Starting phenix.real_space_refine on Fri Mar 6 11:32:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpa_32680/03_2026/7wpa_32680_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpa_32680/03_2026/7wpa_32680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wpa_32680/03_2026/7wpa_32680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpa_32680/03_2026/7wpa_32680.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpa_32680/03_2026/7wpa_32680_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpa_32680/03_2026/7wpa_32680_neut.cif" } resolution = 2.77 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= 0.001 sd= 0.021 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 Zn 1 6.06 5 S 142 5.16 5 Cl 1 4.86 5 C 19446 2.51 5 N 5000 2.21 5 O 5854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30444 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8329 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 56, 'TRANS': 1004} Chain breaks: 6 Chain: "B" Number of atoms: 8329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8329 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 56, 'TRANS': 1004} Chain breaks: 6 Chain: "C" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8297 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 56, 'TRANS': 1000} Chain breaks: 8 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.94, per 1000 atoms: 0.20 Number of scatterers: 30444 At special positions: 0 Unit cell: (126.896, 139.256, 244.728, 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) Zn 1 29.99 Cl 1 17.00 S 142 16.00 O 5854 8.00 N 5000 7.00 C 19446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.04 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 279 " " NAG A1302 " - " ASN A 613 " " NAG A1303 " - " ASN A 706 " " NAG A1304 " - " ASN A1071 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 714 " " NAG B1301 " - " ASN B 279 " " NAG B1302 " - " ASN B 613 " " NAG B1303 " - " ASN B 706 " " NAG B1304 " - " ASN B1071 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 714 " " NAG C1301 " - " ASN C 279 " " NAG C1302 " - " ASN C 613 " " NAG C1303 " - " ASN C 706 " " NAG C1304 " - " ASN C1071 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 714 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 546 " " NAG E 1 " - " ASN A 328 " " NAG F 1 " - " ASN A 798 " " NAG G 1 " - " ASN A1131 " " NAG H 1 " - " ASN A1095 " " NAG I 1 " - " ASN B 328 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1131 " " NAG L 1 " - " ASN B1095 " " NAG M 1 " - " ASN C 328 " " NAG N 1 " - " ASN C 798 " " NAG O 1 " - " ASN C1131 " " NAG P 1 " - " ASN C1095 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.3 seconds 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7112 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 50 sheets defined 25.1% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.621A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.638A pdb=" N ALA A 623 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.506A pdb=" N TYR A 753 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 750 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.572A pdb=" N GLN A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 removed outlier: 3.732A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.872A pdb=" N ALA A 849 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 850 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 851 " --> pdb=" O CYS A 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 846 through 851' Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.560A pdb=" N THR A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.564A pdb=" N ALA A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.608A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.613A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 removed outlier: 3.504A pdb=" N LYS A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.856A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 974 through 979 removed outlier: 4.490A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 979 " --> pdb=" O ASN A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 974 through 979' Processing helix chain 'A' and resid 982 through 1029 removed outlier: 3.659A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 4.092A pdb=" N SER A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.886A pdb=" N LEU B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 381 through 387 removed outlier: 3.820A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 381 through 387' Processing helix chain 'B' and resid 619 through 624 removed outlier: 4.111A pdb=" N HIS B 622 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 623 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 624 " --> pdb=" O ILE B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 624' Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.238A pdb=" N LEU B 750 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 751 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 