Starting phenix.real_space_refine on Mon Oct 13 10:50:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ww6_37882/10_2025/8ww6_37882.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ww6_37882/10_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_37882/10_2025/8ww6_37882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ww6_37882/10_2025/8ww6_37882.map" model { file = "/net/cci-nas-00/data/ceres_data/8ww6_37882/10_2025/8ww6_37882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ww6_37882/10_2025/8ww6_37882.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 6 5.21 5 S 161 5.16 5 C 21022 2.51 5 N 5549 2.21 5 O 6040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32825 Number of models: 1 Model: "" Number of chains: 14 Chain: "H" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "B" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5347 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 613} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5347 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 613} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5347 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 613} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 5333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5333 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 611} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5328 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 611} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5347 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 613} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.93, per 1000 atoms: 0.24 Number of scatterers: 32825 At special positions: 0 Unit cell: (143.445, 153.3, 148.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 161 16.00 P 47 15.00 Mg 6 11.99 O 6040 8.00 N 5549 7.00 C 21022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 29 sheets defined 51.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'B' and resid 289 through 297 Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 311 through 317 removed outlier: 3.859A pdb=" N TYR B 315 " --> pdb=" O PRO B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 removed outlier: 3.561A pdb=" N THR B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 377 through 386 removed outlier: 3.566A pdb=" N HIS B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 409 Processing helix chain 'B' and resid 414 through 427 Processing helix chain 'B' and resid 466 through 494 removed outlier: 3.520A pdb=" N SER B 474 " --> pdb=" O HIS B 470 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE B 477 " --> pdb=" O ILE B 473 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 479 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 484 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.859A pdb=" N ASN B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 516 removed outlier: 3.908A pdb=" N SER B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 520 through 535 removed outlier: 4.542A pdb=" N PHE B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.709A pdb=" N THR B 620 " --> pdb=" O PHE B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 654 removed outlier: 3.608A pdb=" N LEU B 645 " --> pdb=" O GLY B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 668 removed outlier: 4.037A pdb=" N LEU B 666 " --> pdb=" O ASN B 662 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.644A pdb=" N VAL B 709 " --> pdb=" O LEU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 751 removed outlier: 3.679A pdb=" N ARG B 751 " --> pdb=" O GLY B 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 751' Processing helix chain 'B' and resid 777 through 783 removed outlier: 4.153A pdb=" N ILE B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 808 removed outlier: 3.580A pdb=" N GLN B 791 " --> pdb=" O ASP B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.641A pdb=" N GLU B 826 " --> pdb=" O GLU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 843 removed outlier: 3.708A pdb=" N VAL B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 870 removed outlier: 3.790A pdb=" N VAL B 858 " --> pdb=" O ASN B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 878 No H-bonds generated for 'chain 'B' and resid 876 through 878' Processing helix chain 'B' and resid 879 through 887 removed outlier: 5.174A pdb=" N GLU B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 892 removed outlier: 4.079A pdb=" N LYS B 891 " --> pdb=" O VAL B 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 4.113A pdb=" N HIS A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.721A pdb=" N ILE A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.287A pdb=" N TYR A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 344 through 345 No H-bonds generated for 'chain 'A' and resid 344 through 345' Processing helix chain 'A' and resid 346 through 350 removed outlier: 4.336A pdb=" N LYS A 349 " --> pdb=" O CYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.869A pdb=" N ILE A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 409 Processing helix chain 'A' and resid 414 through 427 Processing helix chain 'A' and resid 466 through 494 removed outlier: 4.225A pdb=" N PHE A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 removed outlier: 3.806A pdb=" N ASN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 520 through 535 removed outlier: 3.521A pdb=" N LYS A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 641 through 654 removed outlier: 3.787A pdb=" N LEU A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 removed outlier: 4.389A pdb=" N LEU A 666 " --> pdb=" O ASN A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 708 removed outlier: 4.151A pdb=" N LYS A 706 " --> pdb=" O THR A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 777 through 783 removed outlier: 4.284A pdb=" N ILE A 781 " --> pdb=" O ASP A 777 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 810 removed outlier: 3.705A pdb=" N GLN A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 833 through 843 removed outlier: 3.625A pdb=" N THR A 840 " --> pdb=" O HIS A 836 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 841 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 842 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 870 removed outlier: 3.827A pdb=" N VAL A 858 " --> pdb=" O ASN A 854 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 866 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 868 " --> pdb=" O GLU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 882 removed outlier: 4.118A pdb=" N GLN A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.149A pdb=" N LYS A 891 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 892 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 893 " --> pdb=" O GLU A 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 888 through 893' Processing helix chain 'C' and resid 290 through 297 removed outlier: 4.175A pdb=" N ASP C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 308 Processing helix chain 'C' and resid 311 through 317 removed outlier: 3.845A pdb=" N TYR C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 331 removed outlier: 3.703A pdb=" N TRP C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 354 through 367 Processing helix chain 'C' and resid 377 through 386 Processing helix chain 'C' and resid 388 through 409 removed outlier: 3.668A pdb=" N GLU C 392 " --> pdb=" O GLN C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 425 Processing helix chain 'C' and resid 466 through 494 removed outlier: 4.166A pdb=" N PHE C 477 " --> pdb=" O ILE C 473 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG C 479 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 516 removed outlier: 4.136A pdb=" N ASN C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LYS C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 520 through 535 removed outlier: 5.293A pdb=" N PHE C 533 