Starting phenix.real_space_refine on Mon Jul 6 00:17:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v60_42986/07_2026/8v60_42986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v60_42986/07_2026/8v60_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_42986/07_2026/8v60_42986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v60_42986/07_2026/8v60_42986.map" model { file = "/net/cci-nas-00/data/ceres_data/8v60_42986/07_2026/8v60_42986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v60_42986/07_2026/8v60_42986.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.025 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 636 Ad-hoc single atom residues: {' K': 6} Unusual residues: {'AJP': 9, 'CLR': 1, 'POV': 6} Classifications: {'undetermined': 16} Link IDs: {None: 14} Chain breaks: 6 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-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 659 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'AJP': 9, 'CLR': 1, 'POV': 8} Classifications: {'undetermined': 18} Link IDs: {None: 16} Chain breaks: 1 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-1': 4, 'POV:plan-2': 3, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 636 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'AJP': 9, 'CLR': 1, 'POV': 6} Classifications: {'undetermined': 16} Link IDs: {None: 14} Chain breaks: 1 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-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 656 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'AJP': 9, 'CLR': 1, 'POV': 8} Classifications: {'undetermined': 18} Link IDs: {None: 16} Chain breaks: 1 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-1': 4, 'POV:plan-2': 3, 'POV:plan-3': 3} 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: 7.92, per 1000 atoms: 0.25 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: 2.77 Conformation dependent library (CDL) restraints added in 1.2 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: 1.29 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: 7.91 Time building geometry restraints manager: 3.60 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: 2.300 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: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.910 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 3.88 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (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 ARG 0.004 0.000 ARG C 393 TYR 0.028 0.002 TYR B1015 PHE 0.016 0.002 PHE D 511 TRP 0.011 0.001 TRP D 23 HIS 0.002 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 (32311) covalent geometry : angle 0.68474 / 0.31 (44216) hydrogen bonds : bond 0.15532 / 10.06 ( 1365) hydrogen bonds : angle 5.80787 / 4.14 ( 3735) *********************** 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 : 1.103 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: 0.8300 (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: 0.7385 (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: 0.7273 (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: 0.6342 time to fit residues: 383.5377 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 : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 534 ASN ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.162009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106609 restraints weight = 36580.838| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.42 r_work: 0.3121 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32311 Z= 0.133 Angle : 0.675 8.771 44216 Z= 0.298 Chirality : 0.044 0.258 5400 Planarity : 0.004 0.054 5089 Dihedral : 16.358 123.496 9490 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.60 % Allowed : 7.26 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3592 helix: 0.93 (0.13), residues: 1660 sheet: 0.40 (0.25), residues: 468 loop : 0.78 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.016 0.001 TYR C 928 PHE 0.024 0.001 PHE D 159 TRP 0.040 0.002 TRP C 23 HIS 0.002 0.000 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (32311) covalent geometry : angle 0.67537 / 0.30 (44216) hydrogen bonds : bond 0.04542 / 2.92 ( 1365) hydrogen bonds : angle 4.64449 / 3.32 ( 3735) *********************** 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 407 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 356 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8293 (mt0) cc_final: 0.8051 (mt0) REVERT: A 182 ASN cc_start: 0.7415 (m-40) cc_final: 0.7114 (m-40) REVERT: A 216 GLN cc_start: 0.7482 (mt0) cc_final: 0.6946 (mm110) REVERT: A 228 LYS cc_start: 0.8430 (mttt) cc_final: 0.8013 (mmtm) REVERT: A 265 ASN cc_start: 0.8601 (m-40) cc_final: 0.8188 (t0) REVERT: A 517 ILE cc_start: 0.8390 (mt) cc_final: 0.8158 (mm) REVERT: A 565 MET cc_start: 0.9356 (ttp) cc_final: 0.9152 (ttp) REVERT: A 699 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8160 (mp0) REVERT: A 712 MET cc_start: 0.8367 (mmm) cc_final: 0.8136 (mmp) REVERT: A 831 GLN cc_start: 0.8455 (mt0) cc_final: 0.7933 (mm110) REVERT: A 871 THR cc_start: 0.7634 (t) cc_final: 0.7297 (t) REVERT: A 960 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8188 (ttp80) REVERT: A 984 ASP cc_start: 0.7449 (p0) cc_final: 0.7026 (t0) REVERT: B 151 GLN cc_start: 0.8361 (mt0) cc_final: 0.8122 (mt0) REVERT: B 182 ASN cc_start: 0.7382 (m-40) cc_final: 0.7081 (m-40) REVERT: B 216 GLN cc_start: 0.7469 (mt0) cc_final: 0.6940 (mm110) REVERT: B 228 LYS cc_start: 0.8436 (mttt) cc_final: 0.8030 (mmtm) REVERT: B 265 ASN cc_start: 0.8605 (m-40) cc_final: 0.8157 (t0) REVERT: B 517 ILE cc_start: 0.8390 (mt) cc_final: 0.8154 (mm) REVERT: B 565 MET cc_start: 0.9356 (ttp) cc_final: 0.9146 (ttp) REVERT: B 699 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8145 (mp0) REVERT: B 712 MET cc_start: 0.8367 (mmm) cc_final: 0.8133 (mmp) REVERT: B 831 GLN cc_start: 0.8434 (mt0) cc_final: 0.7913 (mm110) REVERT: B 871 THR cc_start: 0.7641 (t) cc_final: 0.7303 (t) REVERT: B 960 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.8194 (ttp80) REVERT: B 984 ASP cc_start: 0.7415 (p0) cc_final: 0.6994 (t0) REVERT: C 151 GLN cc_start: 0.8322 (mt0) cc_final: 0.8076 (mt0) REVERT: C 166 LEU cc_start: 0.6977 (mp) cc_final: 0.6774 (tt) REVERT: C 182 ASN cc_start: 0.7416 (m-40) cc_final: 0.7125 (m-40) REVERT: C 216 GLN cc_start: 0.7517 (mt0) cc_final: 0.6968 (mm110) REVERT: C 228 LYS cc_start: 0.8444 (mttt) cc_final: 0.8040 (mmtm) REVERT: C 265 ASN cc_start: 0.8557 (m-40) cc_final: 0.8142 (t0) REVERT: C 517 ILE cc_start: 0.8392 (mt) cc_final: 0.8156 (mm) REVERT: C 565 MET cc_start: 0.9356 (ttp) cc_final: 0.9143 (ttp) REVERT: C 699 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8140 (mp0) REVERT: C 712 MET cc_start: 0.8360 (mmm) cc_final: 0.8124 (mmp) REVERT: C 831 GLN cc_start: 0.8461 (mt0) cc_final: 0.7934 (mm110) REVERT: C 871 THR cc_start: 0.7634 (t) cc_final: 0.7296 (t) REVERT: C 960 ARG cc_start: 0.8502 (ttp-110) cc_final: 0.8180 (ttp80) REVERT: C 984 ASP cc_start: 0.7417 (p0) cc_final: 0.6983 (t0) REVERT: D 21 MET cc_start: 0.8022 (pmm) cc_final: 0.7756 (mpp) REVERT: D 151 GLN cc_start: 0.8332 (mt0) cc_final: 0.8085 (mt0) REVERT: D 182 ASN cc_start: 0.7420 (m-40) cc_final: 0.7133 (m-40) REVERT: D 216 GLN cc_start: 0.7506 (mt0) cc_final: 0.6962 (mm110) REVERT: D 228 LYS cc_start: 0.8424 (mttt) cc_final: 0.8011 (mmtm) REVERT: D 265 ASN cc_start: 0.8603 (m-40) cc_final: 0.8238 (t0) REVERT: D 374 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8231 (mm-30) REVERT: D 517 ILE cc_start: 0.8393 (mt) cc_final: 0.8158 (mm) REVERT: D 565 MET cc_start: 0.9352 (ttp) cc_final: 0.9142 (ttp) REVERT: D 699 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8152 (mp0) REVERT: D 712 MET cc_start: 0.8377 (mmm) cc_final: 0.8147 (mmp) REVERT: D 831 GLN cc_start: 0.8443 (mt0) cc_final: 0.7925 (mm110) REVERT: D 871 THR cc_start: 0.7646 (t) cc_final: 0.7309 (t) REVERT: D 960 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.8186 (ttp80) REVERT: D 984 ASP cc_start: 0.7393 (p0) cc_final: 0.6964 (t0) outliers start: 51 outliers final: 23 residues processed: 388 average time/residue: 0.6146 time to fit residues: 282.8643 Evaluate side-chains 340 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 317 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 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 B residue 399 GLU Chi-restraints excluded: chain B residue 416 ILE 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 C residue 399 GLU Chi-restraints excluded: chain C residue 416 ILE 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 399 GLU Chi-restraints excluded: chain D residue 416 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 78 optimal weight: 0.9990 chunk 344 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.160050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102770 restraints weight = 36673.971| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.44 r_work: 0.3079 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1599 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= 0.146 Angle : 0.609 8.709 44216 Z= 0.282 Chirality : 0.043 0.319 5400 Planarity : 0.004 0.049 5089 Dihedral : 12.848 117.182 9490 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.41 % Allowed : 9.70 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.14), residues: 3592 helix: 1.13 (0.13), residues: 1636 sheet: 0.42 (0.25), residues: 468 loop : 0.81 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.013 0.001 TYR A 928 PHE 0.014 0.001 PHE A 511 TRP 0.034 0.001 TRP C 23 HIS 0.002 0.001 HIS A 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (32311) covalent geometry : angle 0.60927 / 0.28 (44216) hydrogen bonds : bond 0.04820 / 3.11 ( 1365) hydrogen bonds : angle 4.62324 / 3.30 ( 3735) *********************** 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 372 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 327 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8285 (mt0) cc_final: 0.8016 (mt0) REVERT: A 182 ASN cc_start: 0.7378 (m-40) cc_final: 0.7061 (m-40) REVERT: A 216 GLN cc_start: 0.7720 (mt0) cc_final: 0.7101 (mm110) REVERT: A 228 LYS cc_start: 0.8438 (mttt) cc_final: 0.7963 (mmtm) REVERT: A 265 ASN cc_start: 0.8629 (m-40) cc_final: 0.8225 (t0) REVERT: A 374 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8058 (mm-30) REVERT: A 517 ILE cc_start: 0.8377 (mt) cc_final: 0.8155 (mm) REVERT: A 565 MET cc_start: 0.9341 (ttp) cc_final: 0.9114 (ttp) REVERT: A 699 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8194 (mp0) REVERT: A 712 MET cc_start: 0.8367 (mmm) cc_final: 0.8112 (mmp) REVERT: A 960 ARG cc_start: 0.8539 (ttp-110) cc_final: 0.8214 (ttp80) REVERT: A 984 ASP cc_start: 0.7404 (p0) cc_final: 0.7020 (t0) REVERT: B 104 MET cc_start: 0.7438 (tpp) cc_final: 0.7121 (tpt) REVERT: B 151 GLN cc_start: 0.8373 (mt0) cc_final: 0.8116 (mt0) REVERT: B 182 ASN cc_start: 0.7449 (m-40) cc_final: 0.7126 (m-40) REVERT: B 216 GLN cc_start: 0.7722 (mt0) cc_final: 0.7021 (mm110) REVERT: B 228 LYS cc_start: 0.8422 (mttt) cc_final: 0.7968 (mmtm) REVERT: B 265 ASN cc_start: 0.8543 (m-40) cc_final: 0.8148 (t0) REVERT: B 517 ILE cc_start: 0.8371 (mt) cc_final: 0.8148 (mm) REVERT: B 565 MET cc_start: 0.9336 (ttp) cc_final: 0.9104 (ttp) REVERT: B 699 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8192 (mp0) REVERT: B 712 MET cc_start: 0.8377 (mmm) cc_final: 0.8119 (mmp) REVERT: B 960 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8218 (ttp80) REVERT: B 984 ASP cc_start: 0.7367 (p0) cc_final: 0.6981 (t0) REVERT: C 151 GLN cc_start: 0.8300 (mt0) cc_final: 0.8032 (mt0) REVERT: C 182 ASN cc_start: 0.7424 (m-40) cc_final: 0.7101 (m-40) REVERT: C 216 GLN cc_start: 0.7737 (mt0) cc_final: 0.7147 (mm110) REVERT: C 228 LYS cc_start: 0.8443 (mttt) cc_final: 0.8139 (mmtp) REVERT: C 265 ASN cc_start: 0.8550 (m-40) cc_final: 0.8166 (t0) REVERT: C 517 ILE cc_start: 0.8377 (mt) cc_final: 0.8151 (mm) REVERT: C 565 MET cc_start: 0.9340 (ttp) cc_final: 0.9107 (ttp) REVERT: C 699 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8175 (mp0) REVERT: C 712 MET cc_start: 0.8359 (mmm) cc_final: 0.8096 (mmp) REVERT: C 960 ARG cc_start: 0.8540 (ttp-110) cc_final: 0.8211 (ttp80) REVERT: C 984 ASP cc_start: 0.7372 (p0) cc_final: 0.6993 (p0) REVERT: D 21 MET cc_start: 0.7955 (pmm) cc_final: 0.7364 (mpp) REVERT: D 23 TRP cc_start: 0.7749 (p-90) cc_final: 0.7427 (p90) REVERT: D 151 GLN cc_start: 0.8327 (mt0) cc_final: 0.8050 (mt0) REVERT: D 182 ASN cc_start: 0.7385 (m-40) cc_final: 0.7078 (m-40) REVERT: D 216 GLN cc_start: 0.7685 (mt0) cc_final: 0.7130 (mm110) REVERT: D 228 LYS cc_start: 0.8422 (mttt) cc_final: 0.8110 (mmtp) REVERT: D 265 ASN cc_start: 