (m100) REVERT: F 435 ASP cc_start: 0.8851 (p0) cc_final: 0.8530 (p0) REVERT: F 666 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9025 (tm) outliers start: 52 outliers final: 30 residues processed: 211 average time/residue: 0.4090 time to fit residues: 147.4495 Evaluate side-chains 199 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 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 290 LEU 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 426 MET Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain E residue 945 TRP Chi-restraints excluded: chain F residue 358 LEU 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 745 THR Chi-restraints excluded: chain F residue 892 TYR 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 376 optimal weight: 9.9990 chunk 342 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 202 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 HIS B 491 HIS ** 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** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.077748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057810 restraints weight = 181294.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.058839 restraints weight = 120074.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.059474 restraints weight = 93998.042| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 33826 Z= 0.135 Angle : 0.632 14.178 46003 Z= 0.317 Chirality : 0.041 0.155 4826 Planarity : 0.004 0.058 5717 Dihedral : 13.050 177.467 4659 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.42 % Favored : 91.34 % Rotamer: Outliers : 1.49 % Allowed : 16.57 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3847 helix: 0.82 (0.13), residues: 1758 sheet: -0.64 (0.28), residues: 337 loop : -1.39 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 945 HIS 0.007 0.001 HIS C 367 PHE 0.022 0.001 PHE A 912 TYR 0.019 0.001 TYR B 866 ARG 0.004 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1282) hydrogen bonds : angle 5.28316 ( 3756) covalent geometry : bond 0.00300 (33826) covalent geometry : angle 0.63167 (46003) *********************** 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 215 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 4.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8922 (tpp) cc_final: 0.8647 (tpp) REVERT: B 631 MET cc_start: 0.8730 (tpt) cc_final: 0.7482 (tpp) REVERT: B 666 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8611 (pp) REVERT: B 745 THR cc_start: 0.9591 (OUTLIER) cc_final: 0.9371 (p) REVERT: B 853 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.7125 (t80) REVERT: A 452 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7460 (pmm) REVERT: A 615 MET cc_start: 0.9549 (tpp) cc_final: 0.9289 (tpp) REVERT: A 631 MET cc_start: 0.8525 (tpp) cc_final: 0.8083 (tpp) REVERT: C 340 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8842 (tp30) REVERT: C 452 MET cc_start: 0.8759 (pmm) cc_final: 0.8504 (pmm) REVERT: C 728 MET cc_start: 0.8307 (ppp) cc_final: 0.8100 (ppp) REVERT: D 290 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7475 (tp) REVERT: D 341 TRP cc_start: 0.9034 (t60) cc_final: 0.8455 (t60) REVERT: D 412 MET cc_start: 0.8750 (mpp) cc_final: 0.8194 (mpp) REVERT: D 416 TYR cc_start: 0.8509 (t80) cc_final: 0.8069 (t80) REVERT: D 426 MET cc_start: 0.8211 (tmm) cc_final: 0.7997 (tmm) REVERT: D 477 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8756 (m-80) REVERT: D 646 MET cc_start: 0.9332 (mpp) cc_final: 0.8752 (mpp) REVERT: E 335 TYR cc_start: 0.8783 (m-80) cc_final: 0.8385 (m-80) REVERT: E 477 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: E 482 ASP cc_start: 0.8601 (m-30) cc_final: 0.8232 (m-30) REVERT: E 728 MET cc_start: 0.7760 (pmm) cc_final: 0.7177 (pmm) REVERT: E 732 MET cc_start: 0.8845 (mmm) cc_final: 0.8626 (mmm) REVERT: E 753 LEU cc_start: 0.9511 (mt) cc_final: 0.9029 (mt) REVERT: F 335 TYR cc_start: 0.9518 (m-80) cc_final: 0.9137 (m-10) REVERT: F 341 TRP cc_start: 0.8087 (m100) cc_final: 0.7414 (m100) REVERT: F 435 ASP cc_start: 0.8877 (p0) cc_final: 0.8560 (p0) outliers start: 52 outliers final: 35 residues processed: 201 average time/residue: 0.4493 time to fit residues: 153.7575 Evaluate side-chains 204 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 4.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 314 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 431 VAL 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 290 LEU 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 417 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 821 ILE Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain E residue 945 TRP 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 672 THR Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 900 THR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 181 optimal weight: 0.9980 chunk 288 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 318 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 159 optimal weight: 0.0980 chunk 380 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.077498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057605 restraints weight = 182230.