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 605 Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.799A pdb=" N THR C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 654 removed outlier: 3.959A pdb=" N LEU C 645 " --> pdb=" O GLY C 641 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C 646 " --> pdb=" O LYS C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 4.152A pdb=" N LEU C 666 " --> pdb=" O ASN C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 682 removed outlier: 3.864A pdb=" N PHE C 680 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 681 " --> pdb=" O SER C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 710 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.516A pdb=" N ARG C 752 " --> pdb=" O GLY C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 783 removed outlier: 4.266A pdb=" N ILE C 781 " --> pdb=" O ASP C 777 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS C 782 " --> pdb=" O PRO C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 808 removed outlier: 3.505A pdb=" N GLN C 791 " --> pdb=" O ASP C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 831 removed outlier: 3.538A pdb=" N GLU C 826 " --> pdb=" O GLU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 843 Processing helix chain 'C' and resid 855 through 870 removed outlier: 3.853A pdb=" N THR C 860 " --> pdb=" O SER C 856 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR C 868 " --> pdb=" O GLU C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 876 through 881 removed outlier: 3.936A pdb=" N LEU C 880 " --> pdb=" O ILE C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 891 removed outlier: 3.651A pdb=" N LYS C 891 " --> pdb=" O VAL C 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 888 through 891' Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.591A pdb=" N ARG D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 317 removed outlier: 3.995A pdb=" N TYR D 315 " --> pdb=" O PRO D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 331 removed outlier: 3.740A pdb=" N THR D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.713A pdb=" N GLN D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 removed outlier: 3.753A pdb=" N TRP D 350 " --> pdb=" O PRO D 347 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN D 351 " --> pdb=" O GLU D 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 347 through 351' Processing helix chain 'D' and resid 353 through 366 removed outlier: 3.936A pdb=" N LYS D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 388 through 409 removed outlier: 3.615A pdb=" N TYR D 409 " --> pdb=" O TYR D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 427 Processing helix chain 'D' and resid 466 through 476 Processing helix chain 'D' and resid 476 through 494 removed outlier: 4.314A pdb=" N VAL D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN D 494 " --> pdb=" O TYR D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 removed outlier: 4.013A pdb=" N LEU D 501 " --> pdb=" O GLU D 497 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LYS D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 520 through 535 removed outlier: 4.970A pdb=" N PHE D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 605 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.600A pdb=" N THR D 620 " --> pdb=" O PHE D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 623 No H-bonds generated for 'chain 'D' and resid 621 through 623' Processing helix chain 'D' and resid 641 through 654 removed outlier: 3.697A pdb=" N LEU D 645 " --> pdb=" O GLY D 641 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET D 646 " --> pdb=" O LYS D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 666 Processing helix chain 'D' and resid 679 through 683 removed outlier: 3.691A pdb=" N LEU D 683 " --> pdb=" O PHE D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 710 Processing helix chain 'D' and resid 746 through 752 removed outlier: 3.679A pdb=" N TRP D 750 " --> pdb=" O ASP D 746 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG D 752 " --> pdb=" O GLY D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 783 removed outlier: 3.520A pdb=" N ILE D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 810 removed outlier: 3.573A pdb=" N GLN D 791 " --> pdb=" O ASP D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 831 removed outlier: 3.702A pdb=" N SER D 823 " --> pdb=" O PRO D 819 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N THR D 825 " --> pdb=" O ILE D 821 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 831 " --> pdb=" O ALA D 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 843 Processing helix chain 'D' and resid 854 through 870 removed outlier: 4.265A pdb=" N VAL D 858 " --> pdb=" O ASN D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 887 removed outlier: 4.015A pdb=" N GLN D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 893 removed outlier: 3.948A pdb=" N LYS D 891 " --> pdb=" O VAL D 888 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 893 " --> pdb=" O GLU D 890 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 297 through 310 removed outlier: 3.937A pdb=" N ARG E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 317 Processing helix chain 'E' and resid 317 through 331 removed outlier: 3.567A pdb=" N THR E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 343 Processing helix chain 'E' and resid 353 through 366 removed outlier: 4.280A pdb=" N GLU E 359 " --> pdb=" O LYS E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 386 Processing helix chain 'E' and resid 388 through 409 Processing helix chain 'E' and resid 414 through 427 removed outlier: 3.674A pdb=" N ILE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 476 removed outlier: 3.623A pdb=" N SER E 474 " --> pdb=" O HIS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 494 removed outlier: 3.834A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 516 removed outlier: 3.961A pdb=" N ASN E 502 " --> pdb=" O SER E 498 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR E 504 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LYS E 505 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER E 516 " --> pdb=" O GLU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 519 No H-bonds generated for 'chain 'E' and resid 517 through 519' Processing helix chain 'E' and resid 520 through 535 removed outlier: 3.869A pdb=" N PHE E 533 " --> pdb=" O ARG E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 605 Processing helix chain 'E' and resid 607 through 620 removed outlier: 3.547A pdb=" N THR E 620 " --> pdb=" O PHE E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 623 No H-bonds generated for 'chain 'E' and resid 621 through 623' Processing helix chain 'E' and resid 641 through 654 Processing helix chain 'E' and resid 662 through 666 Processing helix chain 'E' and resid 678 through 682 Processing helix chain 'E' and resid 705 through 710 Processing helix chain 'E' and resid 746 through 752 Processing helix chain 'E' and resid 777 through 783 removed outlier: 4.123A pdb=" N ILE E 781 " --> pdb=" O ASP E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 810 removed outlier: 3.747A pdb=" N GLN E 791 " --> pdb=" O ASP E 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 816 removed outlier: 3.502A pdb=" N VAL E 816 " --> pdb=" O ILE E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 819 through 831 removed outlier: 3.918A pdb=" N SER E 823 " --> pdb=" O PRO E 819 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N THR E 825 " --> pdb=" O ILE E 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 843 removed outlier: 3.729A pdb=" N ARG E 837 " --> pdb=" O ASP E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 854 through 870 removed outlier: 3.783A pdb=" N VAL E 858 " --> pdb=" O ASN E 854 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR E 868 " --> pdb=" O GLU E 864 " (cutoff:3.500A) Processing helix chain 'E' and resid 