0.8622 (m-40) cc_final: 0.8248 (t0) REVERT: D 517 ILE cc_start: 0.8368 (mt) cc_final: 0.8145 (mm) REVERT: D 565 MET cc_start: 0.9335 (ttp) cc_final: 0.9101 (ttp) REVERT: D 699 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8195 (mp0) REVERT: D 712 MET cc_start: 0.8360 (mmm) cc_final: 0.8110 (mmp) REVERT: D 960 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8224 (ttp80) REVERT: D 984 ASP cc_start: 0.7382 (p0) cc_final: 0.7000 (t0) outliers start: 45 outliers final: 36 residues processed: 359 average time/residue: 0.6440 time to fit residues: 275.0524 Evaluate side-chains 346 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 310 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 179 LEU 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 578 ARG Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 179 LEU 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 578 ARG Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 816 GLN Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 179 LEU 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 578 ARG Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 816 GLN Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 179 LEU 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 578 ARG Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 816 GLN Chi-restraints excluded: chain D residue 941 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 187 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 chunk 335 optimal weight: 0.0470 chunk 281 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 126 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 245 optimal weight: 0.3980 chunk 221 optimal weight: 6.9990 chunk 277 optimal weight: 20.0000 chunk 299 optimal weight: 2.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 HIS A 476 ASN B 379 HIS B 476 ASN C 379 HIS C 476 ASN D 379 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.161782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105416 restraints weight = 36574.427| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.39 r_work: 0.3114 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32311 Z= 0.106 Angle : 0.560 9.807 44216 Z= 0.257 Chirality : 0.041 0.329 5400 Planarity : 0.004 0.048 5089 Dihedral : 11.248 120.369 9490 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.38 % Allowed : 10.55 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.14), residues: 3592 helix: 1.25 (0.13), residues: 1668 sheet: 0.55 (0.25), residues: 464 loop : 0.84 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.010 0.001 TYR D 279 PHE 0.026 0.001 PHE C 159 TRP 0.030 0.001 TRP C 23 HIS 0.002 0.000 HIS B 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (32311) covalent geometry : angle 0.56027 / 0.26 (44216) hydrogen bonds : bond 0.03955 / 2.54 ( 1365) hydrogen bonds : angle 4.47393 / 3.20 ( 3735) *********************** 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 358 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 314 time to evaluate : 1.099 Fit side-chains REVERT: A 104 MET cc_start: 0.7453 (tpp) cc_final: 0.7127 (tpt) REVERT: A 151 GLN cc_start: 0.8325 (mt0) cc_final: 0.8062 (mt0) REVERT: A 182 ASN cc_start: 0.7374 (m-40) cc_final: 0.7039 (m-40) REVERT: A 216 GLN cc_start: 0.7557 (mt0) cc_final: 0.6841 (mm110) REVERT: A 228 LYS cc_start: 0.8437 (mttt) cc_final: 0.7932 (mmtm) REVERT: A 265 ASN cc_start: 0.8649 (m-40) cc_final: 0.8257 (t0) REVERT: A 324 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 374 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8046 (mm-30) REVERT: A 604 GLU cc_start: 0.8235 (mp0) cc_final: 0.7903 (pm20) REVERT: A 699 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8184 (mp0) REVERT: A 960 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8220 (ttp80) REVERT: A 984 ASP cc_start: 0.7416 (p0) cc_final: 0.7026 (t0) REVERT: B 104 MET cc_start: 0.7481 (tpp) cc_final: 0.7188 (tpt) REVERT: B 151 GLN cc_start: 0.8334 (mt0) cc_final: 0.8080 (mt0) REVERT: B 182 ASN cc_start: 0.7358 (m-40) cc_final: 0.7014 (m-40) REVERT: B 216 GLN cc_start: 0.7594 (mt0) cc_final: 0.6902 (mm110) REVERT: B 228 LYS cc_start: 0.8426 (mttt) cc_final: 0.8110 (mmtp) REVERT: B 265 ASN cc_start: 0.8546 (m-40) cc_final: 0.8154 (t0) REVERT: B 517 ILE cc_start: 0.8326 (mt) cc_final: 0.8124 (mm) REVERT: B 604 GLU cc_start: 0.8243 (mp0) cc_final: 0.7909 (pm20) REVERT: B 699 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8175 (mp0) REVERT: B 900 ASP cc_start: 0.8096 (p0) cc_final: 0.7889 (p0) REVERT: B 960 ARG cc_start: 0.8541 (ttp-110) cc_final: 0.8209 (ttp80) REVERT: B 984 ASP cc_start: 0.7427 (p0) cc_final: 0.7063 (p0) REVERT: C 104 MET cc_start: 0.7402 (tpp) cc_final: 0.7033 (tpt) REVERT: C 151 GLN cc_start: 0.8346 (mt0) cc_final: 0.8075 (mt0) REVERT: C 182 ASN cc_start: 0.7366 (m-40) cc_final: 0.7048 (m-40) REVERT: C 216 GLN cc_start: 0.7772 (mt0) cc_final: 0.6992 (mm110) REVERT: C 228 LYS cc_start: 0.8449 (mttt) cc_final: 0.7997 (mmtm) REVERT: C 265 ASN cc_start: 0.8555 (m-40) cc_final: 0.8173 (t0) REVERT: C 324 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7189 (mt-10) REVERT: C 517 ILE cc_start: 0.8340 (mt) cc_final: 0.8137 (mm) REVERT: C 565 MET cc_start: 0.9349 (ttp) cc_final: 0.9148 (ttp) REVERT: C 604 GLU cc_start: 0.8241 (mp0) cc_final: 0.7908 (pm20) REVERT: C 699 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8170 (mp0) REVERT: C 960 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8222 (ttp80) REVERT: C 984 ASP cc_start: 0.7417 (p0) cc_final: 0.7052 (p0) REVERT: D 21 MET cc_start: 0.8016 (pmm) cc_final: 0.7379 (mpp) REVERT: D 23 TRP cc_start: 0.7748 (p-90) cc_final: 0.7414 (p90) REVERT: D 104 MET cc_start: 0.7421 (tpp) cc_final: 0.7134 (tpt) REVERT: D 151 GLN cc_start: 0.8317 (mt0) cc_final: 0.8044 (mt0) REVERT: D 182 ASN cc_start: 0.7362 (m-40) cc_final: 0.7059 (m-40) REVERT: D 216 GLN cc_start: 0.7824 (mt0) cc_final: 0.7106 (mm110) REVERT: D 228 LYS cc_start: 0.8433 (mttt) cc_final: 0.7975 (mmtm) REVERT: D 265 ASN cc_start: 0.8631 (m-40) cc_final: 0.8273 (t0) REVERT: D 324 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7184 (mt-10) REVERT: D 517 ILE cc_start: 0.8322 (mt) cc_final: 0.8119 (mm) REVERT: D 565 MET cc_start: 0.9347 (ttp) cc_final: 0.9146 (ttp) REVERT: D 604 GLU cc_start: 0.8240 (mp0) cc_final: 0.7908 (pm20) REVERT: D 699 