Starting phenix.real_space_refine on Fri Jun 27 05:45:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v60_42986/06_2025/8v60_42986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v60_42986/06_2025/8v60_42986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v60_42986/06_2025/8v60_42986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v60_42986/06_2025/8v60_42986.map" model { file = "/net/cci-nas-00/data/ceres_data/8v60_42986/06_2025/8v60_42986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v60_42986/06_2025/8v60_42986.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.025 sd= 0.199 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 K 9 8.98 5 P 20 5.49 5 S 192 5.16 5 C 20646 2.51 5 N 4728 2.21 5 O 5869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31464 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7212 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7212 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7212 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 7212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7212 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 642 Unusual residues: {' K': 6, 'AJP': 9, 'CLR': 1, 'POV': 6} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 909 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 660 Unusual residues: {' K': 1, 'AJP': 9, 'CLR': 1, 'POV': 8} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 807 Unresolved non-hydrogen dihedrals: 981 Unresolved non-hydrogen chiralities: 155 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 3, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 637 Unusual residues: {' K': 1, 'AJP': 9, 'CLR': 1, 'POV': 6} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 909 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 657 Unusual residues: {' K': 1, 'AJP': 9, 'CLR': 1, 'POV': 8} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 811 Unresolved non-hydrogen dihedrals: 983 Unresolved non-hydrogen chiralities: 155 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 18.70, per 1000 atoms: 0.59 Number of scatterers: 31464 At special positions: 0 Unit cell: (168.3, 168.3, 135, 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) K 9 19.00 S 192 16.00 P 20 15.00 O 5869 8.00 N 4728 7.00 C 20646 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: 7.80 Conformation dependent library (CDL) restraints added in 4.1 seconds 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6872 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 24 sheets defined 56.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.839A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 37 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.704A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 200 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.570A pdb=" N ARG A 210 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 260 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.541A pdb=" N GLU A 264 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 318 Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.533A pdb=" N ASN A 465 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 466 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A 467 " --> pdb=" O HIS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 523 through 533 removed outlier: 4.185A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.547A pdb=" N VAL A 546 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.974A pdb=" N ALA A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 767 removed outlier: 4.107A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.632A pdb=" N CYS A 797 " --> pdb=" O ILE A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 816 Processing helix chain 'A' and resid 817 through 830 removed outlier: 3.526A pdb=" N SER A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.998A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 892 removed outlier: 3.522A pdb=" N ASN A 887 " --> pdb=" O ASN A 884 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 892 " --> pdb=" O GLN A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 917 through 930 removed outlier: 4.102A pdb=" N ASP A 921 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 922 " --> pdb=" O SER A 918 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 4.019A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 972 Processing helix chain 'A' and resid 995 through 1008 removed outlier: 3.566A pdb=" N LEU A 999 " --> pdb=" O CYS A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1021 No H-bonds generated for 'chain 'A' and resid 1019 through 1021' Processing helix chain 'B' and resid 21 through 46 removed outlier: 3.855A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 37 " --> pdb=" O PHE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 148 through 170 Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.704A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 200 Proline residue: B 191 - end of helix Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.558A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 229 through 260 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 318 Processing helix chain 'B' and resid 318 through 327 Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 462 through 472 removed outlier: 3.503A pdb=" N ASN B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 466 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 467 " --> pdb=" O HIS B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 523 through 533 removed outlier: 4.186A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.549A pdb=" N VAL B 546 " --> pdb=" O SER B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 699 through 703 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 743 removed outlier: 3.974A pdb=" N ALA B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 747 through 751 Processing helix chain 'B' and resid 759 through 767 removed outlier: 4.107A pdb=" N ARG B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 766 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 793 through 797 removed outlier: 3.621A pdb=" N CYS B 797 " --> pdb=" O ILE B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 816 Processing helix chain 'B' and resid 817 through 830 removed outlier: 3.523A pdb=" N SER B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.999A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 removed outlier: 3.522A pdb=" N ASN B 887 " --> pdb=" O ASN B 884 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 892 " --> pdb=" O GLN B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 918 through 930 removed outlier: 3.599A pdb=" N SER B 922 " --> pdb=" O SER B 918 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 942 removed outlier: 4.017A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 965 through 972 Processing helix chain 'B' and resid 995 through 1008 removed outlier: 3.560A pdb=" N LEU B 999 " --> pdb=" O CYS B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1021 No H-bonds generated for 'chain 'B' and resid 1019 through 1021' Processing helix chain 'C' and resid 21 through 46 removed outlier: 3.846A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU C 37 " --> pdb=" O PHE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 148 through 170 Processing helix chain 'C' and resid 173 through 179 removed outlier: 3.703A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.512A pdb=" N ARG C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 215 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 229 through 260 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 318 Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 462 through 472 removed outlier: 3.536A pdb=" N ASN C 465 " --> pdb=" O GLN C 462 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 466 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA C 467 " --> pdb=" O HIS C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.186A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.547A pdb=" N VAL C 546 " --> pdb=" O SER C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 603 through 605 No H-bonds generated for 'chain 'C' and resid 603 through 605' Processing helix chain 'C' and resid 606 through 611 Processing helix chain 'C' and resid 621 through 625 Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 743 removed outlier: 3.973A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 747 through 751 Processing helix chain 'C' and resid 759 through 767 removed outlier: 3.776A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 793 through 797 removed outlier: 3.632A pdb=" N CYS C 797 " --> pdb=" O ILE C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 816 Processing helix chain 'C' and resid 817 through 830 removed outlier: 3.524A pdb=" N SER C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 876 removed outlier: 3.998A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.535A pdb=" N ASN C 887 " --> pdb=" O ASN C 884 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 918 through 930 removed outlier: 3.598A pdb=" N