876 through 886 removed outlier: 3.702A pdb=" N LEU E 880 " --> pdb=" O ILE E 876 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN E 882 " --> pdb=" O LEU E 878 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 883 " --> pdb=" O GLU E 879 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU E 885 " --> pdb=" O SER E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 893 removed outlier: 3.728A pdb=" N LYS E 891 " --> pdb=" O VAL E 888 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR E 892 " --> pdb=" O LEU E 889 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 893 " --> pdb=" O GLU E 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 888 through 893' Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 297 through 310 removed outlier: 3.831A pdb=" N ARG F 301 " --> pdb=" O ASP F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 317 removed outlier: 4.236A pdb=" N TYR F 315 " --> pdb=" O PRO F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 330 Processing helix chain 'F' and resid 335 through 344 Processing helix chain 'F' and resid 358 through 367 Processing helix chain 'F' and resid 377 through 384 Processing helix chain 'F' and resid 388 through 409 removed outlier: 3.782A pdb=" N GLU F 392 " --> pdb=" O GLN F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.560A pdb=" N ILE F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 494 removed outlier: 3.617A pdb=" N SER F 474 " --> pdb=" O HIS F 470 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE F 477 " --> pdb=" O ILE F 473 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER F 478 " --> pdb=" O SER F 474 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG F 479 " --> pdb=" O GLU F 475 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.843A pdb=" N LEU F 501 " --> pdb=" O GLU F 497 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR F 504 " --> pdb=" O ILE F 500 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS F 505 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER F 516 " --> pdb=" O GLU F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 519 No H-bonds generated for 'chain 'F' and resid 517 through 519' Processing helix chain 'F' and resid 520 through 535 removed outlier: 4.343A pdb=" N PHE F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU F 534 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 605 Processing helix chain 'F' and resid 607 through 620 removed outlier: 3.531A pdb=" N THR F 620 " --> pdb=" O PHE F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 654 Processing helix chain 'F' and resid 662 through 668 removed outlier: 4.086A pdb=" N LEU F 666 " --> pdb=" O ASN F 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 677 through 682 removed outlier: 3.616A pdb=" N MET F 681 " --> pdb=" O ASN F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 704 through 710 removed outlier: 3.707A pdb=" N MET F 708 " --> pdb=" O ARG F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 751 Processing helix chain 'F' and resid 778 through 783 removed outlier: 3.906A pdb=" N HIS F 782 " --> pdb=" O PRO F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 810 removed outlier: 3.558A pdb=" N GLN F 791 " --> pdb=" O ASP F 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 812 through 816 Processing helix chain 'F' and resid 822 through 831 Processing helix chain 'F' and resid 833 through 843 Processing helix chain 'F' and resid 855 through 870 removed outlier: 3.512A pdb=" N THR F 868 " --> pdb=" O GLU F 864 " (cutoff:3.500A) Processing helix chain 'F' and resid 876 through 884 removed outlier: 4.369A pdb=" N LEU F 880 " --> pdb=" O ILE F 876 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN F 882 " --> pdb=" O LEU F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 888 through 893 removed outlier: 3.737A pdb=" N LYS F 891 " --> pdb=" O VAL F 888 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR F 892 " --> pdb=" O LEU F 889 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 893 " --> pdb=" O GLU F 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 888 through 893' Processing sheet with id=AA1, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.717A pdb=" N TRP B 442 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 550 through 553 Processing sheet with id=AA3, first strand: chain 'B' and resid 631 through 635 Processing sheet with id=AA4, first strand: chain 'B' and resid 658 through 660 removed outlier: 3.571A pdb=" N SER B 659 " --> pdb=" O TYR B 688 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 690 " --> pdb=" O SER B 659 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY B 689 " --> pdb=" O VAL B 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 698 through 699 removed outlier: 6.706A pdb=" N GLU B 698 " --> pdb=" O ILE B 741 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 713 through 716 removed outlier: 3.618A pdb=" N VAL B 714 " --> pdb=" O PHE B 726 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 761 through 762 removed outlier: 7.077A pdb=" N LYS B 761 " --> pdb=" O LYS B 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.801A pdb=" N TRP A 442 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 550 through 553 Processing sheet with id=AB1, first strand: chain 'A' and resid 658 through 660 removed outlier: 4.102A pdb=" N TYR A 690 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 689 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA A 735 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 691 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 632 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 714 through 718 removed outlier: 3.783A pdb=" N VAL A 714 " --> pdb=" O PHE A 726 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 718 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 431 through 434 removed outlier: 3.793A pdb=" N TRP C 442 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 550 through 553 Processing sheet with id=AB5, first strand: chain 'C' and resid 632 through 635 Processing sheet with id=AB6, first strand: chain 'C' and resid 658 through 661 removed outlier: 3.921A pdb=" N TYR C 690 " --> pdb=" O SER C 659 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 713 through 716 removed outlier: 3.502A pdb=" N GLU C 724 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 893 through 895 Processing sheet with id=AB9, first strand: chain 'D' and resid 430 through 434 removed outlier: 3.644A pdb=" N TRP D 442 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 550 through 553 removed outlier: 3.597A pdb=" N GLY D 556 " --> pdb=" O VAL D 553 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 658 through 660 removed outlier: 3.708A pdb=" N TYR D 690 " --> pdb=" O SER D 659 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 733 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 735 " --> pdb=" O PHE D 691 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU D 632 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N MET D 631 " --> pdb=" O ARG D 754 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR D 756 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU D 633 " --> pdb=" O TYR D 756 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 714 through 716 removed outlier: 3.930A pdb=" N VAL D 714 " --> pdb=" O PHE D 726 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE D 726 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA D 716 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU D 724 " --> pdb=" O ALA D 716 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 430 through 434 removed outlier: 3.772A pdb=" N TRP E 442 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 550 through 553 Processing sheet with id=AC6, first strand: chain 'E' and resid 658 through 660 removed outlier: 3.924A pdb=" N TYR E 690 " --> pdb=" O SER E 659 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU E 632 " --> pdb=" O ALA E 734 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 430 through 434 removed outlier: 3.931A pdb=" N TRP F 442 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 550 through 553 Processing sheet with id=AC9, first strand: chain 'F' and resid 658 through 660 removed outlier: 3.816A pdb=" N TYR F 690 " --> pdb=" O SER F 659 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA F 735 " --> pdb=" O PHE F 691 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU F 632 " --> pdb=" O ALA F 734 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N SER F 736 " --> pdb=" O LEU F 632 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TRP F 634 " --> pdb=" O SER F 736 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 698 through 699 removed outlier: 6.514A pdb=" N GLU F 698 " --> pdb=" O ILE F 741 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 714 through 717 1282 hydrogen bonds defined for protein. 