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8188 (mp0) REVERT: D 960 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.8284 (ttp80) REVERT: D 984 ASP cc_start: 0.7410 (p0) cc_final: 0.7048 (p0) outliers start: 44 outliers final: 22 residues processed: 336 average time/residue: 0.6657 time to fit residues: 265.4378 Evaluate side-chains 327 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 305 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 416 ILE 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 B residue 179 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 416 ILE 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 C residue 385 LEU 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 816 GLN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 813 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 296 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 251 optimal weight: 0.3980 chunk 309 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 chunk 293 optimal weight: 0.9990 chunk 337 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 ASN B 771 HIS C 225 ASN D 771 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.162594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105846 restraints weight = 36711.949| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.53 r_work: 0.3146 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1946 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= 0.099 Angle : 0.533 9.586 44216 Z= 0.247 Chirality : 0.040 0.306 5400 Planarity : 0.003 0.047 5089 Dihedral : 9.714 121.981 9490 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.41 % Allowed : 10.55 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.14), residues: 3592 helix: 1.46 (0.13), residues: 1664 sheet: 0.67 (0.25), residues: 468 loop : 0.91 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.010 0.001 TYR C 279 PHE 0.017 0.001 PHE A 511 TRP 0.037 0.001 TRP A 23 HIS 0.002 0.000 HIS B 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (32311) covalent geometry : angle 0.53327 / 0.25 (44216) hydrogen bonds : bond 0.03719 / 2.38 ( 1365) hydrogen bonds : angle 4.35165 / 3.11 ( 3735) *********************** 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 361 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 1.159 Fit side-chains REVERT: A 104 MET cc_start: 0.7339 (tpp) cc_final: 0.7083 (tpt) REVERT: A 151 GLN cc_start: 0.8302 (mt0) cc_final: 0.8036 (mt0) REVERT: A 182 ASN cc_start: 0.7390 (m-40) cc_final: 0.7076 (m-40) REVERT: A 216 GLN cc_start: 0.7801 (mt0) cc_final: 0.7051 (mm110) REVERT: A 228 LYS cc_start: 0.8423 (mttt) cc_final: 0.8109 (mmtp) REVERT: A 265 ASN cc_start: 0.8637 (m-40) cc_final: 0.8252 (t0) REVERT: A 324 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 374 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8004 (mm-30) REVERT: A 604 GLU cc_start: 0.8241 (mp0) cc_final: 0.7796 (pm20) REVERT: A 699 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8175 (mp0) REVERT: A 960 ARG cc_start: 0.8537 (ttp-110) cc_final: 0.8146 (ttm170) REVERT: A 984 ASP cc_start: 0.7352 (p0) cc_final: 0.7006 (t0) REVERT: B 151 GLN cc_start: 0.8243 (mt0) cc_final: 0.7989 (mt0) REVERT: B 182 ASN cc_start: 0.7395 (m-40) cc_final: 0.7047 (m-40) REVERT: B 216 GLN cc_start: 0.7802 (mt0) cc_final: 0.7072 (mm110) REVERT: B 220 ILE cc_start: 0.7847 (mm) cc_final: 0.7605 (mm) REVERT: B 228 LYS cc_start: 0.8444 (mttt) cc_final: 0.7987 (mmtm) REVERT: B 265 ASN cc_start: 0.8539 (m-40) cc_final: 0.8170 (t0) REVERT: B 324 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7215 (mt-10) REVERT: B 604 GLU cc_start: 0.8265 (mp0) cc_final: 0.7816 (pm20) REVERT: B 699 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8163 (mp0) REVERT: B 960 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.8271 (ttp80) REVERT: B 984 ASP cc_start: 0.7375 (p0) cc_final: 0.7025 (p0) REVERT: C 104 MET cc_start: 0.7403 (tpp) cc_final: 0.7117 (tpt) REVERT: C 151 GLN cc_start: 0.8262 (mt0) cc_final: 0.7978 (mt0) REVERT: C 182 ASN cc_start: 0.7373 (m-40) cc_final: 0.7066 (m-40) REVERT: C 216 GLN cc_start: 0.7735 (mt0) cc_final: 0.7077 (mm110) REVERT: C 265 ASN cc_start: 0.8549 (m-40) cc_final: 0.8186 (t0) REVERT: C 324 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7258 (mt-10) REVERT: C 604 GLU cc_start: 0.8256 (mp0) cc_final: 0.7809 (pm20) REVERT: C 699 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8144 (mp0) REVERT: C 960 ARG cc_start: 0.8535 (ttp-110) cc_final: 0.8142 (ttm170) REVERT: C 984 ASP cc_start: 0.7370 (p0) cc_final: 0.7021 (p0) REVERT: D 21 MET cc_start: 0.8045 (pmm) cc_final: 0.7448 (mpp) REVERT: D 23 TRP cc_start: 0.7801 (p-90) cc_final: 0.7444 (p90) REVERT: D 104 MET cc_start: 0.7346 (tpp) cc_final: 0.7089 (tpt) REVERT: D 151 GLN cc_start: 0.8310 (mt0) cc_final: 0.8027 (mt0) REVERT: D 182 ASN cc_start: 0.7392 (m-40) cc_final: 0.7131 (m-40) REVERT: D 216 GLN cc_start: 0.7733 (mt0) cc_final: 0.7066 (mm110) REVERT: D 228 LYS cc_start: 0.8425 (mttt) cc_final: 0.8103 (mmtp) REVERT: D 265 ASN cc_start: 0.8597 (m-40) cc_final: 0.8251 (t0) REVERT: D 324 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7194 (mt-10) REVERT: D 604 GLU cc_start: 0.8237 (mp0) cc_final: 0.7790 (pm20) REVERT: D 699 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8183 (mp0) REVERT: D 960 ARG cc_start: 0.8537 (ttp-110) cc_final: 0.8138 (ttm170) REVERT: D 984 ASP cc_start: 0.7350 (p0) cc_final: 0.7007 (p0) outliers start: 45 outliers final: 31 residues processed: 345 average time/residue: 0.6094 time to fit residues: 250.7228 Evaluate side-chains 335 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 B residue 179 LEU 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 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 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 578 ARG Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 816 GLN 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 416 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 337 optimal weight: 0.0670 chunk 67 optimal weight: 0.7980 chunk 352 optimal weight: 8.9990 chunk 320 optimal weight: 9.9990 chunk 265 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 HIS B 225 ASN B 771 HIS C 225 ASN C 771 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 = 0.4007 r_free = 0.4007 target = 