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.058628 restraints weight = 120748.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.059291 restraints weight = 94454.943| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33826 Z= 0.146 Angle : 0.636 12.284 46003 Z= 0.319 Chirality : 0.041 0.168 4826 Planarity : 0.004 0.056 5717 Dihedral : 13.012 175.813 4657 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.71 % Favored : 91.08 % Rotamer: Outliers : 1.49 % Allowed : 16.86 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3847 helix: 0.82 (0.13), residues: 1765 sheet: -0.57 (0.28), residues: 326 loop : -1.40 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 945 HIS 0.007 0.001 HIS C 367 PHE 0.026 0.001 PHE D 342 TYR 0.020 0.001 TYR B 866 ARG 0.006 0.000 ARG C 717 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 1282) hydrogen bonds : angle 5.28517 ( 3756) covalent geometry : bond 0.00322 (33826) covalent geometry : angle 0.63565 (46003) *********************** 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 220 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8936 (tpp) cc_final: 0.8652 (tpp) REVERT: B 631 MET cc_start: 0.8716 (tpt) cc_final: 0.7450 (tpp) REVERT: B 666 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8623 (pp) REVERT: B 745 THR cc_start: 0.9592 (OUTLIER) cc_final: 0.9374 (p) REVERT: B 853 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.7149 (t80) REVERT: A 452 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7559 (pmm) REVERT: A 615 MET cc_start: 0.9547 (tpp) cc_final: 0.9305 (tpp) REVERT: A 631 MET cc_start: 0.8636 (tpp) cc_final: 0.8129 (tpp) REVERT: C 340 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8846 (tp30) REVERT: C 452 MET cc_start: 0.8775 (pmm) cc_final: 0.8523 (pmm) REVERT: D 290 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7459 (tp) REVERT: D 341 TRP cc_start: 0.9028 (t60) cc_final: 0.8591 (t60) REVERT: D 412 MET cc_start: 0.8740 (mpp) cc_final: 0.8200 (mpp) REVERT: D 416 TYR cc_start: 0.8495 (t80) cc_final: 0.8077 (t80) REVERT: D 426 MET cc_start: 0.8255 (tmm) cc_final: 0.7967 (tmm) REVERT: D 477 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: D 646 MET cc_start: 0.9323 (mpp) cc_final: 0.8756 (mpp) REVERT: D 708 MET cc_start: 0.9017 (mmp) cc_final: 0.8773 (mmm) REVERT: E 335 TYR cc_start: 0.8747 (m-80) cc_final: 0.8327 (m-80) REVERT: E 338 LEU cc_start: 0.9711 (tt) cc_final: 0.9478 (tt) REVERT: E 477 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: E 482 ASP cc_start: 0.8558 (m-30) cc_final: 0.8177 (m-30) REVERT: E 728 MET cc_start: 0.7781 (pmm) cc_final: 0.7254 (pmm) REVERT: E 753 LEU cc_start: 0.9506 (mt) cc_final: 0.9026 (mt) REVERT: F 335 TYR cc_start: 0.9509 (m-80) cc_final: 0.9136 (m-10) REVERT: F 341 TRP cc_start: 0.8122 (m100) cc_final: 0.7438 (m100) REVERT: F 435 ASP cc_start: 0.8869 (p0) cc_final: 0.8554 (p0) outliers start: 52 outliers final: 35 residues processed: 205 average time/residue: 0.4295 time to fit residues: 149.4731 Evaluate side-chains 208 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 314 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 431 VAL 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 290 LEU 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 417 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 821 ILE Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain E residue 945 TRP 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 672 THR Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 900 THR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 24 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 348 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 371 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS B 792 ASN B 916 GLN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.077482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.057422 restraints weight = 235322.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.057328 restraints weight = 145055.