3756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 3.48 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 1002)) selection = (chain 'B' and (resid 289 through 916 or resid 937 through 1002)) selection = (chain 'C' and (resid 289 through 916 or resid 937 through 1002)) selection = (chain 'D' and (resid 289 through 916 or resid 937 through 1002)) selection = (chain 'E' and (resid 289 through 916 or resid 937 through 1002)) selection = (chain 'F' and (resid 289 through 916 or resid 937 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 29.300 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- 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 : 16.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.25 % Favored : 90.51 % Rotamer: Outliers : 1.46 % Allowed : 1.09 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.14), residues: 3847 helix: 0.56 (0.13), residues: 1693 sheet: -0.29 (0.30), residues: 327 loop : -1.48 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 717 TYR 0.023 0.001 TYR A 892 PHE 0.023 0.001 PHE D 477 TRP 0.045 0.001 TRP C 381 HIS 0.008 0.001 HIS E 875 Details of bonding type rmsd covalent geometry : bond 0.00375 (33826) covalent geometry : angle 0.67234 (46003) hydrogen bonds : bond 0.19080 ( 1282) hydrogen bonds : angle 7.81330 ( 3756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 MET cc_start: 0.7814 (tmm) cc_final: 0.7535 (tmm) REVERT: A 892 TYR cc_start: 0.7606 (p90) cc_final: 0.7323 (p90) REVERT: C 294 MET cc_start: 0.7875 (mmp) cc_final: 0.7561 (mmm) REVERT: C 452 MET cc_start: 0.8465 (pmm) cc_final: 0.8181 (pmm) REVERT: D 341 TRP cc_start: 0.9159 (t60) cc_final: 0.8795 (t60) REVERT: E 482 ASP cc_start: 0.8586 (m-30) cc_final: 0.8275 (m-30) REVERT: E 728 MET cc_start: 0.7348 (pmm) cc_final: 0.6912 (pmm) REVERT: F 335 TYR cc_start: 0.9435 (m-80) cc_final: 0.8828 (m-80) REVERT: F 362 TRP cc_start: 0.7370 (t-100) cc_final: 0.7118 (t-100) REVERT: F 417 MET cc_start: 0.7874 (mtm) cc_final: 0.7440 (mtm) REVERT: F 426 MET cc_start: 0.8389 (tmm) cc_final: 0.8182 (tmm) outliers start: 51 outliers final: 20 residues processed: 259 average time/residue: 0.2106 time to fit residues: 89.1151 Evaluate side-chains 179 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 874 ARG Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 829 ARG Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 671 GLU Chi-restraints excluded: chain F residue 698 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 308 ASN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS B 491 HIS ** B 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 ASN B 871 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN C 491 HIS C 494 GLN ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 396 GLN D 869 ASN ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 ASN F 640 ASN ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.080298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.060354 restraints weight = 235853.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.060391 restraints weight = 144881.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.060853 restraints weight = 109177.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.061090 restraints weight = 95385.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.061199 restraints weight = 89497.439| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33826 Z= 0.132 Angle : 0.649 16.873 46003 Z= 0.333 Chirality : 0.043 0.206 4826 Planarity : 0.004 0.064 5717 Dihedral : 13.486 172.959 4705 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.50 % Favored : 91.27 % Rotamer: Outliers : 0.89 % Allowed : 7.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.14), residues: 3847 helix: 0.48 (0.12), residues: 1741 sheet: -0.21 (0.29), residues: 335 loop : -1.41 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 829 TYR 0.028 0.002 TYR B 756 PHE 0.016 0.001 PHE D 838 TRP 0.043 0.001 TRP C 381 HIS 0.011 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00279 (33826) covalent geometry : angle 0.64933 (46003) hydrogen bonds : bond 0.05042 ( 1282) hydrogen bonds : angle 6.13008 ( 3756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 708 MET cc_start: 0.9583 (mmp) cc_final: 0.9380 (mmp) REVERT: A 452 MET cc_start: 0.7805 (pmm) cc_final: 0.7364 (pmm) REVERT: A 615 MET cc_start: 0.9294 (tpp) cc_final: 0.9012 (tpp) REVERT: A 892 TYR cc_start: 0.7423 (p90) cc_final: 0.7180 (p90) REVERT: C 452 MET cc_start: 0.8532 (pmm) cc_final: 0.8310 (pmm) REVERT: C 681 MET cc_start: 0.9165 (mmp) cc_final: 0.8941 (mmp) REVERT: D 341 TRP cc_start: 0.9200 (t60) cc_final: 0.8664 (t60) REVERT: D 412 MET cc_start: 0.8547 (mpp) cc_final: 0.8106 (mpp) REVERT: D 646 MET cc_start: 0.9379 (mpp) cc_final: 0.8969 (mpp) REVERT: D 708 MET cc_start: 0.9001 (mmp) cc_final: 0.8774 (mmp) REVERT: E 341 TRP cc_start: 0.9321 (t60) cc_final: 0.9111 (t60) REVERT: E 426 MET cc_start: 0.8366 (tmm) cc_final: 0.8096 (ttt) REVERT: E 482 ASP cc_start: 0.8536 (m-30) cc_final: 0.8193 (m-30) REVERT: E 728 MET cc_start: 0.7383 (pmm) cc_final: 0.6861 (pmm) REVERT: E 753 LEU cc_start: 0.9471 (mt) cc_final: 0.8921 (mt) REVERT: F 335 TYR cc_start: 0.9549 (m-80) cc_final: 0.9054 (m-10) REVERT: F 341 TRP cc_start: 0.8039 (m100) cc_final: 0.7311 (m100) REVERT: F 666 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9017 (tm) outliers start: 31 outliers final: 16 residues processed: 205 average time/residue: 0.2079 time to fit residues: 71.4146 Evaluate side-chains 180 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 945 TRP Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 820 THR Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 892 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 366 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 377 optimal weight: 5.9990 chunk 362 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 301 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 C 496 HIS ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 916 GLN ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.077612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.056853 restraints weight = 238442.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056868 restraints weight = 148008.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.057292 restraints weight = 114196.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.057516 restraints weight = 100022.