754 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.784A pdb=" N ALA B 763 " --> pdb=" O GLN B 759 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 822 Processing helix chain 'B' and resid 845 through 852 Processing helix chain 'B' and resid 863 through 882 removed outlier: 3.692A pdb=" N THR B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.962A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 905 " --> pdb=" O TYR B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.633A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 916 " --> pdb=" O VAL B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 910 through 916' Processing helix chain 'B' and resid 916 through 936 removed outlier: 3.661A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.946A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.565A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 3.744A pdb=" N GLU B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 995 " --> pdb=" O ASP B 991 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.867A pdb=" N LEU C 368 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.567A pdb=" N GLN C 406 " --> pdb=" O GLU C 403 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C 408 " --> pdb=" O ARG C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 408' Processing helix chain 'C' and resid 620 through 627 removed outlier: 3.803A pdb=" N ASP C 624 " --> pdb=" O ILE C 621 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN C 625 " --> pdb=" O HIS C 622 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 627 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.638A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 779 removed outlier: 3.649A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 removed outlier: 4.047A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 853 removed outlier: 3.722A pdb=" N ALA C 849 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN C 850 " --> pdb=" O ILE C 847 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 851 " --> pdb=" O CYS C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 879 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.502A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 removed outlier: 3.624A pdb=" N ASN C 904 " --> pdb=" O ALA C 900 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 905 " --> pdb=" O TYR C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.575A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 936 removed outlier: 3.523A pdb=" N LYS C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 961 removed outlier: 4.072A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.682A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.577A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 996 " --> pdb=" O ARG C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.544A pdb=" N SER C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.929A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 67 removed outlier: 3.817A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 77 removed outlier: 4.795A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 98 removed outlier: 3.695A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 110 through 125 removed outlier: 3.639A pdb=" N THR D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 154 removed outlier: 4.198A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 removed outlier: 4.699A pdb=" N GLU D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 186 removed outlier: 4.253A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL D 184 " --> pdb=" O TYR D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.631A pdb=" N ARG D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.884A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 228 through 232 removed outlier: 4.071A pdb=" N GLU D 232 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.747A pdb=" N GLU D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.590A pdb=" N LEU D 278 " --> pdb=" O TRP D 275 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 275 through 279' Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.775A pdb=" N ALA D 296 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET D 297 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.758A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 383 removed outlier: 4.259A pdb=" N THR D 371 " --> pdb=" O ASP D 367 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 408 removed outlier: 3.755A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.730A pdb=" N TYR D 454 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 456 " --> pdb=" O PHE D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 484 removed outlier: 3.767A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 479 through 484' Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.589A pdb=" N LEU D 503 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 521 No H-bonds generated for 'chain 'D' and resid 