0.160310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104422 restraints weight = 36414.178| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.55 r_work: 0.3091 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32311 Z= 0.131 Angle : 0.546 7.498 44216 Z= 0.262 Chirality : 0.041 0.281 5400 Planarity : 0.004 0.045 5089 Dihedral : 9.353 122.407 9490 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.57 % Allowed : 11.37 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.14), residues: 3592 helix: 1.36 (0.13), residues: 1680 sheet: 0.48 (0.24), residues: 492 loop : 0.85 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.012 0.001 TYR A 928 PHE 0.029 0.001 PHE B 159 TRP 0.042 0.001 TRP C 23 HIS 0.002 0.001 HIS B 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (32311) covalent geometry : angle 0.54589 / 0.26 (44216) hydrogen bonds : bond 0.04406 / 2.83 ( 1365) hydrogen bonds : angle 4.44834 / 3.19 ( 3735) *********************** 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 368 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 318 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7548 (mpp) cc_final: 0.6618 (mmm) REVERT: A 151 GLN cc_start: 0.8226 (mt0) cc_final: 0.7960 (mt0) REVERT: A 182 ASN cc_start: 0.7436 (m-40) cc_final: 0.7053 (m-40) REVERT: A 216 GLN cc_start: 0.7656 (mt0) cc_final: 0.6908 (mm110) REVERT: A 265 ASN cc_start: 0.8580 (m-40) cc_final: 0.8241 (t0) REVERT: A 324 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7166 (mt-10) REVERT: A 374 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8005 (mm-30) REVERT: A 604 GLU cc_start: 0.8238 (mp0) cc_final: 0.7498 (pm20) REVERT: A 699 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8163 (mp0) REVERT: A 960 ARG cc_start: 0.8568 (ttp-110) cc_final: 0.8276 (ttp80) REVERT: A 984 ASP cc_start: 0.7386 (p0) cc_final: 0.7026 (p0) REVERT: B 21 MET cc_start: 0.7562 (mpp) cc_final: 0.6732 (mmm) REVERT: B 151 GLN cc_start: 0.8233 (mt0) cc_final: 0.7961 (mt0) REVERT: B 182 ASN cc_start: 0.7425 (m-40) cc_final: 0.7079 (m-40) REVERT: B 216 GLN cc_start: 0.7761 (mt0) cc_final: 0.7077 (mm110) REVERT: B 265 ASN cc_start: 0.8540 (m-40) cc_final: 0.8166 (t0) REVERT: B 324 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7173 (mt-10) REVERT: B 699 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8153 (mp0) REVERT: B 960 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8270 (ttp80) REVERT: B 984 ASP cc_start: 0.7438 (p0) cc_final: 0.7082 (p0) REVERT: C 21 MET cc_start: 0.7622 (mpp) cc_final: 0.6757 (mmm) REVERT: C 104 MET cc_start: 0.7448 (tpp) cc_final: 0.7141 (tpt) REVERT: C 151 GLN cc_start: 0.8243 (mt0) cc_final: 0.7975 (mt0) REVERT: C 182 ASN cc_start: 0.7422 (m-40) cc_final: 0.7145 (m-40) REVERT: C 216 GLN cc_start: 0.7774 (mt0) cc_final: 0.7051 (mm110) REVERT: C 265 ASN cc_start: 0.8528 (m-40) cc_final: 0.8174 (t0) REVERT: C 324 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7272 (mt-10) REVERT: C 604 GLU cc_start: 0.8226 (mp0) cc_final: 0.7499 (pm20) REVERT: C 699 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8133 (mp0) REVERT: C 960 ARG cc_start: 0.8566 (ttp-110) cc_final: 0.8277 (ttp80) REVERT: C 984 ASP cc_start: 0.7409 (p0) cc_final: 0.7056 (p0) REVERT: D 104 MET cc_start: 0.7362 (tpp) cc_final: 0.7097 (tpt) REVERT: D 151 GLN cc_start: 0.8222 (mt0) cc_final: 0.7931 (mt0) REVERT: D 182 ASN cc_start: 0.7432 (m-40) cc_final: 0.7120 (m-40) REVERT: D 216 GLN cc_start: 0.7767 (mt0) cc_final: 0.6994 (mm110) REVERT: D 265 ASN cc_start: 0.8590 (m-40) cc_final: 0.8226 (t0) REVERT: D 324 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7219 (mt-10) REVERT: D 604 GLU cc_start: 0.8241 (mp0) cc_final: 0.7506 (pm20) REVERT: D 699 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8163 (mp0) REVERT: D 960 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.8270 (ttp80) REVERT: D 984 ASP cc_start: 0.7409 (p0) cc_final: 0.7049 (p0) outliers start: 50 outliers final: 33 residues processed: 349 average time/residue: 0.6402 time to fit residues: 266.3423 Evaluate side-chains 347 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 314 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 385 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 416 ILE 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 385 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 416 ILE 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 385 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 416 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 79 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 262 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 301 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 187 optimal weight: 0.0040 chunk 108 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 ASN B 225 ASN B 771 HIS B 957 ASN C 225 ASN C 771 HIS C 957 ASN D 372 ASN D 771 HIS D 957 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.162725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107503 restraints weight = 36737.895| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.56 r_work: 0.3139 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2101 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= 0.093 Angle : 0.491 7.691 44216 Z= 0.236 Chirality : 0.039 0.244 5400 Planarity : 0.003 0.045 5089 Dihedral : 8.902 119.111 9490 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.41 % Allowed : 12.37 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.14), residues: 3592 helix: 1.53 (0.13), residues: 1672 sheet: 0.58 (0.24), residues: 492 loop : 0.91 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.010 0.001 TYR D 279 PHE 0.015 0.001 PHE B 511 TRP 0.030 0.001 TRP C 23 HIS 0.003 0.000 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (32311) covalent geometry : angle 0.49079 / 0.24 (44216) hydrogen bonds : bond 0.03540 / 2.27 ( 1365) hydrogen bonds : angle 4.31178 / 3.09 ( 3735) *********************** 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 352 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 307 time to evaluate : 1.100 Fit side-chains REVERT: A 21 MET cc_start: 0.7492 (mpp) cc_final: 0.6619 (mmm) REVERT: A 182 ASN cc_start: 0.7342 (m-40) cc_final: 0.7034 (m-40) REVERT: A 216 GLN cc_start: 0.7758 (mt0) cc_final: 0.6959 (mm110) REVERT: A 228 LYS cc_start: 0.8441 (mttt) cc_final: 0.8083 (mmtp) REVERT: A 234 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7957 (ptpt) REVERT: A 265 ASN cc_start: 0.8637 (m-40) cc_final: 0.8254 (t0) REVERT: A 324 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7170 (mt-10) REVERT: A 374 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7966 (mm-30) REVERT: A 699 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8144 (mp0) REVERT: A 960 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8145 (ttm170) REVERT: A 984 ASP cc_start: 0.7399 (p0) cc_final: 0.7042 (p0) REVERT: B 182 ASN cc_start: 0.7359 (m-40) cc_final: 0.7045 (m-40) REVERT: B 216 GLN cc_start: 0.7585 (mt0) cc_final: 0.6904 (mm110) REVERT: B 234 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7989 (ptpt) REVERT: B 265 ASN cc_start: 0.8519 (m-40) cc_final: 0.8168 (t0) REVERT: B 324 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7136 (mt-10) REVERT: B 604 GLU cc_start: 0.8174 (mp0) cc_final: 0.7799 (pm20) REVERT: B 699 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8174 (mp0) REVERT: B 960 ARG cc_start: 0.8520 (ttp-110) cc_final: 0.8113 (ttm170) REVERT: B 984 ASP cc_start: 0.7443 (p0) cc_final: 0.7090 (p0) REVERT: C 104 MET cc_start: 0.7426 (tpp) cc_final: 0.7146 (tpt) REVERT: C 151 GLN cc_start: 0.8243 (mt0) cc_final: 0.7993 (mt0) REVERT: C 182 ASN cc_start: 0.7308 (m-40) cc_final: 0.7063 (m-40) REVERT: C 216 GLN cc_start: 0.7707 (mt0) cc_final: 0.6998 (mm110) REVERT: C 234 LYS cc_start: 0.8307 (ttpt) cc_final: 0.7986 (ptpt) REVERT: C 265 ASN cc_start: 0.8527 (m-40) cc_final: 0.8190 (t0) REVERT: C 324 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7229 (mt-10) REVERT: C 699 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8129 (mp0) REVERT: C 960 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.8119 (ttm170) REVERT: C 984 ASP cc_start: 0.7397 (p0) cc_final: 0.7071 (p0) REVERT: D 151 GLN cc_start: 0.8227 (mt0) cc_final: 0.8001 (mt0) REVERT: D 182 ASN cc_start: 0.7247 (m-40) cc_final: 0.7005 (m-40) REVERT: D 216 GLN cc_start: 0.7612 (mt0) cc_final: 0.6938 (mm110) REVERT: D 234 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7975 (ptpt) REVERT: D 265 ASN cc_start: 0.8580 (m-40) cc_final: 0.8229 (t0) REVERT: D 324 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7206 (mt-10) REVERT: D 604 GLU cc_start: 0.8246 (mp0) cc_final: 0.7795 (pm20) REVERT: D 699 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8176 (mp0) REVERT: D 960 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8151 (ttm170) REVERT: D 984 ASP cc_start: 0.7388 (p0) cc_final: 0.7033 (p0) outliers start: 45 outliers final: 23 residues processed: 329 average time/residue: 0.6641 time to fit residues: 258.7103 Evaluate side-chains 323 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 300 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 385 LEU 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 983 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 578 ARG Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 385 LEU 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 983 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 109 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 299 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 287 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 ASN B 225 ASN B 771 HIS B 957 ASN C 225 ASN C 771 HIS C 957 ASN D 771 HIS D 957 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.161502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105517 restraints weight = 36598.211| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.48 r_work: 0.3108 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32311 Z= 0.109 Angle : 0.508 8.312 44216 Z= 0.246 Chirality : 0.039 0.221 5400 Planarity : 0.004 0.044 5089 Dihedral : 8.761 116.906 9490 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.10 % Allowed : 12.91 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.14), residues: 3592 helix: 1.49 (0.13), residues: 1676 sheet: 0.61 (0.24), residues: 492 loop : 0.90 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 790 TYR 0.019 0.001 TYR D 163 PHE 0.029 0.001 PHE B 159 TRP 0.045 0.001 TRP C 23 HIS 0.004 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (32311) covalent geometry : angle 0.50815 / 0.25 (44216) hydrogen bonds : bond 0.03915 / 2.52 ( 1365) hydrogen bonds : angle 4.34409 / 3.11 ( 3735) *********************** 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 339 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 304 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.7558 (mpp) cc_final: 0.6679 (mmm) REVERT: A 182 ASN cc_start: 0.7429 (m-40) cc_final: 0.7139 (m-40) REVERT: A 216 GLN cc_start: 0.7618 (mt0) cc_final: 0.6892 (mm110) REVERT: A 234 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7987 (ptpt) REVERT: A 265 ASN cc_start: 0.8637 (m-40) cc_final: 0.8252 (t0) REVERT: A 324 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7146 (mt-10) REVERT: A 601 ASP cc_start: 0.7995 (t0) cc_final: 0.7776 (t0) REVERT: A 604 GLU cc_start: 0.8172 (mp0) cc_final: 0.7725 (pm20) REVERT: A 691 MET cc_start: 0.8311 (mtp) cc_final: 0.8082 (mtm) REVERT: A 699 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8154 (mp0) REVERT: A 960 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8152 (ttm170) REVERT: A 984 ASP cc_start: 0.7421 (p0) cc_final: 0.7075 (p0) REVERT: B 182 ASN cc_start: 0.7406 (m-40) cc_final: 0.7065 (m-40) REVERT: B 216 GLN cc_start: 0.7731 (mt0) cc_final: 0.7005 (mm110) REVERT: B 265 ASN cc_start: 0.8521 (m-40) cc_final: 0.8174 (t0) REVERT: B 324 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7126 (mt-10) REVERT: B 604 GLU cc_start: 0.8185 (mp0) cc_final: 0.7633 (pm20) REVERT: B 699 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8162 (mp0) REVERT: B 960 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8141 (ttm170) REVERT: B 984 ASP cc_start: 0.7435 (p0) cc_final: 0.7088 (p0) REVERT: C 151 GLN cc_start: 0.8229 (mt0) cc_final: 0.7987 (mt0) REVERT: C 182 ASN cc_start: 0.7322 (m-40) cc_final: 0.7061 (m-40) REVERT: C 216 GLN cc_start: 0.7778 (mt0) cc_final: 0.7004 (mm110) REVERT: C 265 ASN cc_start: 0.8515 (m-40) cc_final: 0.8172 (t0) REVERT: C 324 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 601 ASP cc_start: 0.7987 (t0) cc_final: 0.7778 (t0) REVERT: C 604 GLU cc_start: 0.8180 (mp0) cc_final: 