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.057641 restraints weight = 94143.651| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33826 Z= 0.232 Angle : 0.665 14.230 46003 Z= 0.347 Chirality : 0.043 0.286 4826 Planarity : 0.004 0.057 5717 Dihedral : 13.300 179.077 4667 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.20 % Favored : 90.56 % Rotamer: Outliers : 1.29 % Allowed : 10.88 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.14), residues: 3847 helix: 0.47 (0.12), residues: 1758 sheet: -0.58 (0.28), residues: 348 loop : -1.52 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 670 TYR 0.024 0.002 TYR D 398 PHE 0.020 0.002 PHE A 912 TRP 0.041 0.002 TRP E 945 HIS 0.007 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00494 (33826) covalent geometry : angle 0.66528 (46003) hydrogen bonds : bond 0.04615 ( 1282) hydrogen bonds : angle 6.00666 ( 3756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8925 (tpp) cc_final: 0.8719 (tpp) REVERT: B 708 MET cc_start: 0.9574 (mmp) cc_final: 0.9307 (mmp) REVERT: B 853 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6728 (t80) REVERT: A 417 MET cc_start: 0.8896 (pmm) cc_final: 0.8691 (pmm) REVERT: A 452 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7673 (pmm) REVERT: A 615 MET cc_start: 0.9381 (tpp) cc_final: 0.9099 (tpp) REVERT: A 681 MET cc_start: 0.8729 (ttm) cc_final: 0.8392 (mtt) REVERT: A 892 TYR cc_start: 0.7679 (p90) cc_final: 0.7405 (p90) REVERT: C 452 MET cc_start: 0.8747 (pmm) cc_final: 0.8496 (pmm) REVERT: C 681 MET cc_start: 0.9181 (mmp) cc_final: 0.8879 (mmp) REVERT: C 878 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8820 (tp) REVERT: D 341 TRP cc_start: 0.9206 (t60) cc_final: 0.8710 (t60) REVERT: D 412 MET cc_start: 0.8805 (mpp) cc_final: 0.8281 (mpp) REVERT: D 646 MET cc_start: 0.9367 (mpp) cc_final: 0.8786 (mpp) REVERT: D 708 MET cc_start: 0.9212 (mmp) cc_final: 0.8993 (mmp) REVERT: E 341 TRP cc_start: 0.9351 (t60) cc_final: 0.9106 (t60) REVERT: E 482 ASP cc_start: 0.8656 (m-30) cc_final: 0.8340 (m-30) REVERT: E 728 MET cc_start: 0.7407 (pmm) cc_final: 0.6749 (pmm) REVERT: F 335 TYR cc_start: 0.9516 (m-80) cc_final: 0.9201 (m-80) REVERT: F 341 TRP cc_start: 0.8080 (m100) cc_final: 0.7384 (m100) REVERT: F 666 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9144 (tm) REVERT: F 696 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7689 (ptpp) outliers start: 45 outliers final: 20 residues processed: 193 average time/residue: 0.2072 time to fit residues: 67.5609 Evaluate side-chains 181 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 696 LYS Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 237 optimal weight: 0.0980 chunk 268 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 349 optimal weight: 0.0070 chunk 81 optimal weight: 3.9990 chunk 352 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.0202 ------------------------------------------------------------------------------- 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 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS C 323 ASN D 869 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 792 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.073251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.053620 restraints weight = 208837.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.054778 restraints weight = 123972.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.055480 restraints weight = 91011.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.055942 restraints weight = 76027.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.056123 restraints weight = 68159.313| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1724 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= 0.119 Angle : 0.609 12.974 46003 Z= 0.311 Chirality : 0.042 0.150 4826 Planarity : 0.004 0.061 5717 Dihedral : 13.225 177.781 4661 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.45 % Favored : 91.32 % Rotamer: Outliers : 0.98 % Allowed : 13.30 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.14), residues: 3847 helix: 0.63 (0.13), residues: 1736 sheet: -0.66 (0.28), residues: 337 loop : -1.39 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 301 TYR 0.021 0.001 TYR D 398 PHE 0.023 0.001 PHE A 912 TRP 0.027 0.001 TRP B 321 HIS 0.008 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00255 (33826) covalent geometry : angle 0.60917 (46003) hydrogen bonds : bond 0.03974 ( 1282) hydrogen bonds : angle 5.57149 ( 3756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8987 (tpp) cc_final: 0.8728 (tpp) REVERT: B 666 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8510 (pp) REVERT: B 853 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6673 (t80) REVERT: A 452 MET cc_start: 0.7852 (pmm) cc_final: 0.7561 (pmm) REVERT: A 615 MET cc_start: 0.9451 (tpp) cc_final: 0.9177 (tpp) REVERT: C 452 MET cc_start: 0.8690 (pmm) cc_final: 0.8462 (pmm) REVERT: C 878 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8714 (tp) REVERT: D 341 TRP cc_start: 0.9180 (t60) cc_final: 0.8735 (t60) REVERT: D 412 MET cc_start: 0.8736 (mpp) cc_final: 0.8139 (mpp) REVERT: D 426 MET cc_start: 0.8228 (tmm) cc_final: 0.7855 (tmm) REVERT: D 646 MET cc_start: 0.9395 (mpp) cc_final: 0.8798 (mpp) REVERT: D 708 MET cc_start: 0.9129 (mmp) cc_final: 0.8882 (mmp) REVERT: D 869 ASN cc_start: 0.9376 (OUTLIER) cc_final: 0.8990 (m110) REVERT: E 335 TYR cc_start: 0.8743 (m-80) cc_final: 0.8506 (m-80) REVERT: E 341 TRP cc_start: 0.9287 (t60) cc_final: 0.8906 (t60) REVERT: E 417 MET cc_start: 0.8927 (pmm) cc_final: 0.8610 (pmm) REVERT: E 482 ASP cc_start: 0.8700 (m-30) cc_final: 0.8366 (m-30) REVERT: E 728 MET cc_start: 0.7605 (pmm) cc_final: 0.7018 (pmm) REVERT: E 753 LEU cc_start: 0.9506 (mt) cc_final: 0.8998 (mt) REVERT: F 335 TYR cc_start: 0.9509 (m-80) cc_final: 0.9173 (m-80) REVERT: F 341 TRP cc_start: 0.8036 (m100) cc_final: 0.7260 (m100) REVERT: F 666 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9026 (tm) REVERT: F 696 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7678 (ptpp) outliers start: 34 outliers final: 19 residues processed: 194 average time/residue: 0.2074 time to fit residues: 69.1365 Evaluate side-chains 180 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 820 THR Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 696 LYS Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 235 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 252 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 334 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 371 optimal weight: 6.9990 chunk 375 optimal weight: 0.8980 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 792 ASN B 812 GLN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 916 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.077064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.056256 restraints weight = 236724.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.056312 restraints weight = 147947.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.056744 restraints weight = 113662.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.056976 restraints weight = 100542.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.057093 restraints weight = 93836.605| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33826 Z= 0.243 Angle : 0.673 12.438 46003 Z= 0.349 Chirality : 0.042 0.163 4826 Planarity : 0.004 0.060 5717 Dihedral : 13.249 177.765 4657 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.15 % Favored : 90.64 % Rotamer: Outliers : 1.84 % Allowed : 14.36 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.14), residues: 3847 helix: 0.58 (0.13), residues: 1750 sheet: -0.70 (0.28), residues: 343 loop : -1.54 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 670 TYR 0.023 0.002 TYR D 416 PHE 0.036 0.002 PHE D 838 TRP 0.030 0.002 TRP E 945 HIS 0.007 0.001 HIS D 383 Details of bonding type rmsd covalent geometry : bond 0.00523 (33826) covalent geometry : angle 0.67333 (46003) hydrogen bonds : bond 0.04186 ( 1282) hydrogen bonds : angle 5.74645 ( 3756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 159 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8905 (tpp) cc_final: 0.8690 (tpp) REVERT: B 666 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8578 (pp) REVERT: B 853 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.7033 (t80) REVERT: A 452 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7763 (pmm) REVERT: A 615 MET cc_start: 0.9411 (tpp) cc_final: 0.9117 (tpp) REVERT: A 653 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9152 (tt) REVERT: C 452 MET cc_start: 0.8839 (pmm) cc_final: 0.8580 (pmm) REVERT: C 681 MET cc_start: 0.9135 (mmp) cc_final: 0.8886 (mmp) REVERT: C 700 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8842 (pp) REVERT: D 290 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7355 (tp) REVERT: D 341 TRP cc_start: 0.9186 (t60) cc_final: 0.8555 (t60) REVERT: D 412 MET cc_start: 0.8874 (mpp) cc_final: 0.8265 (mpp) REVERT: D 426 MET cc_start: 0.8179 (tmm) cc_final: 0.7940 (tmm) REVERT: D 646 MET cc_start: 0.9382 (mpp) cc_final: 0.8781 (mpp) REVERT: D 708 MET cc_start: 0.9285 (mmp) cc_final: 0.8974 (mmp) REVERT: E 482 ASP cc_start: 0.8673 (m-30) cc_final: 0.8360 (m-30) REVERT: E 728 MET cc_start: 0.7503 (pmm) cc_final: 0.6706 (pmm) REVERT: F 335 TYR cc_start: 0.9522 (m-80) cc_final: 0.9224 (m-80) REVERT: F 341 TRP cc_start: 0.8116 (m100) cc_final: 0.7375 (m100) REVERT: F 435 ASP cc_start: 0.8801 (p0) cc_final: 0.8461 (p0) REVERT: F 651 MET cc_start: 0.9103 (tpp) cc_final: 0.8755 (tpp) REVERT: F 666 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9194 (tm) REVERT: F 696 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7739 (ptpp) outliers start: 64 outliers final: 39 residues processed: 207 average time/residue: 0.2017 time to fit residues: 71.3688 Evaluate side-chains 205 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 425 MET Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 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 892 TYR 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 417 MET 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 F residue 362 TRP Chi-restraints excluded: chain F residue 662 ASN Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 696 LYS Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 214 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 70 optimal weight: 0.0040 chunk 37 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 337 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 chunk 215 optimal weight: 0.5980 chunk 361 optimal weight: 0.6980 overall best weight: 1.4594 ------------------------------------------------------------------------------- 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** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 581 HIS E 695 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.078573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.058747 restraints weight = 235154.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.058473 restraints weight = 144956.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.058886 restraints weight = 109681.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.059126 restraints weight = 95606.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.059208 restraints weight = 89932.355| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 33826 Z= 0.129 Angle : 0.629 12.118 46003 Z= 0.319 Chirality : 0.042 0.170 4826 Planarity : 0.004 0.053 5717 Dihedral : 13.181 179.423 4657 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.40 % Favored : 91.40 % Rotamer: Outliers : 1.55 % Allowed : 15.71 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.14), residues: 3847 helix: 0.67 (0.13), residues: 1751 sheet: -0.65 (0.29), residues: 328 loop : -1.42 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 670 TYR 0.020 0.001 TYR B 866 PHE 0.025 0.001 PHE D 838 TRP 0.027 0.001 TRP B 321 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00286 (33826) covalent geometry : angle 0.62945 (46003) hydrogen bonds : bond 0.03860 ( 1282) hydrogen bonds : angle 5.44741 ( 3756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8912 (tpp) cc_final: 0.8665 (tpp) REVERT: B 666 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 708 MET cc_start: 0.9560 (mmp) cc_final: 0.9324 (mmp) REVERT: B 745 THR cc_start: 0.9584 (OUTLIER) cc_final: 0.9364 (p) REVERT: B 853 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.7184 (t80) REVERT: A 452 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7693 (pmm) REVERT: A 615 MET cc_start: 0.9401 (tpp) cc_final: 0.9113 (tpp) REVERT: A 653 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9088 (tt) REVERT: C 452 MET cc_start: 0.8755 (pmm) cc_final: 0.8534 (pmm) REVERT: C 681 MET cc_start: 0.9056 (mmp) cc_final: 0.8737 (mmp) REVERT: C 728 MET cc_start: 0.8505 (ppp) cc_final: 0.8287 (ppp) REVERT: D 341 TRP cc_start: 0.9153 (t60) cc_final: 0.8663 (t60) REVERT: D 412 MET cc_start: 0.8857 (mpp) cc_final: 0.8214 (mpp) REVERT: D 426 MET cc_start: 0.8160 (tmm) cc_final: 0.7811 (tmm) REVERT: D 477 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8553 (m-80) REVERT: D 646 MET cc_start: 0.9380 (mpp) cc_final: 0.8818 (mpp) REVERT: D 708 MET cc_start: 0.9253 (mmp) cc_final: 0.8906 (mmp) REVERT: E 335 TYR cc_start: 0.8737 (m-80) cc_final: 0.8479 (m-80) REVERT: E 341 TRP cc_start: 0.9192 (t60) cc_final: 0.8911 (t60) REVERT: E 482 ASP cc_start: 0.8624 (m-30) cc_final: 0.8308 (m-30) REVERT: E 581 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.8230 (p-80) REVERT: E 728 MET cc_start: 0.7551 (pmm) cc_final: 0.6761 (pmm) REVERT: E 753 LEU cc_start: 0.9482 (mt) cc_final: 0.8982 (mt) REVERT: F 335 TYR cc_start: 0.9521 (m-80) cc_final: 0.9183 (m-10) REVERT: F 341 TRP cc_start: 0.8075 (m100) cc_final: 0.7360 (m100) REVERT: F 435 ASP cc_start: 0.8811 (p0) cc_final: 0.8556 (p0) REVERT: F 651 MET cc_start: 0.9102 (tpp) cc_final: 0.8725 (tpp) REVERT: F 666 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9132 (tm) outliers start: 54 outliers final: 33 residues processed: 204 average time/residue: 0.2028 time to fit residues: 70.5771 Evaluate side-chains 199 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 521 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 477 PHE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 581 HIS Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 662 ASN Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 93 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 378 optimal weight: 0.6980 chunk 314 optimal weight: 0.2980 chunk 154 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 346 optimal weight: 4.9990 chunk 370 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 360 optimal weight: 20.0000 chunk 289 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** C 695 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 581 HIS ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.078140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.058134 restraints weight = 182612.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.059151 restraints weight = 119722.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.059831 restraints weight = 93158.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.060197 restraints weight = 80934.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.060380 restraints weight = 75191.054| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 33826 Z= 0.115 Angle : 0.626 14.589 46003 Z= 0.315 Chirality : 0.041 0.191 4826 Planarity : 0.004 0.054 5717 Dihedral : 13.098 179.307 4657 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.47 % Favored : 91.29 % Rotamer: Outliers : 1.78 % Allowed : 15.80 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.14), residues: 3847 helix: 0.73 (0.13), residues: 1753 sheet: -0.51 (0.29), residues: 314 loop : -1.38 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 529 TYR 0.031 0.001 TYR A 853 PHE 0.023 0.001 PHE A 912 TRP 0.026 0.001 TRP B 321 HIS 0.038 0.001 HIS E 581 Details of bonding type rmsd covalent geometry : bond 0.00254 (33826) covalent geometry : angle 0.62597 (46003) hydrogen bonds : bond 0.03621 ( 1282) hydrogen bonds : angle 5.30230 ( 3756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8872 (tpp) cc_final: 0.8625 (tpp) REVERT: B 631 MET cc_start: 0.8436 (tpt) cc_final: 0.7985 (tpp) REVERT: B 666 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8551 (pp) REVERT: B 745 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9329 (p) REVERT: B 853 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7133 (t80) REVERT: A 452 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7624 (pmm) REVERT: A 615 MET cc_start: 0.9544 (tpp) cc_final: 0.9294 (tpp) REVERT: C 452 MET cc_start: 0.8770 (pmm) cc_final: 0.8524 (pmm) REVERT: C 475 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8182 (mm-30) REVERT: C 728 MET cc_start: 0.8399 (ppp) cc_final: 0.8184 (ppp) REVERT: D 290 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7497 (tp) REVERT: D 341 TRP cc_start: 0.9004 (t60) cc_final: 0.8398 (t60) REVERT: D 412 MET cc_start: 0.8710 (mpp) cc_final: 0.8156 (mpp) REVERT: D 426 MET cc_start: 0.8258 (tmm) cc_final: 0.7800 (tmm) REVERT: D 477 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: D 646 MET cc_start: 0.9329 (mpp) cc_final: 0.8751 (mpp) REVERT: D 708 MET cc_start: 0.9157 (mmp) cc_final: 0.8914 (mmp) REVERT: E 335 TYR cc_start: 0.8785 (m-80) cc_final: 0.8426 (m-80) REVERT: E 482 ASP cc_start: 0.8641 (m-30) cc_final: 0.8312 (m-30) REVERT: E 728 MET cc_start: 0.7917 (pmm) cc_final: 0.7231 (pmm) REVERT: E 753 LEU cc_start: 0.9512 (mt) cc_final: 0.9042 (mt) REVERT: F 335 TYR cc_start: 0.9516 (m-80) cc_final: 0.9107 (m-10) REVERT: F 341 TRP cc_start: 0.8084 (m100) cc_final: 0.7405 (m100) REVERT: F 435 ASP cc_start: 0.8806 (p0) cc_final: 0.8487 (p0) REVERT: F 651 MET cc_start: 0.9097 (tpp) cc_final: 0.8733 (tpp) REVERT: F 666 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9023 (tm) outliers start: 62 outliers final: 32 residues processed: 215 average time/residue: 0.1972 time to fit residues: 72.9762 Evaluate side-chains 198 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 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 694 THR Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 243 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 325 optimal weight: 7.9990 chunk 337 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 254 optimal weight: 8.9990 chunk 368 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.077562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057691 restraints weight = 182523.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.058683 restraints weight = 120900.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059341 restraints weight = 94620.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.059693 restraints weight = 82846.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.059902 restraints weight = 76870.063| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33826 Z= 0.157 Angle : 0.650 11.950 46003 Z= 0.325 Chirality : 0.042 0.169 4826 Planarity : 0.004 0.055 5717 Dihedral : 13.075 177.236 4657 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.68 % Favored : 91.11 % Rotamer: Outliers : 1.64 % Allowed : 16.00 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.14), residues: 3847 helix: 0.76 (0.13), residues: 1765 sheet: -0.57 (0.29), residues: 323 loop : -1.39 (0.16), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 529 TYR 0.025 0.001 TYR A 853 PHE 0.022 0.001 PHE A 912 TRP 0.025 0.001 TRP B 321 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00346 (33826) covalent geometry : angle 0.64998 (46003) hydrogen bonds : bond 0.03671 ( 1282) hydrogen bonds : angle 5.35035 ( 3756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8905 (tpp) cc_final: 0.8643 (tpp) REVERT: B 631 MET cc_start: 0.8115 (tpt) cc_final: 0.7458 (tpt) REVERT: B 666 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8620 (pp) REVERT: B 745 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9362 (p) REVERT: B 853 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.7291 (t80) REVERT: A 452 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7660 (pmm) REVERT: A 615 MET cc_start: 0.9557 (tpp) cc_final: 0.9295 (tpp) REVERT: A 631 MET cc_start: 0.8565 (tpp) cc_final: 0.8150 (tpp) REVERT: C 340 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8822 (tp30) REVERT: C 452 MET cc_start: 0.8800 (pmm) cc_final: 0.8553 (pmm) REVERT: C 728 MET cc_start: 0.8430 (ppp) cc_final: 0.8213 (ppp) REVERT: D 290 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7462 (tp) REVERT: D 341 TRP cc_start: 0.8993 (t60) cc_final: 0.8407 (t60) REVERT: D 412 MET cc_start: 0.8725 (mpp) cc_final: 0.8191 (mpp) REVERT: D 426 MET cc_start: 0.8236 (tmm) cc_final: 0.7928 (tmm) REVERT: D 477 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8726 (m-80) REVERT: D 646 MET cc_start: 0.9304 (mpp) cc_final: 0.9016 (mpp) REVERT: D 708 MET cc_start: 0.9135 (mmp) cc_final: 0.8860 (mmp) REVERT: E 335 TYR cc_start: 0.8808 (m-80) cc_final: 0.8431 (m-80) REVERT: E 482 ASP cc_start: 0.8681 (m-30) cc_final: 0.8363 (m-30) REVERT: E 728 MET cc_start: 0.7855 (pmm) cc_final: 0.7185 (pmm) REVERT: E 732 MET cc_start: 0.8821 (mmm) cc_final: 0.8614 (mmm) REVERT: E 753 LEU cc_start: 0.9494 (mt) cc_final: 0.9005 (mt) REVERT: F 335 TYR cc_start: 0.9516 (m-80) cc_final: 0.9113 (m-10) REVERT: F 341 TRP cc_start: 0.8132 (m100) cc_final: 0.7435 (m100) REVERT: F 435 ASP cc_start: 0.8849 (p0) cc_final: 0.8545 (p0) REVERT: F 651 MET cc_start: 0.9127 (tpp) cc_final: 0.8773 (tpp) REVERT: F 666 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9043 (tm) outliers start: 57 outliers final: 41 residues processed: 202 average time/residue: 0.2052 time to fit residues: 71.5649 Evaluate side-chains 209 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 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 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 477 PHE Chi-restraints excluded: chain D residue 900 THR Chi-restraints excluded: chain E residue 417 MET 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 723 GLN Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 662 ASN Chi-restraints excluded: chain F residue 666 LEU Chi-restraints excluded: chain F residue 672 THR Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 892 TYR Chi-restraints excluded: chain F residue 900 THR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 308 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 352 optimal weight: 0.7980 chunk 93 optimal weight: 0.0970 chunk 248 optimal weight: 2.9990 chunk 289 optimal weight: 0.2980 chunk 204 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 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** ** 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 = 0.3732 r_free = 0.3732 target = 0.078101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.058217 restraints weight = 181538.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059259 restraints weight = 119376.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.059957 restraints weight = 92890.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.060333 restraints weight = 80602.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.060536 restraints weight = 74956.522| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 33826 Z= 0.114 Angle : 0.645 12.092 46003 Z= 0.320 Chirality : 0.041 0.173 4826 Planarity : 0.004 0.055 5717 Dihedral : 13.020 177.356 4657 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 : 1.46 % Allowed : 16.28 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.14), residues: 3847 helix: 0.79 (0.13), residues: 1753 sheet: -0.69 (0.27), residues: 365 loop : -1.30 (0.16), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 529 TYR 0.026 0.001 TYR A 853 PHE 0.029 0.001 PHE D 342 TRP 0.027 0.001 TRP B 321 HIS 0.011 0.001 HIS E 304 Details of bonding type rmsd covalent geometry : bond 0.00253 (33826) covalent geometry : angle 0.64543 (46003) hydrogen bonds : bond 0.03497 ( 1282) hydrogen bonds : angle 5.20815 ( 3756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8833 (tpp) cc_final: 0.8577 (tpp) REVERT: B 631 MET cc_start: 0.8163 (tpt) cc_final: 0.7414 (tpt) REVERT: B 666 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8608 (pp) REVERT: B 745 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9286 (p) REVERT: B 853 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7289 (t80) REVERT: A 452 