SER C 922 " --> pdb=" O SER C 918 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 942 removed outlier: 4.017A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 965 through 972 Processing helix chain 'C' and resid 995 through 1008 removed outlier: 3.566A pdb=" N LEU C 999 " --> pdb=" O CYS C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'D' and resid 21 through 46 removed outlier: 3.829A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU D 37 " --> pdb=" O PHE D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 148 through 170 Processing helix chain 'D' and resid 173 through 179 removed outlier: 3.704A pdb=" N PHE D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 200 Proline residue: D 191 - end of helix Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.573A pdb=" N ARG D 210 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 229 through 260 Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.542A pdb=" N GLU D 264 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 318 Processing helix chain 'D' and resid 318 through 327 Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 462 through 472 removed outlier: 3.535A pdb=" N ASN D 465 " --> pdb=" O GLN D 462 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 466 " --> pdb=" O TYR D 463 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D 467 " --> pdb=" O HIS D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.185A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.546A pdb=" N VAL D 546 " --> pdb=" O SER D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 603 through 605 No H-bonds generated for 'chain 'D' and resid 603 through 605' Processing helix chain 'D' and resid 606 through 611 Processing helix chain 'D' and resid 621 through 625 Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.972A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 759 through 767 removed outlier: 4.107A pdb=" N ARG D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU D 766 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 793 through 797 removed outlier: 3.615A pdb=" N CYS D 797 " --> pdb=" O ILE D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 816 Processing helix chain 'D' and resid 817 through 830 removed outlier: 3.526A pdb=" N SER D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 876 removed outlier: 3.998A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 892 removed outlier: 3.523A pdb=" N ASN D 887 " --> pdb=" O ASN D 884 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP D 892 " --> pdb=" O GLN D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 917 through 930 removed outlier: 4.102A pdb=" N ASP D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 922 " --> pdb=" O SER D 918 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 942 removed outlier: 4.017A pdb=" N THR D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 965 through 972 Processing helix chain 'D' and resid 995 through 1008 removed outlier: 3.567A pdb=" N LEU D 999 " --> pdb=" O CYS D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1021 No H-bonds generated for 'chain 'D' and resid 1019 through 1021' Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 401 removed outlier: 6.778A pdb=" N LYS A 343 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL A 376 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A 421 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 540 removed outlier: 6.922A pdb=" N LEU A 594 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE A 568 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE A 596 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.382A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.419A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU A 803 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS A 722 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 975 through 981 removed outlier: 3.965A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AA8, first strand: chain 'B' and resid 398 through 401 removed outlier: 6.784A pdb=" N LYS B 343 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL B 376 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE B 345 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 378 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 347 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 421 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.923A pdb=" N LEU B 594 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE B 568 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 564 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.381A pdb=" N TYR B 686 " --> pdb=" O GLY B 962 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.416A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 720 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU B 803 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS B 722 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 975 through 981 removed outlier: 3.966A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB5, first strand: chain 'C' and resid 398 through 401 removed outlier: 6.778A pdb=" N LYS C 343 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL C 376 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 345 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU C 378 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C 347 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA C 421 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 535 through 540 removed outlier: 6.923A pdb=" N LEU C 594 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE C 568 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE C 596 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.382A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.420A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL C 720 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU C 803 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS C 722 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 975 through 981 removed outlier: 3.965A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AC2, first strand: chain 'D' and resid 398 through 401 removed outlier: 6.779A pdb=" N LYS D 343 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL D 376 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE D 345 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU D 378 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 347 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA D 421 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS D 422 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLN D 459 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE D 424 " --> pdb=" O GLN D 459 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 535 through 540 removed outlier: 6.923A pdb=" N LEU D 594 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE D 568 " --> pdb=" O LEU D 594 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE D 596 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 564 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.382A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.418A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU D 803 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N CYS D 722 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 975 through 981 removed outlier: 3.965A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1365 hydrogen bonds defined for protein. 3735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.31 Time building geometry restraints manager: 8.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4914 1.32 - 1.44: 8583 1.44 - 1.57: 18490 1.57 - 1.69: 40 1.69 - 1.81: 284 Bond restraints: 32311 Sorted by residual: bond pdb=" C21 POV D1107 " pdb=" O22 POV D1107 " ideal model delta sigma weight residual 1.205 1.332 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 POV A1110 " pdb=" O22 POV A1110 " ideal model delta sigma weight residual 1.205 1.331 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C21 POV C1105 " pdb=" O22 POV C1105 " ideal model delta sigma weight residual 1.205 1.330 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C21 POV A1110 " pdb=" O21 POV A1110 " ideal model delta sigma weight residual 1.330 1.205 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C21 POV D1107 " pdb=" O21 POV D1107 " ideal model delta sigma weight residual 1.330 1.205 0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 32306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 43832 3.02 - 6.03: 374 6.03 - 9.05: 0 9.05 - 12.07: 0 12.07 - 15.08: 10 Bond angle restraints: 44216 Sorted by residual: angle pdb=" C32 POV B1102 " pdb=" C31 POV B1102 " pdb=" O32 POV B1102 " ideal model delta sigma weight residual 125.74 110.66 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C32 POV B1102 " pdb=" C31 POV B1102 " pdb=" O31 POV B1102 " ideal model delta sigma weight residual 110.66 125.74 -15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C22 POV D1107 " pdb=" C21 POV D1107 " pdb=" O22 POV D1107 " ideal model delta sigma weight residual 125.44 111.12 