0.7741 (pm20) REVERT: C 699 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8155 (mp0) REVERT: C 960 ARG cc_start: 0.8568 (ttp-110) cc_final: 0.8151 (ttm170) REVERT: C 984 ASP cc_start: 0.7436 (p0) cc_final: 0.7089 (p0) REVERT: D 151 GLN cc_start: 0.8236 (mt0) cc_final: 0.8023 (mt0) REVERT: D 182 ASN cc_start: 0.7313 (m-40) cc_final: 0.7070 (m-40) REVERT: D 216 GLN cc_start: 0.7707 (mt0) cc_final: 0.6968 (mm110) REVERT: D 265 ASN cc_start: 0.8556 (m-40) cc_final: 0.8206 (t0) REVERT: D 324 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7144 (mt-10) REVERT: D 604 GLU cc_start: 0.8238 (mp0) cc_final: 0.7530 (pm20) REVERT: D 699 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8168 (mp0) REVERT: D 960 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.8144 (ttm170) REVERT: D 984 ASP cc_start: 0.7363 (p0) cc_final: 0.7014 (p0) outliers start: 35 outliers final: 23 residues processed: 324 average time/residue: 0.6406 time to fit residues: 246.9133 Evaluate side-chains 326 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 578 ARG Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 312 LEU 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 578 ARG Chi-restraints excluded: chain B residue 813 THR 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 578 ARG Chi-restraints excluded: chain C residue 813 THR 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 416 ILE Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 813 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 267 optimal weight: 9.9990 chunk 249 optimal weight: 0.0870 chunk 188 optimal weight: 8.9990 chunk 344 optimal weight: 0.0050 chunk 167 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 302 optimal weight: 4.9990 chunk 170 optimal weight: 0.0970 chunk 193 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.8374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 ASN B 225 ASN B 771 HIS B 957 ASN C 225 ASN C 771 HIS C 957 ASN D 771 HIS D 957 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.160006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101670 restraints weight = 36540.464| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.11 r_work: 0.3104 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32311 Z= 0.132 Angle : 0.531 9.360 44216 Z= 0.260 Chirality : 0.040 0.195 5400 Planarity : 0.004 0.043 5089 Dihedral : 8.657 112.853 9490 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.32 % Allowed : 12.75 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.14), residues: 3592 helix: 1.37 (0.13), residues: 1676 sheet: 0.57 (0.24), residues: 492 loop : 0.89 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 790 TYR 0.019 0.001 TYR A 163 PHE 0.018 0.001 PHE D 187 TRP 0.026 0.001 TRP C 23 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (32311) covalent geometry : angle 0.53107 / 0.26 (44216) hydrogen bonds : bond 0.04437 / 2.85 ( 1365) hydrogen bonds : angle 4.47358 / 3.20 ( 3735) *********************** 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 348 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.7681 (mpp) cc_final: 0.6818 (mmm) REVERT: A 182 ASN cc_start: 0.7465 (m-40) cc_final: 0.7164 (m-40) REVERT: A 216 GLN cc_start: 0.7833 (mt0) cc_final: 0.7122 (mm110) REVERT: A 265 ASN cc_start: 0.8631 (m-40) cc_final: 0.8281 (t0) REVERT: A 324 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7200 (mt-10) REVERT: A 374 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8025 (mm-30) REVERT: A 601 ASP cc_start: 0.8051 (t0) cc_final: 0.7690 (t0) REVERT: A 604 GLU cc_start: 0.8171 (mp0) cc_final: 0.7564 (pm20) REVERT: A 699 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8184 (mp0) REVERT: A 960 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8277 (ttp80) REVERT: A 984 ASP cc_start: 0.7290 (p0) cc_final: 0.6978 (p0) REVERT: B 23 TRP cc_start: 0.7807 (p-90) cc_final: 0.7585 (p90) REVERT: B 182 ASN cc_start: 0.7468 (m-40) cc_final: 0.7158 (m-40) REVERT: B 216 GLN cc_start: 0.7694 (mt0) cc_final: 0.6982 (mm110) REVERT: B 234 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8072 (ptpt) REVERT: B 265 ASN cc_start: 0.8519 (m-40) cc_final: 0.8209 (t0) REVERT: B 324 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7240 (mt-10) REVERT: B 699 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8203 (mp0) REVERT: B 960 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8274 (ttp80) REVERT: B 984 ASP cc_start: 0.7351 (p0) cc_final: 0.7042 (p0) REVERT: C 151 GLN cc_start: 0.8232 (mt0) cc_final: 0.7779 (mt0) REVERT: C 182 ASN cc_start: 0.7336 (m-40) cc_final: 0.7090 (m-40) REVERT: C 216 GLN cc_start: 0.7650 (mt0) cc_final: 0.6955 (mm110) REVERT: C 265 ASN cc_start: 0.8506 (m-40) cc_final: 0.8205 (t0) REVERT: C 324 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7268 (mt-10) REVERT: C 601 ASP cc_start: 0.8042 (t0) cc_final: 0.7691 (t0) REVERT: C 604 GLU cc_start: 0.8166 (mp0) cc_final: 0.7565 (pm20) REVERT: C 699 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8190 (mp0) REVERT: C 960 ARG cc_start: 0.8563 (ttp-110) cc_final: 0.8270 (ttp80) REVERT: C 984 ASP cc_start: 0.7347 (p0) cc_final: 0.7039 (p0) REVERT: D 151 GLN cc_start: 0.8248 (mt0) cc_final: 0.7883 (mt0) REVERT: D 182 ASN cc_start: 0.7298 (m-40) cc_final: 0.7057 (m-40) REVERT: D 216 GLN cc_start: 0.7560 (mt0) cc_final: 0.6937 (mm110) REVERT: D 265 ASN cc_start: 0.8541 (m-40) cc_final: 0.8221 (t0) REVERT: D 324 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7195 (mt-10) REVERT: D 604 GLU cc_start: 0.8238 (mp0) cc_final: 0.7552 (pm20) REVERT: D 699 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8215 (mp0) REVERT: D 960 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.8282 (ttp80) REVERT: D 984 ASP cc_start: 0.7263 (p0) cc_final: 0.6952 (p0) outliers start: 42 outliers final: 29 residues processed: 333 average time/residue: 0.6702 time to fit residues: 265.8905 Evaluate side-chains 330 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 301 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 578 ARG Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 312 LEU 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 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 416 ILE 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 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 416 ILE Chi-restraints