519 through 521' Processing helix chain 'D' and resid 522 through 527 Processing helix chain 'D' and resid 528 through 531 removed outlier: 4.249A pdb=" N GLN D 531 " --> pdb=" O ALA D 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 528 through 531' Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 554 through 559 removed outlier: 3.853A pdb=" N LEU D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 554 through 559' Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 588 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.683A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 91 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 186 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 201 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 190 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 197 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.869A pdb=" N PHE A 43 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 583 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.869A pdb=" N PHE A 43 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 583 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.344A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.616A pdb=" N LEU A 82 " --> pdb=" O PHE A 235 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY A 101 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 127 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 124 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A 167 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.930A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.750A pdb=" N LYS A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 394 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 513 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 535 through 540 removed outlier: 3.659A pdb=" N GLY A 545 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 657 removed outlier: 5.003A pdb=" N THR A 693 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN A 655 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 698 through 701 removed outlier: 6.375A pdb=" N ALA A 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS C 787 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN A 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.899A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.899A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.268A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 784 through 786 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.490A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.535A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 264 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 186 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 201 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE B 196 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASP B 225 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE B 198 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 221 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.901A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.629A pdb=" N ARG B 234 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP B 102 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 114 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 129 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.857A pdb=" N GLY B 590 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 315 " --> pdb=" O GLY B 590 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AC8, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.593A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA B 432 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 373 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 470 through 471 removed outlier: 4.027A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 657 removed outlier: 6.257A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 688 " --> pdb=" O GLN B 672 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 672 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 663 " --> pdb=" O ILE B 667 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 714 through 725 removed outlier: 7.539A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.422A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 784 through 787 removed outlier: 6.063A pdb=" N ILE B 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1117 through 1119 removed outlier: 3.769A pdb=" N CYS B1079 " --> pdb=" O VAL B1130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.775A pdb=" N GLU C 186 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C 201 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N HIS C 202 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N ALA C 219 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.513A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE2, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AE3, first strand: chain 'C' and resid 114 through 