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C22 POV D1107 " pdb=" C21 POV D1107 " pdb=" O21 POV D1107 " ideal model delta sigma weight residual 111.03 125.34 -14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C22 POV A1110 " pdb=" C21 POV A1110 " pdb=" O22 POV A1110 " ideal model delta sigma weight residual 125.44 111.15 14.29 3.00e+00 1.11e-01 2.27e+01 ... (remaining 44211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.20: 21182 25.20 - 50.41: 1029 50.41 - 75.61: 365 75.61 - 100.82: 170 100.82 - 126.02: 296 Dihedral angle restraints: 23042 sinusoidal: 12434 harmonic: 10608 Sorted by residual: dihedral pdb=" O31 AJP B1111 " pdb=" C30 AJP B1111 " pdb=" C32 AJP B1111 " pdb=" O33 AJP B1111 " ideal model delta sinusoidal sigma weight residual 177.28 -56.70 -126.02 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" O31 AJP C1109 " pdb=" C30 AJP C1109 " pdb=" C32 AJP C1109 " pdb=" O33 AJP C1109 " ideal model delta sinusoidal sigma weight residual 177.28 -57.22 -125.50 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C29 AJP B1111 " pdb=" C30 AJP B1111 " pdb=" C32 AJP B1111 " pdb=" O33 AJP B1111 " ideal model delta sinusoidal sigma weight residual -60.96 64.18 -125.14 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 23039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3851 0.045 - 0.091: 1139 0.091 - 0.136: 270 0.136 - 0.182: 88 0.182 - 0.227: 52 Chirality restraints: 5400 Sorted by residual: chirality pdb=" C22 AJP C1109 " pdb=" C21 AJP C1109 " pdb=" C23 AJP C1109 " pdb=" O79 AJP C1109 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C22 AJP A1114 " pdb=" C21 AJP A1114 " pdb=" C23 AJP A1114 " pdb=" O79 AJP A1114 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C35 AJP A1115 " pdb=" C36 AJP A1115 " pdb=" O34 AJP A1115 " pdb=" O40 AJP A1115 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 5397 not shown) Planarity restraints: 5089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 898 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO D 899 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 899 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 899 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 898 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO B 899 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 899 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 899 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 898 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO C 899 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 899 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 899 " -0.035 5.00e-02 4.00e+02 ... (remaining 5086 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.77: 6192 2.77 - 3.37: 33585 3.37 - 3.96: 58827 3.96 - 4.55: 82280 4.55 - 5.14: 122035 Nonbonded interactions: 302919 Sorted by model distance: nonbonded pdb=" NH2 ARG B 790 " pdb=" O GLN B 831 " model vdw 2.183 3.120 nonbonded pdb=" NH2 ARG D 790 " pdb=" O GLN D 831 " model vdw 2.183 3.120 nonbonded pdb=" NH2 ARG C 790 " pdb=" O GLN C 831 " model vdw 2.186 3.120 nonbonded pdb=" NH2 ARG A 790 " pdb=" O GLN A 831 " model vdw 2.186 3.120 nonbonded pdb=" OD1 ASP C 898 " pdb=" OG1 THR C 901 " model vdw 2.245 3.040 ... (remaining 302914 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 19 through 1057 or (resid 1106 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or (resid 1114 through 1117 and (na \ me C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 o \ r name C08 or name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24 or name C26 or name C27 or name C28 or name C29 o \ r name C30 or name C32 or name C80 or name C81 or name C83 or name C85 or name O \ 09 or name O25 or name O31 or name O33 or name O34 or name O77 or name O78 or na \ me O79 or name O82 or name O84)))) selection = (chain 'B' and (resid 19 through 1057 or (resid 1106 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or (resid 1114 through 1117 and (na \ me C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 o \ r name C08 or name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24 or name C26 or name C27 or name C28 or name C29 o \ r name C30 or name C32 or name C80 or name C81 or name C83 or name C85 or name O \ 09 or name O25 or name O31 or name O33 or name O34 or name O77 or name O78 or na \ me O79 or name O82 or name O84)))) selection = (chain 'C' and (resid 19 through 1057 or (resid 1106 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or (resid 1114 through 1117 and (na \ me C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 o \ r name C08 or name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24 or name C26 or name C27 or name C28 or name C29 o \ r name C30 or name C32 or name C80 or name C81 or name C83 or name C85 or name O \ 09 or name O25 or name O31 or name O33 or name O34 or name O77 or name O78 or na \ me O79 or name O82 or name O84)))) selection = (chain 'D' and (resid 19 through 1057 or (resid 1106 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or (resid 1114 through 1117 and (na \ me C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 o \ r name C08 or name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24 or name C26 or name C27 or name C28 or name C29 o \ r name C30 or name C32 or name C80 or name C81 or name C83 or name C85 or name O \ 09 or name O25 or name O31 or name O33 or name O34 or name O77 or name O78 or na \ me O79 or name O82 or name O84)))) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.350 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 69.010 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.120 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.005 0.127 32311 Z= 0.241 Angle : 0.685 15.083 44216 Z= 0.309 Chirality : 0.051 0.227 5400 Planarity : 0.004 0.065 5089 Dihedral : 23.399 126.025 16170 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3592 helix: 0.38 (0.13), residues: 1660 sheet: 0.21 (0.24), residues: 468 loop : 0.57 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 23 HIS 0.002 0.001 HIS A 394 PHE 0.016 0.002 PHE D 511 TYR 0.028 0.002 TYR B1015 ARG 0.004 0.000 ARG C 393 Details of bonding type rmsd hydrogen bonds : bond 0.15532 ( 1365) hydrogen bonds : angle 5.80787 ( 3735) covalent geometry : bond 0.00517 (32311) covalent geometry : angle 0.68474 (44216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 3.564 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.7804 (pmm) cc_final: 0.7515 (pmm) REVERT: A 151 GLN cc_start: 0.8310 (mt0) cc_final: 0.8032 (mt0) REVERT: A 166 LEU cc_start: 0.7125 (mp) cc_final: 0.6830 (tt) REVERT: A 182 ASN cc_start: 0.7273 (m-40) cc_final: 0.6944 (m-40) REVERT: A 216 GLN cc_start: 0.7396 (mt0) cc_final: 0.7015 (mm-40) REVERT: A 228 LYS cc_start: 0.8418 (mttt) cc_final: 0.7979 (mmtm) REVERT: A 265 ASN cc_start: 0.8556 (m-40) cc_final: 0.8189 (t0) REVERT: A 393 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7938 (mtm-85) REVERT: A 517 ILE cc_start: 0.8351 (mt) cc_final: 0.8093 (mm) REVERT: A 556 LEU cc_start: 0.8542 (mt) cc_final: 0.8313 (tt) REVERT: A 565 MET cc_start: 0.9343 (ttp) cc_final: 0.9098 (ttp) REVERT: A 601 ASP cc_start: 0.8192 (t70) cc_final: 0.7676 (t0) REVERT: A 603 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7789 (mtmm) REVERT: A 699 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8126 (mp0) REVERT: A 831 GLN cc_start: 0.8792 (mt0) cc_final: 0.8409 (mm-40) REVERT: A 871 THR cc_start: 0.7624 (t) cc_final: 0.7408 (t) REVERT: A 984 ASP cc_start: 0.7307 (p0) cc_final: 0.6858 (t0) REVERT: B 21 MET cc_start: 0.7820 (pmm) cc_final: 0.7215 (mpp) REVERT: B 151 GLN cc_start: 0.8307 (mt0) cc_final: 0.8000 (mt0) REVERT: B 166 LEU cc_start: 0.7134 (mp) cc_final: 0.6825 (tt) REVERT: B 182 ASN cc_start: 0.7282 (m-40) cc_final: 0.6924 (m-40) REVERT: B 216 GLN cc_start: 0.7396 (mt0) cc_final: 0.7045 (mm-40) REVERT: B 228 LYS cc_start: 0.8420 (mttt) cc_final: 0.7987 (mmtm) REVERT: B 265 ASN cc_start: 0.8627 (m-40) cc_final: 0.8200 (t0) REVERT: B 342 ARG cc_start: 0.7398 (ttm170) cc_final: 0.7090 (ttm170) REVERT: B 393 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: B 517 ILE cc_start: 0.8356 (mt) cc_final: 0.8068 (mm) REVERT: B 556 LEU cc_start: 0.8524 (mt) cc_final: 0.8301 (tt) REVERT: B 565 MET cc_start: 0.9346 (ttp) cc_final: 0.9100 (ttp) REVERT: B 601 ASP cc_start: 0.8215 (t70) cc_final: 0.7681 (t0) REVERT: B 603 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7775 (mtmm) REVERT: B 699 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8125 (mp0) REVERT: B 831 GLN cc_start: 0.8785 (mt0) cc_final: 0.8399 (mm-40) REVERT: B 871 THR cc_start: 0.7627 (t) cc_final: 0.7413 (t) REVERT: B 984 ASP cc_start: 0.7314 (p0) cc_final: 0.6861 (t0) REVERT: C 21 MET cc_start: 0.7823 (pmm) cc_final: 0.7524 (pmm) REVERT: C 151 GLN cc_start: 0.8307 (mt0) cc_final: 0.8013 (mt0) REVERT: C 166 LEU cc_start: 0.7129 (mp) cc_final: 0.6830 (tt) REVERT: C 182 ASN cc_start: 0.7278 (m-40) cc_final: 0.6958 (m-40) REVERT: C 216 GLN cc_start: 0.7404 (mt0) cc_final: 0.7020 (mm-40) REVERT: C 228 LYS cc_start: 0.8454 (mttt) cc_final: 0.8007 (mmtm) REVERT: C 265 ASN cc_start: 0.8567 (m-40) cc_final: 0.8197 (t0) REVERT: C 342 ARG cc_start: 0.7384 (ttm170) cc_final: 0.7064 (ttm170) REVERT: C 393 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7922 (mtm-85) REVERT: C 517 ILE cc_start: 0.8344 (mt) cc_final: 0.8094 (mm) REVERT: C 556 LEU cc_start: 0.8534 (mt) cc_final: 0.8308 (tt) REVERT: C 565 MET cc_start: 0.9343 (ttp) cc_final: 0.9095 (ttp) REVERT: C 601 ASP cc_start: 0.8176 (t70) cc_final: 0.7679 (t0) REVERT: C 603 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7775 (mtmm) REVERT: C 699 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8126 (mp0) REVERT: C 831 GLN cc_start: 0.8797 (mt0) cc_final: 0.8412 (mm-40) REVERT: C 871 THR cc_start: 0.7627 (t) cc_final: 0.7412 (t) REVERT: C 984 ASP cc_start: 0.7347 (p0) cc_final: 0.6857 (t0) REVERT: D 151 GLN cc_start: 0.8328 (mt0) cc_final: 0.8030 (mt0) REVERT: D 166 LEU cc_start: 0.7160 (mp) cc_final: 0.6858 (tt) REVERT: D 182 ASN cc_start: 0.7272 (m-40) cc_final: 0.6929 (m-40) REVERT: D 216 GLN cc_start: 0.7386 (mt0) cc_final: 0.7000 (mm-40) REVERT: D 228 LYS cc_start: 0.8449 (mttt) cc_final: 0.7995 (mmtm) REVERT: D 265 ASN cc_start: 0.8545 (m-40) cc_final: 0.8187 (t0) REVERT: D 342 ARG cc_start: 0.7387 (ttm170) cc_final: 0.7068 (ttm170) REVERT: D 393 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7925 (mtm-85) REVERT: D 517 ILE cc_start: 0.8350 (mt) cc_final: 0.8092 (mm) REVERT: D 556 LEU cc_start: 0.8534 (mt) cc_final: 0.8306 (tt) REVERT: D 565 MET cc_start: 0.9344 (ttp) cc_final: 0.9099 (ttp) REVERT: D 601 ASP cc_start: 0.8201 (t70) cc_final: 0.7691 (t0) REVERT: D 603 LYS cc_start: 0.8367 (mtpp) cc_final: 0.7804 (mtmm) REVERT: D 699 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8130 (mp0) REVERT: D 831 GLN cc_start: 0.8788 (mt0) cc_final: 0.8404 (mm-40) REVERT: D 871 THR cc_start: 0.7625 (t) cc_final: 0.7411 (t) REVERT: D 984 ASP cc_start: 0.7308 (p0) cc_final: 0.6859 (t0) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 1.2918 time to fit residues: 782.8461 Evaluate side-chains 318 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 745 ASN B 745 ASN C 745 ASN D 534 ASN D 745 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.156314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097355 restraints weight = 36086.765| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.10 r_work: 0.3036 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 32311 Z= 0.303 Angle : 0.823 9.095 44216 Z= 0.380 Chirality : 0.051 0.245 5400 Planarity : 0.006 0.057 5089 Dihedral : 17.285 123.280 9490 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.82 % Allowed : 6.94 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3592 helix: 0.49 (0.12), residues: 1680 sheet: 0.39 (0.24), residues: 456 loop : 0.51 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 23 HIS 0.005 0.001 HIS B 693 PHE 0.019 0.003 PHE B 159 TYR 0.022 0.003 TYR C 928 ARG 0.005 0.001 ARG C 413 Details of bonding type rmsd hydrogen bonds : bond 0.06937 ( 1365) hydrogen bonds : angle 5.03633 ( 3735) covalent geometry : bond 0.00744 (32311) covalent geometry : angle 0.82287 (44216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 353 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8086 (pmm) cc_final: 0.7679 (mmm) REVERT: A 151 GLN cc_start: 0.8337 (mt0) cc_final: 0.8046 (mt0) REVERT: A 182 ASN cc_start: 0.7615 (m-40) cc_final: 0.7357 (m-40) REVERT: A 216 GLN cc_start: 0.7628 (mt0) cc_final: 0.7039 (mm110) REVERT: A 265 ASN cc_start: 0.8591 (m-40) cc_final: 0.8224 (t0) REVERT: A 374 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8224 (tp30) REVERT: A 517 ILE cc_start: 0.8470 (mt) cc_final: 0.8236 (mm) REVERT: A 603 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8095 (mtmm) REVERT: A 712 MET cc_start: 0.8464 (mmm) cc_final: 0.8218 (mmp) REVERT: A 831 GLN cc_start: 0.8688 (mt0) cc_final: 0.8165 (mm110) REVERT: A 984 ASP cc_start: 0.7335 (p0) cc_final: 0.6962 (p0) REVERT: B 21 MET cc_start: 0.8135 (pmm) cc_final: 0.7764 (mmm) REVERT: B 151 GLN cc_start: 0.8416 (mt0) cc_final: 0.8129 (mt0) REVERT: B 182 ASN cc_start: 0.7644 (m-40) cc_final: 0.7392 (m-40) REVERT: B 216 GLN cc_start: 0.7650 (mt0) cc_final: 0.7068 (mm110) REVERT: B 265 ASN cc_start: 0.8597 (m-40) cc_final: 0.8169 (t0) REVERT: B 374 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8230 (mm-30) REVERT: B 517 ILE cc_start: 0.8513 (mt) cc_final: 0.8276 (mm) REVERT: B 603 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8107 (mtmm) REVERT: B 699 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8270 (mp0) REVERT: B 712 MET cc_start: 0.8456 (mmm) cc_final: 0.8212 (mmp) REVERT: B 831 GLN cc_start: 0.8702 (mt0) cc_final: 0.8176 (mm110) REVERT: B 984 ASP cc_start: 0.7307 (p0) cc_final: 0.6936 (p0) REVERT: C 21 MET cc_start: 0.7998 (pmm) cc_final: 0.7680 (mmm) REVERT: C 151 GLN cc_start: 0.8341 (mt0) cc_final: 0.8035 (mt0) REVERT: C 166 LEU cc_start: 0.6934 (mp) cc_final: 0.6694 (tt) REVERT: C 182 ASN cc_start: 0.7616 (m-40) cc_final: 0.7358 (m-40) REVERT: C 216 GLN cc_start: 0.7634 (mt0) cc_final: 0.7054 (mm110) REVERT: C 228 LYS cc_start: 0.8483 (mttt) cc_final: 0.7251 (pmtt) REVERT: C 265 ASN cc_start: 0.8598 (m-40) cc_final: 0.8189 (t0) REVERT: C 374 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8206 (mm-30) REVERT: C 517 ILE cc_start: 0.8510 (mt) cc_final: 0.8272 (mm) REVERT: C 603 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8100 (mtmm) REVERT: C 699 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8269 (mp0) REVERT: C 712 MET cc_start: 0.8471 (mmm) cc_final: 0.8228 (mmp) REVERT: C 831 GLN cc_start: 0.8715 (mt0) cc_final: 0.8190 (mm110) REVERT: C 900 ASP cc_start: 0.7977 (p0) cc_final: 0.7684 (p0) REVERT: C 984 ASP cc_start: 0.7346 (p0) cc_final: 0.6945 (p0) REVERT: D 151 GLN cc_start: 0.8350 (mt0) cc_final: 0.8041 (mt0) REVERT: D 182 ASN cc_start: 0.7621 (m-40) cc_final: 0.7350 (m-40) REVERT: D 216 GLN cc_start: 0.7617 (mt0) cc_final: 0.7039 (mm110) REVERT: D 265 ASN cc_start: 0.8562 (m-40) cc_final: 0.8210 (t0) REVERT: D 374 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8223 (mm-30) REVERT: D 517 ILE cc_start: 0.8508 (mt) cc_final: 0.8272 (mm) REVERT: D 601 ASP cc_start: 0.8397 (t70) cc_final: 0.7882 (t70) REVERT: D 603 LYS cc_start: 0.8474 (mtpp) cc_final: 0.7856 (mtmm) REVERT: D 699 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8278 (mp0) REVERT: D 712 MET cc_start: 0.8460 (mmm) cc_final: 0.8217 (mmp) REVERT: D 831 GLN cc_start: 0.8711 (mt0) cc_final: 0.8185 (mm-40) REVERT: D 984 ASP cc_start: 0.7380 (p0) cc_final: 0.6993 (p0) outliers start: 58 outliers final: 36 residues processed: 391 average time/residue: 2.0960 time to fit residues: 971.5071 Evaluate side-chains 359 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 323 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 1057 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 578 ARG Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1057 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1057 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 139 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 349 optimal weight: 5.9990 chunk 328 optimal weight: 0.0670 chunk 2 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS B 771 HIS C 379 HIS C 771 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.157536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.101014 restraints weight = 36358.661| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.46 r_work: 0.3039 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32311 Z= 0.185 Angle : 0.647 9.073 44216 Z= 0.304 Chirality : 0.044 0.312 5400 Planarity : 0.004 0.054 5089 Dihedral : 13.165 119.096 9490 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.35 % Allowed : 10.08 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.14), residues: 3592 helix: 0.76 (0.13), residues: 1680 sheet: 0.54 (0.24), residues: 456 loop : 0.55 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 23 HIS 0.003 0.001 HIS C 693 PHE 0.014 0.002 PHE D 511 TYR 0.013 0.002 TYR C 928 ARG 0.003 0.000 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.05542 ( 1365) hydrogen bonds : angle 4.83110 ( 3735) covalent geometry : bond 0.00449 (32311) covalent geometry : angle 0.64747 (44216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 341 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8052 (pmm) cc_final: 0.7656 (mmm) REVERT: A 104 MET cc_start: 0.7465 (tpp) cc_final: 0.7151 (tpt) REVERT: A 151 GLN cc_start: 0.8401 (mt0) cc_final: 0.8129 (mt0) REVERT: A 182 ASN cc_start: 0.7562 (m-40) cc_final: 0.7284 (m-40) REVERT: A 216 GLN cc_start: 0.7693 (mt0) cc_final: 0.7029 (mm110) REVERT: A 265 ASN cc_start: 0.8575 (m-40) cc_final: 0.8202 (t0) REVERT: A 517 ILE cc_start: 0.8431 (mt) cc_final: 0.8209 (mm) REVERT: A 601 ASP cc_start: 0.8306 (t70) cc_final: 0.7865 (t70) REVERT: A 603 LYS cc_start: 0.8401 (mtpp) cc_final: 0.7990 (mtmm) REVERT: A 831 GLN cc_start: 0.8526 (mt0) cc_final: 0.7965 (mm110) REVERT: A 960 ARG cc_start: 0.8566 (ttp-110) cc_final: 0.8225 (ttp80) REVERT: A 984 ASP cc_start: 0.7404 (p0) cc_final: 0.7016 (p0) REVERT: B 21 MET cc_start: 0.7996 (pmm) cc_final: 