excluded: chain D residue 578 ARG 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 3 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 115 optimal weight: 0.0670 chunk 227 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 ASN A 957 ASN B 225 ASN B 771 HIS B 957 ASN C 225 ASN C 771 HIS C 957 ASN ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 HIS D 957 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.162477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105894 restraints weight = 36621.521| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.41 r_work: 0.3128 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32311 Z= 0.092 Angle : 0.480 10.670 44216 Z= 0.236 Chirality : 0.038 0.160 5400 Planarity : 0.003 0.045 5089 Dihedral : 8.386 108.374 9490 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.26 % Allowed : 13.07 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.14), residues: 3592 helix: 1.55 (0.13), residues: 1676 sheet: 0.58 (0.24), residues: 492 loop : 0.91 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.020 0.001 TYR C 163 PHE 0.029 0.001 PHE D 159 TRP 0.028 0.001 TRP C 23 HIS 0.003 0.000 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (32311) covalent geometry : angle 0.47983 / 0.24 (44216) hydrogen bonds : bond 0.03560 / 2.28 ( 1365) hydrogen bonds : angle 4.33016 / 3.11 ( 3735) ********************** 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 337 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 1.288 Fit side-chains REVERT: A 21 MET cc_start: 0.7697 (mpp) cc_final: 0.6878 (mmm) REVERT: A 182 ASN cc_start: 0.7360 (m-40) cc_final: 0.7081 (m-40) REVERT: A 216 GLN cc_start: 0.7643 (mt0) cc_final: 0.6926 (mm110) REVERT: A 265 ASN cc_start: 0.8610 (m-40) cc_final: 0.8250 (t0) REVERT: A 324 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7188 (mt-10) REVERT: A 374 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8015 (mm-30) REVERT: A 601 ASP cc_start: 0.7969 (t0) cc_final: 0.7682 (t0) REVERT: A 604 GLU cc_start: 0.8161 (mp0) cc_final: 0.7592 (pm20) REVERT: A 699 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8145 (mp0) REVERT: A 960 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.8279 (ttp80) REVERT: A 984 ASP cc_start: 0.7454 (p0) cc_final: 0.7135 (p0) REVERT: B 182 ASN cc_start: 0.7397 (m-40) cc_final: 0.7095 (m-40) REVERT: B 216 GLN cc_start: 0.7745 (mt0) cc_final: 0.7001 (mm110) REVERT: B 234 LYS cc_start: 0.8303 (ttpt) cc_final: 0.7981 (ptmt) REVERT: B 265 ASN cc_start: 0.8517 (m-40) cc_final: 0.8181 (t0) REVERT: B 324 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7158 (mt-10) REVERT: B 601 ASP cc_start: 0.8008 (t0) cc_final: 0.7672 (t0) REVERT: B 604 GLU cc_start: 0.8173 (mp0) cc_final: 0.7680 (pm20) REVERT: B 699 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8179 (mp0) REVERT: B 960 ARG cc_start: 0.8545 (ttp-110) cc_final: 0.8278 (ttp80) REVERT: B 984 ASP cc_start: 0.7455 (p0) cc_final: 0.7137 (p0) REVERT: C 21 MET cc_start: 0.7350 (mpp) cc_final: 0.6449 (mmm) REVERT: C 182 ASN cc_start: 0.7295 (m-40) cc_final: 0.7056 (m-40) REVERT: C 216 GLN cc_start: 0.7781 (mt0) cc_final: 0.7010 (mm110) REVERT: C 265 ASN cc_start: 0.8507 (m-40) cc_final: 0.8177 (t0) REVERT: C 324 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7084 (mt-10) REVERT: C 601 ASP cc_start: 0.7958 (t0) cc_final: 0.7679 (t0) REVERT: C 604 GLU cc_start: 0.8179 (mp0) cc_final: 0.7612 (pm20) REVERT: C 699 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8158 (mp0) REVERT: C 960 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.8289 (ttp80) REVERT: C 984 ASP cc_start: 0.7451 (p0) cc_final: 0.7135 (p0) REVERT: D 182 ASN cc_start: 0.7210 (m-40) cc_final: 0.6964 (m-40) REVERT: D 216 GLN cc_start: 0.7751 (mt0) cc_final: 0.6982 (mm110) REVERT: D 220 ILE cc_start: 0.7798 (mm) cc_final: 0.7579 (mm) REVERT: D 265 ASN cc_start: 0.8542 (m-40) cc_final: 0.8196 (t0) REVERT: D 324 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7156 (mt-10) REVERT: D 604 GLU cc_start: 0.8223 (mp0) cc_final: 0.7563 (pm20) REVERT: D 699 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8178 (mp0) REVERT: D 960 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8335 (ttp80) REVERT: D 984 ASP cc_start: 0.7374 (p0) cc_final: 0.7052 (p0) outliers start: 40 outliers final: 30 residues processed: 322 average time/residue: 0.6688 time to fit residues: 256.4855 Evaluate side-chains 325 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 578 ARG Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 312 LEU 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 578 ARG Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 941 VAL 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 416 ILE 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 983 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 578 ARG 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 283 optimal weight: 6.9990 chunk 169 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 341 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 92 optimal weight: 0.0770 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 ASN B 225 ASN B 771 HIS B 957 ASN C 225 ASN C 771 HIS C 957 ASN D 771 HIS D 957 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.163457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106888 restraints weight = 36677.905| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.50 r_work: 0.3206 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32311 Z= 0.090 Angle : 0.481 11.118 44216 Z= 0.236 Chirality : 0.038 0.144 5400 Planarity : 0.003 0.045 5089 Dihedral : 8.263 108.966 9490 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.16 % Allowed : 13.00 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.14), residues: 3592 helix: 1.58 (0.13), residues: 1676 sheet: 0.63 (0.24), residues: 492 loop : 0.92 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 607 TYR 0.010 0.001 TYR C 163 PHE 0.023 0.001 PHE D 187 TRP 0.031 0.001 TRP B 23 HIS 0.002 0.000 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (32311) covalent geometry : angle 0.48080 / 0.24 (44216) hydrogen bonds : bond 0.03451 / 2.22 ( 1365) hydrogen bonds : angle 4.28694 / 3.07 ( 3735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15662.83 seconds wall clock time: 266 minutes 17.34 seconds (15977.34 seconds total)