119 removed outlier: 3.839A pdb=" N SER C 167 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.604A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.809A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ASN C 539 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY C 547 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 582 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 573 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AE7, first strand: chain 'C' and resid 395 through 399 removed outlier: 3.745A pdb=" N PHE C 397 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 449 through 450 Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.056A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 688 " --> pdb=" O GLN C 672 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.546A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 722 " --> pdb=" O PHE C1059 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.546A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 722 " --> pdb=" O PHE C1059 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.345A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF5, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.853A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 2.88 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: 5057 1.32 - 1.45: 8649 1.45 - 1.57: 17265 1.57 - 1.70: 0 1.70 - 1.82: 190 Bond restraints: 31161 Sorted by residual: bond pdb=" C ARG D 582 " pdb=" N PRO D 583 " ideal model delta sigma weight residual 1.337 1.379 -0.043 9.80e-03 1.04e+04 1.91e+01 bond pdb=" C PRO B 983 " pdb=" O PRO B 983 " ideal model delta sigma weight residual 1.240 1.196 0.045 1.12e-02 7.97e+03 1.59e+01 bond pdb=" C GLN C1139 " pdb=" N PRO C1140 " ideal model delta sigma weight residual 1.335 1.385 -0.050 1.36e-02 5.41e+03 1.35e+01 bond pdb=" C PRO A 983 " pdb=" O PRO A 983 " ideal model delta sigma weight residual 1.240 1.209 0.032 1.12e-02 7.97e+03 8.00e+00 bond pdb=" CA ALA A 986 " pdb=" CB ALA A 986 " ideal model delta sigma weight residual 1.528 1.485 0.044 1.59e-02 3.96e+03 7.49e+00 ... (remaining 31156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 42252 4.27 - 8.55: 123 8.55 - 12.82: 10 12.82 - 17.10: 0 17.10 - 21.37: 1 Bond angle restraints: 42386 Sorted by residual: angle pdb=" N PRO C 983 " pdb=" CA PRO C 983 " pdb=" C PRO C 983 " ideal model delta sigma weight residual 110.70 122.80 -12.10 1.22e+00 6.72e-01 9.83e+01 angle pdb=" C LEU A 458 " pdb=" N LYS A 459 " pdb=" CA LYS A 459 " ideal model delta sigma weight residual 122.21 143.58 -21.37 2.87e+00 1.21e-01 5.55e+01 angle pdb=" N VAL C 619 " pdb=" CA VAL C 619 " pdb=" C VAL C 619 " ideal model delta sigma weight residual 111.77 104.70 7.07 1.04e+00 9.25e-01 4.62e+01 angle pdb=" N PRO B 983 " pdb=" CA PRO B 983 " pdb=" C PRO B 983 " ideal model delta sigma weight residual 110.70 118.98 -8.28 1.22e+00 6.72e-01 4.60e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 120.79 129.08 -8.29 1.39e+00 5.18e-01 3.55e+01 ... (remaining 42381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 17220 17.71 - 35.42: 1483 35.42 - 53.13: 320 53.13 - 70.85: 58 70.85 - 88.56: 32 Dihedral angle restraints: 19113 sinusoidal: 8082 harmonic: 11031 Sorted by residual: dihedral pdb=" CB CYS C1079 " pdb=" SG CYS C1079 " pdb=" SG CYS C1123 " pdb=" CB CYS C1123 " ideal model delta sinusoidal sigma weight residual -86.00 2.56 -88.56 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS B1079 " pdb=" SG CYS B1079 " pdb=" SG CYS B1123 " pdb=" CB CYS B1123 " ideal model delta sinusoidal sigma weight residual -86.00 -14.28 -71.72 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CB CYS A 477 " pdb=" SG CYS A 477 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual 93.00 159.87 -66.87 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 19110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4759 0.118 - 0.237: 114 0.237 - 0.355: 1 0.355 - 0.473: 3 0.473 - 0.591: 2 Chirality restraints: 4879 Sorted by residual: chirality pdb=" CA PRO C 983 " pdb=" N PRO C 983 " pdb=" C PRO C 983 " pdb=" CB PRO C 983 " both_signs ideal model delta sigma weight residual False 2.72 2.13 0.59 2.00e-01 2.50e+01 8.74e+00 chirality pdb=" CA PRO B 983 " pdb=" N PRO B 983 " pdb=" C PRO B 983 " pdb=" CB PRO B 983 " both_signs ideal model delta sigma weight residual False 2.72 2.20 0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 4876 not shown) Planarity restraints: 5454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1139 " -0.050 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO A1140 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A1140 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1140 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 980 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.15e+00 pdb=" C ARG C 980 " -0.049 2.00e-02 2.50e+03 pdb=" O ARG C 980 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 981 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 980 