0.7615 (mmm) REVERT: B 104 MET cc_start: 0.7475 (tpp) cc_final: 0.7158 (tpt) REVERT: B 151 GLN cc_start: 0.8341 (mt0) cc_final: 0.8083 (mt0) REVERT: B 182 ASN cc_start: 0.7585 (m-40) cc_final: 0.7308 (m-40) REVERT: B 216 GLN cc_start: 0.7685 (mt0) cc_final: 0.7015 (mm110) REVERT: B 228 LYS cc_start: 0.8465 (mttt) cc_final: 0.7208 (pmtt) REVERT: B 265 ASN cc_start: 0.8563 (m-40) cc_final: 0.8125 (t0) REVERT: B 517 ILE cc_start: 0.8422 (mt) cc_final: 0.8195 (mm) REVERT: B 601 ASP cc_start: 0.8297 (t70) cc_final: 0.7854 (t70) REVERT: B 603 LYS cc_start: 0.8406 (mtpp) cc_final: 0.7992 (mtmm) REVERT: B 699 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8165 (mp0) REVERT: B 831 GLN cc_start: 0.8530 (mt0) cc_final: 0.7969 (mm110) REVERT: B 960 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8217 (ttp80) REVERT: B 984 ASP cc_start: 0.7388 (p0) cc_final: 0.7009 (p0) REVERT: C 21 MET cc_start: 0.8045 (pmm) cc_final: 0.7674 (mmm) REVERT: C 151 GLN cc_start: 0.8303 (mt0) cc_final: 0.8035 (mt0) REVERT: C 182 ASN cc_start: 0.7497 (m-40) cc_final: 0.7218 (m-40) REVERT: C 216 GLN cc_start: 0.7708 (mt0) cc_final: 0.7044 (mm110) REVERT: C 265 ASN cc_start: 0.8535 (m-40) cc_final: 0.8132 (t0) REVERT: C 517 ILE cc_start: 0.8423 (mt) cc_final: 0.8196 (mm) REVERT: C 601 ASP cc_start: 0.8304 (t70) cc_final: 0.7866 (t70) REVERT: C 603 LYS cc_start: 0.8407 (mtpp) cc_final: 0.7997 (mtmm) REVERT: C 699 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8171 (mp0) REVERT: C 831 GLN cc_start: 0.8538 (mt0) cc_final: 0.7978 (mm110) REVERT: C 960 ARG cc_start: 0.8568 (ttp-110) cc_final: 0.8222 (ttp80) REVERT: C 984 ASP cc_start: 0.7434 (p0) cc_final: 0.7048 (p0) REVERT: D 104 MET cc_start: 0.7420 (tpp) cc_final: 0.7121 (tpt) REVERT: D 151 GLN cc_start: 0.8323 (mt0) cc_final: 0.8052 (mt0) REVERT: D 182 ASN cc_start: 0.7498 (m-40) cc_final: 0.7206 (m-40) REVERT: D 216 GLN cc_start: 0.7694 (mt0) cc_final: 0.7031 (mm110) REVERT: D 265 ASN cc_start: 0.8586 (m-40) cc_final: 0.8217 (t0) REVERT: D 517 ILE cc_start: 0.8443 (mt) cc_final: 0.8209 (mm) REVERT: D 699 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8181 (mp0) REVERT: D 960 ARG cc_start: 0.8572 (ttp-110) cc_final: 0.8226 (ttp80) REVERT: D 984 ASP cc_start: 0.7443 (p0) cc_final: 0.7051 (p0) outliers start: 43 outliers final: 33 residues processed: 365 average time/residue: 1.4102 time to fit residues: 615.3309 Evaluate side-chains 362 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 329 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 578 ARG Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 980 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 356 optimal weight: 0.6980 chunk 171 optimal weight: 20.0000 chunk 335 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS A 771 HIS B 379 HIS B 771 HIS D 379 HIS D 771 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102719 restraints weight = 36584.391| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.52 r_work: 0.3060 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32311 Z= 0.140 Angle : 0.602 10.178 44216 Z= 0.280 Chirality : 0.042 0.339 5400 Planarity : 0.004 0.050 5089 Dihedral : 11.287 122.402 9490 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.79 % Allowed : 11.68 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3592 helix: 0.98 (0.13), residues: 1688 sheet: 0.50 (0.24), residues: 476 loop : 0.70 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 23 HIS 0.007 0.001 HIS C 771 PHE 0.015 0.001 PHE A 511 TYR 0.011 0.001 TYR A 928 ARG 0.003 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 1365) hydrogen bonds : angle 4.64893 ( 3735) covalent geometry : bond 0.00329 (32311) covalent geometry : angle 0.60182 (44216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 335 time to evaluate : 3.513 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.7453 (tpp) cc_final: 0.7172 (tpt) REVERT: A 151 GLN cc_start: 0.8335 (mt0) cc_final: 0.8088 (mt0) REVERT: A 182 ASN cc_start: 0.7581 (m-40) cc_final: 0.7279 (m-40) REVERT: A 216 GLN cc_start: 0.7724 (mt0) cc_final: 0.6979 (mm110) REVERT: A 265 ASN cc_start: 0.8590 (m-40) cc_final: 0.8218 (t0) REVERT: A 374 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8011 (mm-30) REVERT: A 479 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7251 (mm-30) REVERT: A 517 ILE cc_start: 0.8409 (mt) cc_final: 0.8206 (mm) REVERT: A 601 ASP cc_start: 0.8226 (t70) cc_final: 0.7930 (t70) REVERT: A 603 LYS cc_start: 0.8419 (mtpp) cc_final: 0.7988 (mtmm) REVERT: A 604 GLU cc_start: 0.8171 (mp0) cc_final: 0.7805 (pm20) REVERT: A 712 MET cc_start: 0.8340 (mmm) cc_final: 0.8127 (mmp) REVERT: A 960 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8195 (ttp-170) REVERT: A 984 ASP cc_start: 0.7440 (p0) cc_final: 0.7072 (p0) REVERT: B 21 MET cc_start: 0.8102 (pmm) cc_final: 0.7667 (mmm) REVERT: B 104 MET cc_start: 0.7361 (tpp) cc_final: 0.7084 (tpt) REVERT: B 151 GLN cc_start: 0.8297 (mt0) cc_final: 0.8059 (mt0) REVERT: B 182 ASN cc_start: 0.7547 (m-40) cc_final: 0.7227 (m-40) REVERT: B 216 GLN cc_start: 0.7727 (mt0) cc_final: 0.6955 (mm110) REVERT: B 265 ASN cc_start: 0.8528 (m-40) cc_final: 0.8133 (t0) REVERT: B 479 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7232 (mm-30) REVERT: B 517 ILE cc_start: 0.8398 (mt) cc_final: 0.8192 (mm) REVERT: B 601 ASP cc_start: 0.8222 (t70) cc_final: 0.7930 (t70) REVERT: B 603 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7985 (mtmm) REVERT: B 604 GLU cc_start: 0.8173 (mp0) cc_final: 0.7801 (pm20) REVERT: B 699 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8145 (mp0) REVERT: B 712 MET cc_start: 0.8349 (mmm) cc_final: 0.8103 (mmp) REVERT: B 900 ASP cc_start: 0.8040 (p0) cc_final: 0.7833 (p0) REVERT: B 960 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8192 (ttp-170) REVERT: B 984 ASP cc_start: 0.7459 (p0) cc_final: 0.7088 (p0) REVERT: C 104 MET cc_start: 0.7399 (tpp) cc_final: 0.7089 (tpt) REVERT: C 151 GLN cc_start: 0.8276 (mt0) cc_final: 0.8022 (mt0) REVERT: C 182 ASN cc_start: 0.7533 (m-40) cc_final: 0.7209 (m-40) REVERT: C 216 GLN cc_start: 0.7748 (mt0) cc_final: 0.6993 (mm110) REVERT: C 265 ASN cc_start: 0.8523 (m-40) cc_final: 0.8144 (t0) REVERT: C 479 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7249 (mm-30) REVERT: C 517 ILE cc_start: 0.8401 (mt) cc_final: 0.8191 (mm) REVERT: C 601 ASP cc_start: 0.8225 (t70) cc_final: 0.7934 (t70) REVERT: C 603 LYS cc_start: 0.8420 (mtpp) cc_final: 0.7981 (mtmm) REVERT: C 604 GLU cc_start: 0.8160 (mp0) cc_final: 0.7793 (pm20) REVERT: C 699 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8134 (mp0) REVERT: C 712 MET cc_start: 0.8345 (mmm) cc_final: 0.8093 (mmp) REVERT: C 960 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8179 (ttp-170) REVERT: C 984 ASP cc_start: 0.7480 (p0) cc_final: 0.7094 (p0) REVERT: D 104 MET cc_start: 0.7450 (tpp) cc_final: 0.7169 (tpt) REVERT: D 151 GLN cc_start: 0.8391 (mt0) cc_final: 0.8128 (mt0) REVERT: D 182 ASN cc_start: 0.7519 (m-40) cc_final: 0.7228 (m-40) REVERT: D 216 GLN cc_start: 0.7726 (mt0) cc_final: 0.6982 (mm110) REVERT: D 265 ASN cc_start: 0.8565 (m-40) cc_final: 0.8207 (t0) REVERT: D 517 ILE cc_start: 0.8392 (mt) cc_final: 0.8187 (mm) REVERT: D 604 GLU cc_start: 0.8194 (mp0) cc_final: 0.7813 (pm20) REVERT: D 699 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8159 (mp0) REVERT: D 712 MET cc_start: 0.8327 (mmm) cc_final: 0.8086 (mmp) REVERT: D 900 ASP cc_start: 0.8050 (p0) cc_final: 0.7793 (p0) REVERT: D 960 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.8195 (ttp-170) REVERT: D 984 ASP cc_start: 0.7450 (p0) cc_final: 0.7080 (p0) outliers start: 57 outliers final: 42 residues processed: 370 average time/residue: 1.3398 time to fit residues: 592.2143 Evaluate side-chains 364 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 322 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 578 ARG Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 980 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 156 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 182 optimal weight: 20.0000 chunk 350 optimal weight: 20.0000 chunk 314 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 323 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS B 771 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.160665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104920 restraints weight = 36562.143| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.57 r_work: 0.3094 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32311 Z= 0.106 Angle : 0.543 9.417 44216 Z= 0.254 Chirality : 0.040 0.311 5400 Planarity : 0.004 0.049 5089 Dihedral : 9.898 123.160 9490 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.60 % Allowed : 12.44 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 3592 helix: 1.27 (0.13), residues: 1676 sheet: 0.51 (0.24), residues: 492 loop : 0.71 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 23 HIS 0.006 0.001 HIS D 771 PHE 0.027 0.001 PHE C 159 TYR 0.010 0.001 TYR C 279 ARG 0.004 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 1365) hydrogen bonds : angle 4.48785 ( 3735) covalent geometry : bond 0.00233 (32311) covalent geometry : angle 0.54322 (44216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 329 time to evaluate : 3.116 Fit side-chains REVERT: A 21 MET cc_start: 0.7637 (mpp) cc_final: 0.6744 (mmm) REVERT: A 104 MET cc_start: 0.7501 (tpp) cc_final: 0.7198 (tpt) REVERT: A 151 GLN cc_start: 0.8269 (mt0) cc_final: 0.8023 (mt0) REVERT: A 182 ASN cc_start: 0.7453 (m-40) cc_final: 0.7146 (m-40) REVERT: A 216 GLN cc_start: 0.7655 (mt0) cc_final: 0.6894 (mm110) REVERT: A 265 ASN cc_start: 0.8595 (m-40) cc_final: 0.8223 (t0) REVERT: A 324 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7162 (mt-10) REVERT: A 374 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7992 (mm-30) REVERT: A 479 GLU cc_start: 0.7833 (mm-30) cc_final: 0.6660 (pp20) REVERT: A 601 ASP cc_start: 0.8257 (t70) cc_final: 0.7834 (t70) REVERT: A 603 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8002 (mtmm) REVERT: A 960 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8183 (ttp80) REVERT: A 984 ASP cc_start: 0.7457 (p0) cc_final: 0.7112 (p0) REVERT: B 21 MET cc_start: 0.8037 (pmm) cc_final: 0.7630 (mpp) REVERT: B 23 TRP cc_start: 0.7442 (p90) cc_final: 0.7060 (p90) REVERT: B 104 MET cc_start: 0.7505 (tpp) cc_final: 0.7219 (tpt) REVERT: B 151 GLN cc_start: 0.8275 (mt0) cc_final: 0.8014 (mt0) REVERT: B 182 ASN cc_start: 0.7435 (m-40) cc_final: 0.7144 (m-40) REVERT: B 216 GLN cc_start: 0.7670 (mt0) cc_final: 0.6908 (mm110) REVERT: B 265 ASN cc_start: 0.8527 (m-40) cc_final: 0.8134 (t0) REVERT: B 324 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7207 (mt-10) REVERT: B 479 GLU cc_start: 0.7833 (mm-30) cc_final: 0.6669 (pp20) REVERT: B 699 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8127 (mp0) REVERT: B 960 ARG cc_start: 0.8539 (ttp-110) cc_final: 0.8170 (ttp80) REVERT: B 984 ASP cc_start: 0.7462 (p0) cc_final: 0.7115 (p0) REVERT: C 21 MET cc_start: 0.7628 (mpp) cc_final: 0.6714 (mmm) REVERT: C 104 MET cc_start: 0.7500 (tpp) cc_final: 0.7243 (tpt) REVERT: C 151 GLN cc_start: 0.8255 (mt0) cc_final: 0.7993 (mt0) REVERT: C 182 ASN cc_start: 0.7433 (m-40) cc_final: 0.7157 (m-40) REVERT: C 216 GLN cc_start: 0.7656 (mt0) cc_final: 0.6885 (mm110) REVERT: C 265 ASN cc_start: 0.8531 (m-40) cc_final: 0.8147 (t0) REVERT: C 324 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7143 (mt-10) REVERT: C 479 GLU cc_start: 0.7850 (mm-30) cc_final: 0.6662 (pp20) REVERT: C 699 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8096 (mp0) REVERT: C 960 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8175 (ttp80) REVERT: C 984 ASP cc_start: 0.7488 (p0) cc_final: 0.7117 (p0) REVERT: D 104 MET cc_start: 0.7543 (tpp) cc_final: 0.7267 (tpt) REVERT: D 151 GLN cc_start: 0.8294 (mt0) cc_final: 0.8048 (mt0) REVERT: D 182 ASN cc_start: 0.7441 (m-40) cc_final: 0.7137 (m-40) REVERT: D 216 GLN cc_start: 0.7604 (mt0) cc_final: 0.6840 (mm110) REVERT: D 265 ASN cc_start: 0.8555 (m-40) cc_final: 0.8209 (t0) REVERT: D 324 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7141 (mt-10) REVERT: D 699 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8132 (mp0) REVERT: D 960 ARG cc_start: 0.8534 (ttp-110) cc_final: 0.8161 (ttp80) REVERT: D 984 ASP cc_start: 0.7439 (p0) cc_final: 0.7092 (p0) outliers start: 51 outliers final: 33 residues processed: 356 average time/residue: 1.3166 time to fit residues: 562.6157 Evaluate side-chains 352 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 319 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 578 ARG Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 980 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 151 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 355 optimal weight: 0.4980 chunk 210 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 310 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS B 771 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105260 restraints weight = 36630.240| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.57 r_work: 0.3099 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32311 Z= 0.100 Angle : 0.511 7.377 44216 Z= 0.246 Chirality : 0.040 0.283 5400 Planarity : 0.004 0.048 5089 Dihedral : 9.401 121.795 9490 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.79 % Allowed : 12.91 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.14), residues: 3592 helix: 1.32 (0.13), residues: 1700 sheet: 0.63 (0.24), residues: 492 loop : 0.75 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 23 HIS 0.004 0.001 HIS C 771 PHE 0.016 0.001 PHE D 511 TYR 0.009 0.001 TYR C 279 ARG 0.003 0.000 ARG D 707 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 1365) hydrogen bonds : angle 4.38946 ( 3735) covalent geometry : bond 0.00220 (32311) covalent geometry : angle 0.51070 (44216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 330 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8234 (mt0) cc_final: 0.7986 (mt0) REVERT: A 182 ASN cc_start: 0.7410 (m-40) cc_final: 0.7127 (m-40) REVERT: A 216 GLN cc_start: 0.7734 (mt0) cc_final: 0.6962 (mm110) REVERT: A 265 ASN cc_start: 0.8604 (m-40) cc_final: 0.8233 (t0) REVERT: A 324 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7152 (mt-10) REVERT: A 374 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8009 (mm-30) REVERT: A 479 GLU cc_start: 0.7786 (mm-30) cc_final: 0.6775 (pp20) REVERT: A 603 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8268 (mtmm) REVERT: A 604 GLU cc_start: 0.8149 (mp0) cc_final: 0.7699 (pm20) REVERT: A 960 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.8281 (ttp80) REVERT: A 984 ASP cc_start: 0.7485 (p0) cc_final: 0.7147 (p0) REVERT: B 21 MET cc_start: 0.8052 (pmm) cc_final: 0.7544 (mmm) REVERT: B 151 GLN cc_start: 0.8252 (mt0) cc_final: 0.8008 (mt0) REVERT: B 182 ASN cc_start: 0.7493 (m-40) cc_final: 0.7189 (m-40) REVERT: B 216 GLN cc_start: 0.7734 (mt0) cc_final: 0.6969 (mm110) REVERT: B 265 ASN cc_start: 0.8532 (m-40) cc_final: 0.8149 (t0) REVERT: B 324 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7241 (mt-10) REVERT: B 479 GLU cc_start: 0.7813 (mm-30) cc_final: 0.6787 (pp20) REVERT: B 604 GLU cc_start: 0.8177 (mp0) cc_final: 0.7691 (pm20) REVERT: B 699 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8153 (mp0) REVERT: B 960 ARG cc_start: 0.8539 (ttp-110) cc_final: 0.8254 (ttp80) REVERT: B 984 ASP cc_start: 0.7492 (p0) cc_final: 0.7155 (p0) REVERT: C 104 MET cc_start: 0.7440 (tpp) cc_final: 0.7153 (tpt) REVERT: C 151 GLN cc_start: 0.8235 (mt0) cc_final: 0.7976 (mt0) REVERT: C 182 ASN cc_start: 0.7415 (m-40) cc_final: 0.7133 (m-40) REVERT: C 216 GLN cc_start: 0.7793 (mt0) cc_final: 0.7013 (mm110) REVERT: C 265 ASN cc_start: 0.8522 (m-40) cc_final: 0.8159 (t0) REVERT: C 324 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7137 (mt-10) REVERT: C 479 GLU cc_start: 0.7841 (mm-30) cc_final: 0.6793 (pp20) REVERT: C 604 GLU cc_start: 0.8167 (mp0) cc_final: 0.7681 (pm20) REVERT: C 699 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8110 (mp0) REVERT: C 960 ARG cc_start: 0.8560 (ttp-110) cc_final: 0.8273 (ttp80) REVERT: C 984 ASP cc_start: 0.7478 (p0) cc_final: 0.7116 (p0) REVERT: D 151 GLN cc_start: 0.8243 (mt0) cc_final: 0.7986 (mt0) REVERT: D 182 ASN cc_start: 0.7428 (m-40) cc_final: 0.7146 (m-40) REVERT: D 216 GLN cc_start: 0.7766 (mt0) cc_final: 0.6991 (mm110) REVERT: D 265 ASN cc_start: 0.8551 (m-40) cc_final: 0.8178 (t0) REVERT: D 324 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7145 (mt-10) REVERT: D 604 GLU cc_start: 0.8106 (mp0) cc_final: 0.7724 (pm20) REVERT: D 699 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8138 (mp0) REVERT: D 960 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.8264 (ttp80) REVERT: D 984 ASP cc_start: 0.7452 (p0) cc_final: 0.7115 (p0) outliers start: 57 outliers final: 34 residues processed: 367 average time/residue: 1.2909 time to fit residues: 567.6389 Evaluate side-chains 350 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 316 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 578 ARG Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 980 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 272 optimal weight: 0.4980 chunk 255 optimal weight: 0.1980 chunk 151 optimal weight: 0.0670 chunk 280 optimal weight: 5.9990 chunk 258 optimal weight: 0.7980 chunk 352 optimal weight: 3.9990 chunk 317 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 137 optimal weight: 0.0980 chunk 297 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS B 771 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.163007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107303 restraints weight = 36798.549| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.62 r_work: 0.3140 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32311 Z= 0.089 Angle : 0.483 7.808 44216 Z= 0.232 Chirality : 0.038 0.232 5400 Planarity : 0.004 0.047 5089 Dihedral : 8.931 117.995 9490 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.32 % Allowed : 13.60 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.14), residues: 3592 helix: 1.48 (0.13), residues: 1696 sheet: 0.73 (0.24), residues: 488 loop : 0.78 