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.057684 restraints weight = 109665.359| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33826 Z= 0.175 Angle : 0.668 13.340 46003 Z= 0.334 Chirality : 0.042 0.167 4826 Planarity : 0.004 0.057 5717 Dihedral : 13.028 175.702 4657 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.94 % Favored : 90.88 % Rotamer: Outliers : 1.55 % Allowed : 17.03 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3847 helix: 0.79 (0.13), residues: 1774 sheet: -0.60 (0.29), residues: 330 loop : -1.43 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 945 HIS 0.007 0.001 HIS C 367 PHE 0.020 0.001 PHE A 912 TYR 0.022 0.002 TYR E 398 ARG 0.007 0.000 ARG A 682 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 1282) hydrogen bonds : angle 5.36877 ( 3756) covalent geometry : bond 0.00385 (33826) covalent geometry : angle 0.66778 (46003) ********************** 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 219 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 3.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8959 (tpp) cc_final: 0.8673 (tpp) REVERT: B 631 MET cc_start: 0.8877 (tpt) cc_final: 0.7629 (tpp) REVERT: B 666 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8663 (pp) REVERT: B 853 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7365 (t80) REVERT: A 452 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7702 (pmm) REVERT: A 615 MET cc_start: 0.9343 (tpp) cc_final: 0.9058 (tpp) REVERT: A 631 MET cc_start: 0.8588 (tpp) cc_final: 0.8063 (tpp) REVERT: C 452 MET cc_start: 0.8827 (pmm) cc_final: 0.8573 (pmm) REVERT: C 728 MET cc_start: 0.8577 (ppp) cc_final: 0.8231 (ppp) REVERT: D 290 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7251 (tp) REVERT: D 341 TRP cc_start: 0.8912 (t60) cc_final: 0.8457 (t60) REVERT: D 412 MET cc_start: 0.8875 (mpp) cc_final: 0.8220 (mpp) REVERT: D 416 TYR cc_start: 0.8649 (t80) cc_final: 0.8306 (t80) REVERT: D 477 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8627 (m-80) REVERT: D 646 MET cc_start: 0.9356 (mpp) cc_final: 0.9117 (mpp) REVERT: E 296 HIS cc_start: 0.8688 (m90) cc_final: 0.8420 (m-70) REVERT: E 335 TYR cc_start: 0.8773 (m-80) cc_final: 0.8444 (m-80) REVERT: E 341 TRP cc_start: 0.9038 (t60) cc_final: 0.8587 (t60) REVERT: E 477 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8162 (m-10) REVERT: E 482 ASP cc_start: 0.8474 (m-30) cc_final: 0.8112 (m-30) REVERT: E 581 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8339 (p-80) REVERT: E 728 MET cc_start: 0.7377 (pmm) cc_final: 0.6725 (pmm) REVERT: E 753 LEU cc_start: 0.9466 (mt) cc_final: 0.8983 (mt) REVERT: F 335 TYR cc_start: 0.9494 (m-80) cc_final: 0.9187 (m-10) REVERT: F 341 TRP cc_start: 0.8076 (m100) cc_final: 0.7402 (m100) REVERT: F 435 ASP cc_start: 0.8869 (p0) cc_final: 0.8611 (p0) outliers start: 54 outliers final: 36 residues processed: 204 average time/residue: 0.4355 time to fit residues: 151.5460 Evaluate side-chains 203 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 4.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 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 314 TYR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 431 VAL 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 290 LEU 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 417 MET Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 477 PHE Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 581 HIS Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain E residue 945 TRP 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 672 THR Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 900 THR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 157 optimal weight: 0.0370 chunk 3 optimal weight: 4.9990 chunk 305 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 130 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 211 optimal weight: 0.8980 overall best weight: 1.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.078516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.058479 restraints weight = 234471.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.058586 restraints weight = 143187.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.059077 restraints weight = 107907.160| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33826 Z= 0.124 Angle : 0.668 13.736 46003 Z= 0.330 Chirality : 0.042 0.192 4826 Planarity : 0.004 0.056 5717 Dihedral : 12.999 175.377 4657 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.58 % Favored : 91.21 % Rotamer: Outliers : 1.26 % Allowed : 17.29 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3847 helix: 0.83 (0.13), residues: 1762 sheet: -0.61 (0.28), residues: 338 loop : -1.35 (0.16), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 945 HIS 0.019 0.001 HIS E 581 PHE 0.035 0.001 PHE D 342 TYR 0.021 0.001 TYR B 866 ARG 0.004 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 1282) hydrogen bonds : angle 5.24766 ( 3756) covalent geometry : bond 0.00277 (33826) covalent geometry : angle 0.66794 (46003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10742.95 seconds wall clock time: 193 minutes 6.27 seconds (11586.27 seconds total)