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7559 (pmm) REVERT: A 615 MET cc_start: 0.9524 (tpp) cc_final: 0.9268 (tpp) REVERT: A 631 MET cc_start: 0.8607 (tpp) cc_final: 0.8126 (tpp) REVERT: C 340 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8844 (tp30) REVERT: C 452 MET cc_start: 0.8741 (pmm) cc_final: 0.8498 (pmm) REVERT: C 475 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8209 (mm-30) REVERT: C 653 LEU cc_start: 0.9450 (tp) cc_final: 0.9234 (tp) REVERT: C 728 MET cc_start: 0.8376 (ppp) cc_final: 0.8135 (ppp) REVERT: D 290 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7411 (tp) REVERT: D 341 TRP cc_start: 0.9001 (t60) cc_final: 0.8441 (t60) REVERT: D 412 MET cc_start: 0.8640 (mpp) cc_final: 0.8112 (mpp) REVERT: D 426 MET cc_start: 0.8122 (tmm) cc_final: 0.7862 (tmm) REVERT: D 477 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8680 (m-80) REVERT: D 646 MET cc_start: 0.9300 (mpp) cc_final: 0.9013 (mpp) REVERT: D 708 MET cc_start: 0.9075 (mmp) cc_final: 0.8802 (mmp) REVERT: E 335 TYR cc_start: 0.8760 (m-80) cc_final: 0.8365 (m-80) REVERT: E 482 ASP cc_start: 0.8578 (m-30) cc_final: 0.8253 (m-30) REVERT: E 728 MET cc_start: 0.7833 (pmm) cc_final: 0.7260 (pmm) REVERT: E 753 LEU cc_start: 0.9493 (mt) cc_final: 0.9002 (mt) REVERT: F 335 TYR cc_start: 0.9506 (m-80) cc_final: 0.9124 (m-10) REVERT: F 341 TRP cc_start: 0.8067 (m100) cc_final: 0.7399 (m100) REVERT: F 435 ASP cc_start: 0.8756 (p0) cc_final: 0.8458 (p0) REVERT: F 651 MET cc_start: 0.9049 (tpp) cc_final: 0.8683 (tpp) REVERT: F 666 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9037 (tm) outliers start: 51 outliers final: 38 residues processed: 200 average time/residue: 0.1981 time to fit residues: 68.3679 Evaluate side-chains 208 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 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 694 THR Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 314 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 945 TRP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 477 PHE Chi-restraints excluded: chain D residue 900 THR Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 417 MET 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 723 GLN Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 632 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 900 THR Chi-restraints excluded: chain F residue 945 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 51 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 168 optimal weight: 0.3980 chunk 225 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 chunk 358 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.075529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.054365 restraints weight = 217426.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.054790 restraints weight = 136208.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.055291 restraints weight = 104206.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.055585 restraints weight = 91264.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.055690 restraints weight = 84985.211| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33826 Z= 0.117 Angle : 0.647 13.716 46003 Z= 0.318 Chirality : 0.041 0.157 4826 Planarity : 0.004 0.055 5717 Dihedral : 12.957 177.329 4657 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.01 % Favored : 91.76 % 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 : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.14), residues: 3847 helix: 0.85 (0.13), residues: 1750 sheet: -0.60 (0.27), residues: 349 loop : -1.29 (0.16), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 529 TYR 0.025 0.001 TYR A 853 PHE 0.021 0.001 PHE A 912 TRP 0.028 0.001 TRP E 362 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00261 (33826) covalent geometry : angle 0.64656 (46003) hydrogen bonds : bond 0.03428 ( 1282) hydrogen bonds : angle 5.17138 ( 3756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8902 (tpp) cc_final: 0.8617 (tpp) REVERT: B 631 MET cc_start: 0.8470 (tpt) cc_final: 0.7596 (tpt) REVERT: B 666 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8676 (pp) REVERT: B 853 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7496 (t80) REVERT: A 452 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7544 (pmm) REVERT: A 615 MET cc_start: 0.9380 (tpp) cc_final: 0.9117 (tpp) REVERT: A 631 MET cc_start: 0.8547 (tpp) cc_final: 0.8064 (tpp) REVERT: C 452 MET cc_start: 0.8738 (pmm) cc_final: 0.8496 (pmm) REVERT: C 475 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8284 (mm-30) REVERT: C 653 LEU cc_start: 0.9420 (tp) cc_final: 0.9186 (tp) REVERT: C 728 MET cc_start: 0.8486 (ppp) cc_final: 0.8135 (ppp) REVERT: D 290 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7382 (tp) REVERT: D 341 TRP cc_start: 0.9114 (t60) cc_final: 0.8609 (t60) REVERT: D 412 MET cc_start: 0.8807 (mpp) cc_final: 0.8162 (mpp) REVERT: D 477 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8678 (m-80) REVERT: D 646 MET cc_start: 0.9346 (mpp) cc_final: 0.8752 (mpp) REVERT: D 708 MET cc_start: 0.9237 (mmp) cc_final: 0.8895 (mmp) REVERT: D 743 ASP cc_start: 0.9013 (t0) cc_final: 0.8659 (p0) REVERT: E 296 HIS cc_start: 0.8883 (m90) cc_final: 0.8481 (m-70) REVERT: E 335 TYR cc_start: 0.8854 (m-80) cc_final: 0.8555 (m-80) REVERT: E 482 ASP cc_start: 0.8661 (m-30) cc_final: 0.8317 (m-30) REVERT: E 728 MET cc_start: 0.7378 (pmm) cc_final: 0.6742 (pmm) REVERT: E 753 LEU cc_start: 0.9504 (mt) cc_final: 0.8996 (mt) REVERT: F 335 TYR cc_start: 0.9521 (m-80) cc_final: 0.9176 (m-10) REVERT: F 341 TRP cc_start: 0.8003 (m100) cc_final: 0.7368 (m100) REVERT: F 435 ASP cc_start: 0.8844 (p0) cc_final: 0.8608 (p0) REVERT: F 651 MET cc_start: 0.9078 (tpp) cc_final: 0.8701 (tpp) outliers start: 52 outliers final: 37 residues processed: 199 average time/residue: 0.2052 time to fit residues: 69.6067 Evaluate side-chains 205 residues out of total 3524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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 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 694 THR Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain C residue 376 ARG 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 417 MET 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 557 VAL Chi-restraints excluded: chain E residue 723 GLN Chi-restraints excluded: chain E residue 822 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 632 LEU 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 244 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 373 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.077666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.057177 restraints weight = 235803.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.057228 restraints weight = 144518.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.057652 restraints weight = 110609.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.057837 restraints weight = 97098.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.057943 restraints weight = 91412.903| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33826 Z= 0.182 Angle : 0.682 13.268 46003 Z= 0.339 Chirality : 0.042 0.209 4826 Planarity : 0.004 0.055 5717 Dihedral : 12.952 175.681 4655 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.97 % Favored : 90.82 % Rotamer: Outliers : 1.41 % Allowed : 16.63 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.14), residues: 3847 helix: 0.81 (0.13), residues: 1770 sheet: -0.55 (0.29), residues: 325 loop : -1.36 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 529 TYR 0.026 0.002 TYR A 853 PHE 0.035 0.001 PHE D 342 TRP 0.035 0.001 TRP E 362 HIS 0.007 0.001 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00398 (33826) covalent geometry : angle 0.68181 (46003) hydrogen bonds : bond 0.03665 ( 1282) hydrogen bonds : angle 5.33503 ( 3756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6904.62 seconds wall clock time: 120 minutes 21.10 seconds (7221.10 seconds total)