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 23 HIS 0.002 0.000 HIS D 771 PHE 0.029 0.001 PHE D 159 TYR 0.009 0.001 TYR C 528 ARG 0.004 0.000 ARG C 707 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 1365) hydrogen bonds : angle 4.25491 ( 3735) covalent geometry : bond 0.00185 (32311) covalent geometry : angle 0.48269 (44216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 3.376 Fit side-chains revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8236 (mt0) cc_final: 0.7950 (mt0) REVERT: A 182 ASN cc_start: 0.7428 (m-40) cc_final: 0.7141 (m-40) REVERT: A 216 GLN cc_start: 0.7661 (mt0) cc_final: 0.6865 (mm110) REVERT: A 265 ASN cc_start: 0.8592 (m-40) cc_final: 0.8255 (t0) REVERT: A 324 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7172 (mt-10) REVERT: A 374 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8000 (mm-30) REVERT: A 479 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 603 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8298 (mtmm) REVERT: A 604 GLU cc_start: 0.8127 (mp0) cc_final: 0.7674 (pm20) REVERT: A 960 ARG cc_start: 0.8609 (ttp-110) cc_final: 0.8329 (ttp80) REVERT: A 984 ASP cc_start: 0.7472 (p0) cc_final: 0.7151 (p0) REVERT: B 21 MET cc_start: 0.8054 (pmm) cc_final: 0.7661 (mpp) REVERT: B 23 TRP cc_start: 0.7449 (p90) cc_final: 0.6983 (p90) REVERT: B 151 GLN cc_start: 0.8235 (mt0) cc_final: 0.7942 (mt0) REVERT: B 182 ASN cc_start: 0.7412 (m-40) cc_final: 0.7127 (m-40) REVERT: B 216 GLN cc_start: 0.7660 (mt0) cc_final: 0.6909 (mm110) REVERT: B 265 ASN cc_start: 0.8495 (m-40) cc_final: 0.8152 (t0) REVERT: B 324 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7102 (mt-10) REVERT: B 479 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 604 GLU cc_start: 0.8168 (mp0) cc_final: 0.7668 (pm20) REVERT: B 699 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8157 (mp0) REVERT: B 960 ARG cc_start: 0.8542 (ttp-110) cc_final: 0.8262 (ttp80) REVERT: B 984 ASP cc_start: 0.7456 (p0) cc_final: 0.7138 (p0) REVERT: C 104 MET cc_start: 0.7377 (tpp) cc_final: 0.7105 (tpt) REVERT: C 151 GLN cc_start: 0.8213 (mt0) cc_final: 0.7969 (mt0) REVERT: C 182 ASN cc_start: 0.7436 (m-40) cc_final: 0.7151 (m-40) REVERT: C 216 GLN cc_start: 0.7608 (mt0) cc_final: 0.6878 (mm110) REVERT: C 265 ASN cc_start: 0.8472 (m-40) cc_final: 0.8141 (t0) REVERT: C 324 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7117 (mt-10) REVERT: C 479 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7482 (mm-30) REVERT: C 604 GLU cc_start: 0.8154 (mp0) cc_final: 0.7658 (pm20) REVERT: C 699 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8104 (mp0) REVERT: C 960 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8310 (ttp80) REVERT: C 984 ASP cc_start: 0.7463 (p0) cc_final: 0.7119 (p0) REVERT: D 151 GLN cc_start: 0.8237 (mt0) cc_final: 0.7999 (mt0) REVERT: D 182 ASN cc_start: 0.7411 (m-40) cc_final: 0.7137 (m-40) REVERT: D 216 GLN cc_start: 0.7611 (mt0) cc_final: 0.6877 (mm110) REVERT: D 265 ASN cc_start: 0.8542 (m-40) cc_final: 0.8193 (t0) REVERT: D 324 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7137 (mt-10) REVERT: D 601 ASP cc_start: 0.8040 (t0) cc_final: 0.7706 (t0) REVERT: D 604 GLU cc_start: 0.8131 (mp0) cc_final: 0.7599 (pm20) REVERT: D 699 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8138 (mp0) REVERT: D 960 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8330 (ttp80) REVERT: D 984 ASP cc_start: 0.7423 (p0) cc_final: 0.7103 (p0) outliers start: 42 outliers final: 28 residues processed: 348 average time/residue: 1.3585 time to fit residues: 568.5722 Evaluate side-chains 344 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 316 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 211 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 297 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS A 957 ASN B 771 HIS B 957 ASN C 957 ASN D 957 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.159168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100457 restraints weight = 36490.480| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.11 r_work: 0.3076 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32311 Z= 0.143 Angle : 0.537 8.016 44216 Z= 0.265 Chirality : 0.041 0.216 5400 Planarity : 0.004 0.045 5089 Dihedral : 8.947 115.523 9490 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.60 % Allowed : 13.29 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.14), residues: 3592 helix: 1.26 (0.13), residues: 1708 sheet: 0.63 (0.24), residues: 492 loop : 0.82 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 23 HIS 0.006 0.001 HIS D 771 PHE 0.014 0.001 PHE A 511 TYR 0.012 0.001 TYR D 279 ARG 0.003 0.000 ARG A 790 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 1365) hydrogen bonds : angle 4.47092 ( 3735) covalent geometry : bond 0.00341 (32311) covalent geometry : angle 0.53725 (44216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 3.673 Fit side-chains revert: symmetry clash REVERT: A 23 TRP cc_start: 0.7823 (p-90) cc_final: 0.7239 (p90) REVERT: A 151 GLN cc_start: 0.8256 (mt0) cc_final: 0.8022 (mt0) REVERT: A 182 ASN cc_start: 0.7444 (m-40) cc_final: 0.7174 (m-40) REVERT: A 216 GLN cc_start: 0.7752 (mt0) cc_final: 0.6995 (mm110) REVERT: A 265 ASN cc_start: 0.8541 (m-40) cc_final: 0.8219 (t0) REVERT: A 374 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8034 (mm-30) REVERT: A 479 GLU cc_start: 0.7703 (mm-30) cc_final: 0.6724 (pp20) REVERT: A 603 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8327 (mtmm) REVERT: A 604 GLU cc_start: 0.8161 (mp0) cc_final: 0.7550 (pm20) REVERT: A 984 ASP cc_start: 0.7409 (p0) cc_final: 0.7101 (p0) REVERT: B 21 MET cc_start: 0.8079 (pmm) cc_final: 0.7572 (mmm) REVERT: B 151 GLN cc_start: 0.8243 (mt0) cc_final: 0.8005 (mt0) REVERT: B 182 ASN cc_start: 0.7463 (m-40) cc_final: 0.7191 (m-40) REVERT: B 216 GLN cc_start: 0.7767 (mt0) cc_final: 0.7013 (mm110) REVERT: B 265 ASN cc_start: 0.8495 (m-40) cc_final: 0.8183 (t0) REVERT: B 324 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 479 GLU cc_start: 0.7702 (mm-30) cc_final: 0.6728 (pp20) REVERT: B 604 GLU cc_start: 0.8197 (mp0) cc_final: 0.7486 (pm20) REVERT: B 699 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8204 (mp0) REVERT: B 984 ASP cc_start: 0.7408 (p0) cc_final: 0.7101 (p0) REVERT: C 23 TRP cc_start: 0.7802 (p-90) cc_final: 0.6998 (p90) REVERT: C 151 GLN cc_start: 0.8235 (mt0) cc_final: 0.7996 (mt0) REVERT: C 182 ASN cc_start: 0.7452 (m-40) cc_final: 0.7163 (m-40) REVERT: C 216 GLN cc_start: 0.7776 (mt0) cc_final: 0.7044 (mm110) REVERT: C 265 ASN cc_start: 0.8481 (m-40) cc_final: 0.8167 (t0) REVERT: C 324 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7127 (mt-10) REVERT: C 479 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6727 (pp20) REVERT: C 604 GLU cc_start: 0.8189 (mp0) cc_final: 0.7499 (pm20) REVERT: C 699 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8137 (mp0) REVERT: C 984 ASP cc_start: 0.7402 (p0) cc_final: 0.7070 (p0) REVERT: D 151 GLN cc_start: 0.8251 (mt0) cc_final: 0.8018 (mt0) REVERT: D 182 ASN cc_start: 0.7389 (m-40) cc_final: 0.7103 (m-40) REVERT: D 216 GLN cc_start: 0.7820 (mt0) cc_final: 0.7092 (mm110) REVERT: D 265 ASN cc_start: 0.8561 (m-40) cc_final: 0.8218 (t0) REVERT: D 324 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7132 (mt-10) REVERT: D 601 ASP cc_start: 0.8171 (t0) cc_final: 0.7828 (t0) REVERT: D 604 GLU cc_start: 0.8161 (mp0) cc_final: 0.7676 (pm20) REVERT: D 699 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8160 (mp0) REVERT: D 984 ASP cc_start: 0.7362 (p0) cc_final: 0.7055 (p0) outliers start: 51 outliers final: 34 residues processed: 356 average time/residue: 1.4841 time to fit residues: 632.4395 Evaluate side-chains 354 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 320 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 578 ARG Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 941 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 220 optimal weight: 0.6980 chunk 30 optimal weight: 0.0470 chunk 192 optimal weight: 0.9980 chunk 242 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 347 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 251 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS A 957 ASN B 771 HIS B 957 ASN C 957 ASN D 957 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105284 restraints weight = 36562.143| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.49 r_work: 0.3121 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32311 Z= 0.091 Angle : 0.488 9.553 44216 Z= 0.238 Chirality : 0.038 0.175 5400 Planarity : 0.004 0.047 5089 Dihedral : 8.616 109.504 9490 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.29 % Allowed : 13.76 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.14), residues: 3592 helix: 1.42 (0.13), residues: 1704 sheet: 0.73 (0.24), residues: 488 loop : 0.82 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 23 HIS 0.004 0.001 HIS D 771 PHE 0.030 0.001 PHE C 159 TYR 0.009 0.001 TYR D 279 ARG 0.004 0.000 ARG B 790 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 1365) hydrogen bonds : angle 4.31348 ( 3735) covalent geometry : bond 0.00194 (32311) covalent geometry : angle 0.48775 (44216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 320 time to evaluate : 3.094 Fit side-chains revert: symmetry clash REVERT: A 182 ASN cc_start: 0.7382 (m-40) cc_final: 0.7091 (m-40) REVERT: A 216 GLN cc_start: 0.7672 (mt0) cc_final: 0.6959 (mm110) REVERT: A 234 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7935 (ptpt) REVERT: A 265 ASN cc_start: 0.8610 (m-40) cc_final: 0.8236 (t0) REVERT: A 324 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7132 (mt-10) REVERT: A 342 ARG cc_start: 0.7504 (ttm170) cc_final: 0.7263 (ttm170) REVERT: A 374 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7977 (mm-30) REVERT: A 479 GLU cc_start: 0.7723 (mm-30) cc_final: 0.6715 (pp20) REVERT: A 601 ASP cc_start: 0.8070 (t0) cc_final: 0.7821 (t0) REVERT: A 603 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8153 (mtmm) REVERT: A 604 GLU cc_start: 0.8124 (mp0) cc_final: 0.7636 (pm20) REVERT: A 984 ASP cc_start: 0.7439 (p0) cc_final: 0.7128 (p0) REVERT: B 21 MET cc_start: 0.8071 (pmm) cc_final: 0.7588 (mmm) REVERT: B 151 GLN cc_start: 0.8244 (mt0) cc_final: 0.7823 (mt0) REVERT: B 182 ASN cc_start: 0.7452 (m-40) cc_final: 0.7137 (m-40) REVERT: B 216 GLN cc_start: 0.7686 (mt0) cc_final: 0.6963 (mm110) REVERT: B 234 LYS cc_start: 0.8300 (ttpt) cc_final: 0.8004 (ptpt) REVERT: B 265 ASN cc_start: 0.8512 (m-40) cc_final: 0.8194 (t0) REVERT: B 324 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7124 (mt-10) REVERT: B 479 GLU cc_start: 0.7719 (mm-30) cc_final: 0.6714 (pp20) REVERT: B 604 GLU cc_start: 0.8186 (mp0) cc_final: 0.7705 (pm20) REVERT: B 699 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8155 (mp0) REVERT: B 984 ASP cc_start: 0.7414 (p0) cc_final: 0.7106 (p0) REVERT: C 151 GLN cc_start: 0.8217 (mt0) cc_final: 0.7778 (mt0) REVERT: C 182 ASN cc_start: 0.7385 (m-40) cc_final: 0.7070 (m-40) REVERT: C 216 GLN cc_start: 0.7717 (mt0) cc_final: 0.6961 (mm110) REVERT: C 234 LYS cc_start: 0.8301 (ttpt) cc_final: 0.8000 (ptpt) REVERT: C 265 ASN cc_start: 0.8482 (m-40) cc_final: 0.8178 (t0) REVERT: C 324 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7060 (mt-10) REVERT: C 479 GLU cc_start: 0.7753 (mm-30) cc_final: 0.6727 (pp20) REVERT: C 604 GLU cc_start: 0.8176 (mp0) cc_final: 0.7665 (pm20) REVERT: C 699 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8124 (mp0) REVERT: C 984 ASP cc_start: 0.7417 (p0) cc_final: 0.7081 (p0) REVERT: D 151 GLN cc_start: 0.8223 (mt0) cc_final: 0.7782 (mt0) REVERT: D 182 ASN cc_start: 0.7336 (m-40) cc_final: 0.7070 (m-40) REVERT: D 216 GLN cc_start: 0.7658 (mt0) cc_final: 0.6975 (mm110) REVERT: D 234 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8003 (ptpt) REVERT: D 265 ASN cc_start: 0.8534 (m-40) cc_final: 0.8200 (t0) REVERT: D 324 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7220 (mt-10) REVERT: D 601 ASP cc_start: 0.8094 (t0) cc_final: 0.7799 (t0) REVERT: D 604 GLU cc_start: 0.8130 (mp0) cc_final: 0.7651 (pm20) REVERT: D 699 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8153 (mp0) REVERT: D 984 ASP cc_start: 0.7392 (p0) cc_final: 0.7083 (p0) outliers start: 41 outliers final: 31 residues processed: 347 average time/residue: 1.3526 time to fit residues: 568.8604 Evaluate side-chains 349 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 318 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 156 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 284 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 chunk 323 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS A 957 ASN B 771 HIS B 957 ASN C 957 ASN D 957 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.160273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104050 restraints weight = 36522.408| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.55 r_work: 0.3083 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32311 Z= 0.113 Angle : 0.504 8.171 44216 Z= 0.249 Chirality : 0.039 0.158 5400 Planarity : 0.004 0.045 5089 Dihedral : 8.573 107.006 9490 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.07 % Allowed : 14.26 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.14), residues: 3592 helix: 1.37 (0.13), residues: 1704 sheet: 0.69 (0.24), residues: 492 loop : 0.85 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 23 HIS 0.005 0.001 HIS D 771 PHE 0.016 0.001 PHE A 511 TYR 0.011 0.001 TYR A 279 ARG 0.006 0.000 ARG D 607 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 1365) hydrogen bonds : angle 4.37814 ( 3735) covalent geometry : bond 0.00264 (32311) covalent geometry : angle 0.50396 (44216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 317 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 ASN cc_start: 0.7337 (m-40) cc_final: 0.7059 (m-40) REVERT: A 216 GLN cc_start: 0.7695 (mt0) cc_final: 0.6926 (mm110) REVERT: A 265 ASN cc_start: 0.8564 (m-40) cc_final: 0.8185 (t0) REVERT: A 324 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7110 (mt-10) REVERT: A 342 ARG cc_start: 0.7517 (ttm170) cc_final: 0.7241 (ttm170) REVERT: A 374 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7995 (mm-30) REVERT: A 479 GLU cc_start: 0.7740 (mm-30) cc_final: 0.6677 (pp20) REVERT: A 603 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8328 (mtmm) REVERT: A 604 GLU cc_start: 0.8140 (mp0) cc_final: 0.7579 (pm20) REVERT: A 960 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8278 (ttp80) REVERT: A 984 ASP cc_start: 0.7467 (p0) cc_final: 0.7159 (p0) REVERT: B 21 MET cc_start: 0.8082 (pmm) cc_final: 0.7546 (mmm) REVERT: B 182 ASN cc_start: 0.7257 (m-40) cc_final: 0.6985 (m-40) REVERT: B 216 GLN cc_start: 0.7703 (mt0) cc_final: 0.6940 (mm110) REVERT: B 265 ASN cc_start: 0.8507 (m-40) cc_final: 0.8167 (t0) REVERT: B 324 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7109 (mt-10) REVERT: B 479 GLU cc_start: 0.7710 (mm-30) cc_final: 0.6664 (pp20) REVERT: B 604 GLU cc_start: 0.8186 (mp0) cc_final: 0.7664 (pm20) REVERT: B 699 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8128 (mp0) REVERT: B 960 ARG cc_start: 0.8530 (ttp80) cc_final: 0.8287 (ttp80) REVERT: B 984 ASP cc_start: 0.7468 (p0) cc_final: 0.7159 (p0) REVERT: C 182 ASN cc_start: 0.7267 (m-40) cc_final: 0.6983 (m-40) REVERT: C 216 GLN cc_start: 0.7608 (mt0) cc_final: 0.6835 (mm110) REVERT: C 265 ASN cc_start: 0.8542 (m-40) cc_final: 0.8171 (t0) REVERT: C 324 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7032 (mt-10) REVERT: C 479 GLU cc_start: 0.7749 (mm-30) cc_final: 0.6674 (pp20) REVERT: C 604 GLU cc_start: 0.8179 (mp0) cc_final: 0.7652 (pm20) REVERT: C 699 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8108 (mp0) REVERT: C 960 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8268 (ttp80) REVERT: C 984 ASP cc_start: 0.7462 (p0) cc_final: 0.7128 (p0) REVERT: D 182 ASN cc_start: 0.7309 (m-40) cc_final: 0.7037 (m-40) REVERT: D 216 GLN cc_start: 0.7759 (mt0) cc_final: 0.7016 (mm110) REVERT: D 265 ASN cc_start: 0.8539 (m-40) cc_final: 0.8179 (t0) REVERT: D 324 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7192 (mt-10) REVERT: D 601 ASP cc_start: 0.8199 (t0) cc_final: 0.7959 (t0) REVERT: D 699 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8119 (mp0) REVERT: D 960 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8310 (ttp80) REVERT: D 984 ASP cc_start: 0.7434 (p0) cc_final: 0.7129 (p0) outliers start: 34 outliers final: 29 residues processed: 341 average time/residue: 1.2896 time to fit residues: 528.1227 Evaluate side-chains 341 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 312 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 941 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 122 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 296 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 299 optimal weight: 4.9990 chunk 345 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 341 optimal weight: 0.9980 chunk 293 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS A 957 ASN B 771 HIS B 957 ASN C 957 ASN D 957 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.162632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105594 restraints weight = 36026.955| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.10 r_work: 0.3176 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32311 Z= 0.104 Angle : 0.497 10.148 44216 Z= 0.246 Chirality : 0.039 0.146 5400 Planarity : 0.004 0.046 5089 Dihedral : 8.483 107.076 9490 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.22 % Allowed : 14.10 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.14), residues: 3592 helix: 1.39 (0.13), residues: 1704 sheet: 0.75 (0.24), residues: 488 loop : 0.83 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 275 HIS 0.005 0.001 HIS D 771 PHE 0.026 0.001 PHE A 159 TYR 0.010 0.001 TYR A 279 ARG 0.005 0.000 ARG D 607 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 1365) hydrogen bonds : angle 4.36504 ( 3735) covalent geometry : bond 0.00239 (32311) covalent geometry : angle 0.49688 (44216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36857.72 seconds wall clock time: 640 minutes 52.05 seconds (38452.05 seconds total)