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.34e+00 pdb=" C ARG A 980 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG A 980 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 981 " -0.016 2.00e-02 2.50e+03 ... (remaining 5451 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 9801 2.84 - 3.36: 24303 3.36 - 3.87: 49610 3.87 - 4.39: 54868 4.39 - 4.90: 95187 Nonbonded interactions: 233769 Sorted by model distance: nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 216 " model vdw 2.327 3.040 nonbonded pdb=" OG SER A 881 " pdb=" OG1 THR A 884 " model vdw 2.329 3.040 nonbonded pdb=" O SER A 940 " pdb=" OG SER A 940 " model vdw 2.331 3.040 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 216 " model vdw 2.332 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.335 3.040 ... (remaining 233764 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 17 through 42 or resid 44 through 401 or resid 403 through \ 1306)) selection = (chain 'B' and (resid 17 through 42 or resid 44 through 401 or resid 403 through \ 1306)) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 10.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 26.020 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.110 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:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31229 Z= 0.221 Angle : 0.789 21.374 42567 Z= 0.460 Chirality : 0.051 0.591 4879 Planarity : 0.006 0.075 5421 Dihedral : 13.934 85.564 11932 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 0.45 % Allowed : 5.85 % Favored : 93.70 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.11), residues: 3726 helix: -3.14 (0.12), residues: 842 sheet: -1.81 (0.18), residues: 667 loop : -2.93 (0.10), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 844 TYR 0.014 0.001 TYR D 385 PHE 0.025 0.001 PHE C 152 TRP 0.012 0.001 TRP D 461 HIS 0.005 0.000 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00393 (31161) covalent geometry : angle 0.77973 (42386) SS BOND : bond 0.00244 ( 23) SS BOND : angle 1.15031 ( 46) hydrogen bonds : bond 0.23282 ( 870) hydrogen bonds : angle 9.18288 ( 2466) link_BETA1-4 : bond 0.00863 ( 12) link_BETA1-4 : angle 3.00871 ( 36) link_NAG-ASN : bond 0.00312 ( 33) link_NAG-ASN : angle 1.92163 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 808 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.7773 (m) cc_final: 0.7176 (p) REVERT: A 151 GLU cc_start: 0.0857 (OUTLIER) cc_final: -0.1576 (pp20) REVERT: A 152 PHE cc_start: 0.4977 (OUTLIER) cc_final: 0.4418 (p90) REVERT: A 153 ARG cc_start: 0.5098 (OUTLIER) cc_final: 0.4420 (mtp-110) REVERT: A 185 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.6854 (mtm-85) REVERT: A 187 PHE cc_start: 0.7458 (m-80) cc_final: 0.7224 (m-80) REVERT: A 263 TYR cc_start: 0.7197 (m-80) cc_final: 0.6871 (m-80) REVERT: A 278 GLU cc_start: 0.7314 (pm20) cc_final: 0.7107 (pm20) REVERT: A 363 SER cc_start: 0.8177 (p) cc_final: 0.7966 (p) REVERT: A 393 TYR cc_start: 0.8081 (m-80) cc_final: 0.7620 (m-80) REVERT: A 450 TYR cc_start: 0.7165 (p90) cc_final: 0.6916 (p90) REVERT: A 492 TYR cc_start: 0.6860 (m-80) cc_final: 0.6516 (m-10) REVERT: A 495 ARG cc_start: 0.7474 (mpt-90) cc_final: 0.7233 (tpp-160) REVERT: A 593 SER cc_start: 0.8611 (p) cc_final: 0.8320 (m) REVERT: A 616 GLU cc_start: 0.7101 (pm20) cc_final: 0.6894 (pm20) REVERT: A 947 ASP cc_start: 0.7136 (m-30) cc_final: 0.6908 (m-30) REVERT: A 1028 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7457 (mt-10) REVERT: B 28 TYR cc_start: 0.7832 (m-80) cc_final: 0.7251 (m-80) REVERT: B 43 PHE cc_start: 0.8501 (t80) cc_final: 0.8200 (t80) REVERT: B 201 LYS cc_start: 0.6867 (tttt) cc_final: 0.6629 (ptmm) REVERT: B 221 GLU cc_start: 0.6621 (mp0) cc_final: 0.6310 (mp0) REVERT: B 302 SER cc_start: 0.8377 (m) cc_final: 0.8164 (p) REVERT: B 377 TYR cc_start: 0.7977 (m-80) cc_final: 0.7634 (m-80) REVERT: B 393 TYR cc_start: 0.6917 (m-10) cc_final: 0.5536 (m-10) REVERT: B 448 TYR cc_start: 0.7668 (m-10) cc_final: 0.7427 (m-10) REVERT: B 512 PHE cc_start: 0.6524 (m-80) cc_final: 0.6115 (m-80) REVERT: B 642 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7247 (p) REVERT: B 737 MET cc_start: 0.7001 (ttm) cc_final: 0.6786 (ttm) REVERT: B 800 SER cc_start: 0.8056 (t) cc_final: 0.7769 (p) REVERT: B 954 GLN cc_start: 0.7342 (tt0) cc_final: 0.7090 (tt0) REVERT: B 1016 ARG cc_start: 0.7370 (ttp-110) cc_final: 0.7086 (ttp-110) REVERT: C 94 GLU cc_start: 0.5862 (tp30) cc_final: 0.5118 (tp30) REVERT: C 98 ILE cc_start: 0.7731 (mm) cc_final: 0.7347 (mp) REVERT: C 127 LYS cc_start: 0.7331 (mtpp) cc_final: 0.7126 (mtpp) REVERT: C 263 TYR cc_start: 0.7597 (m-80) cc_final: 0.7266 (m-80) REVERT: C 350 TRP cc_start: 0.7512 (p-90) cc_final: 0.7287 (p-90) REVERT: C 544 LYS cc_start: 0.8312 (mttm) cc_final: 0.8033 (mmmm) REVERT: C 561 GLN cc_start: 0.6853 (tp-100) cc_final: 0.6513 (tp-100) REVERT: C 652 TYR cc_start: 0.8648 (t80) cc_final: 0.8439 (t80) REVERT: C 814 PHE cc_start: 0.5794 (t80) cc_final: 0.5512 (t80) REVERT: C 816 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7150 (mt-10) REVERT: C 820 PHE cc_start: 0.7914 (m-80) cc_final: 0.7624 (m-80) REVERT: C 864 ASP cc_start: 0.7439 (m-30) cc_final: 0.7238 (m-30) REVERT: C 865 GLU cc_start: 0.7260 (mp0) cc_final: 0.6997 (mp0) REVERT: C 987 GLU cc_start: 0.7466 (mp0) cc_final: 0.7187 (mp0) REVERT: D 32 PHE cc_start: 0.7998 (t80) cc_final: 0.7734 (t80) REVERT: D 51 ASN cc_start: 0.7769 (m-40) cc_final: 0.7475 (m-40) REVERT: D 64 ASN cc_start: 0.6362 (p0) cc_final: 0.4207 (m-40) REVERT: D 75 GLU cc_start: 0.6012 (pm20) cc_final: 0.5757 (pm20) REVERT: D 82 MET cc_start: 0.7636 (ptm) cc_final: 0.7022 (tmm) REVERT: D 121 ASN cc_start: 0.7208 (m110) cc_final: 0.6982 (m110) REVERT: D 187 LYS cc_start: 0.4999 (mttp) cc_final: 0.4432 (tttp) REVERT: D 199 TYR cc_start: 0.6059 (t80) cc_final: 0.5822 (t80) REVERT: D 307 ILE cc_start: 0.8638 (mm) cc_final: 0.8371 (mm) REVERT: D 359 LEU cc_start: 0.6257 (tp) cc_final: 0.5878 (pt) REVERT: D 398 GLU cc_start: 0.6603 (tp30) cc_final: 0.6187 (tp30) REVERT: D 456 LEU cc_start: 0.6280 (mm) cc_final: 0.6034 (pp) REVERT: D 579 MET cc_start: 0.2017 (tpt) cc_final: -0.0699 (pmt) outliers start: 15 outliers final: 3 residues processed: 816 average time/residue: 0.5725 time to fit residues: 559.9522 Evaluate side-chains 669 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 662 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 132 GLN A 191 ASN A 311 GLN A 318 GLN A 357 ASN A 391 ASN A 406 GLN A 447 ASN A 474 ASN A 478 ASN A 771 GLN A 898 GLN A 910 GLN A 952 ASN A 999 GLN A1002 GLN A1033 GLN A1051 GLN A1139 GLN B 215 GLN B 340 ASN B 411 GLN B 419 ASN B 478 ASN B 537 ASN B 553 ASN B 850 GLN B 946 GLN B 952 ASN B 999 GLN B1008 GLN B1020 ASN B1033 GLN B1068 GLN B1103 GLN C 97 ASN C 123 ASN C 268 GLN C 340 ASN C 411 GLN C 447 ASN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 ASN C 577 GLN C 774 ASN C 821 ASN C 932 GLN C 946 GLN C 962 GLN C 999 GLN C1020 ASN C1061 HIS D 61 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 340 GLN D 437 ASN D 472 GLN D 505 HIS D 522 GLN D 524 GLN D 578 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.187321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139440 restraints weight = 43397.679| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.34 r_work: 0.3586 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31229 Z= 0.166 Angle : 0.613 11.715 42567 Z= 0.312 Chirality : 0.045 0.221 4879 Planarity : 0.005 0.057 5421 Dihedral : 5.498 57.524 5012 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.29 % Allowed : 14.48 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.95 (0.12), residues: 3726 helix: -1.76 (0.15), residues: 871 sheet: -1.03 (0.19), residues: 646 loop : -2.43 (0.11), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 354 TYR 0.026 0.001 TYR C 901 PHE 0.023 0.001 PHE A 84 TRP 0.016 0.001 TRP A 433 HIS 0.006 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00384 (31161) covalent geometry : angle 0.59876 (42386) SS BOND : bond 0.00549 ( 23) SS BOND : angle 2.39142 ( 46) hydrogen bonds : bond 0.04297 ( 870) hydrogen bonds : angle 5.95167 ( 2466) link_BETA1-4 : bond 0.00504 ( 12) link_BETA1-4 : angle 1.76688 ( 36) link_NAG-ASN : bond 0.00418 ( 33) link_NAG-ASN : angle 2.05354 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 700 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.7850 (m) cc_final: 0.7553 (t) REVERT: A 151 GLU cc_start: 0.0426 (OUTLIER) cc_final: -0.1028 (pp20) REVERT: A 152 PHE cc_start: 0.4513 (OUTLIER) cc_final: 0.4178 (p90) REVERT: A 185 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.7971 (mtm-85) REVERT: A 187 PHE cc_start: 0.8354 (m-80) cc_final: 0.8143 (m-80) REVERT: A 191 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7542 (m-40) REVERT: A 344 PHE cc_start: 0.7194 (m-80) cc_final: 0.6111 (m-10) REVERT: A 393 TYR cc_start: 0.8402 (m-80) cc_final: 0.7952 (m-80) REVERT: A 450 TYR cc_start: 0.7584 (p90) cc_final: 0.7297 (p90) REVERT: A 492 TYR cc_start: 0.7162 (m-80) cc_final: 0.6620 (m-10) REVERT: A 507 VAL cc_start: 0.8094 (t) cc_final: 0.7850 (m) REVERT: A 593 SER cc_start: 0.8836 (p) cc_final: 0.8628 (m) REVERT: A 600 ASN cc_start: 0.8216 (t0) cc_final: 0.7800 (t0) REVERT: A 616 GLU cc_start: 0.7863 (pm20) cc_final: 0.7551 (pm20) REVERT: A 808 LYS cc_start: 0.7535 (mtmt) cc_final: 0.7103 (mttt) REVERT: A 817 ASP cc_start: 0.8012 (m-30) cc_final: 0.7689 (m-30) REVERT: A 1002 GLN cc_start: 0.8363 (tp40) cc_final: 0.8122 (mm-40) REVERT: A 1016 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7948 (ttp-170) REVERT: B 34 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7529 (mpt90) REVERT: B 201 LYS cc_start: 0.8016 (tttt) cc_final: 0.7648 (tttt) REVERT: B 304 THR cc_start: 0.8326 (p) cc_final: 0.8067 (t) REVERT: B 439 ASP cc_start: 0.7808 (m-30) cc_final: 0.7530 (m-30) REVERT: B 448 TYR cc_start: 0.7917 (m-10) cc_final: 0.7572 (m-10) REVERT: B 462 GLU cc_start: 0.7593 (pt0) cc_final: 0.7327 (pt0) REVERT: B 490 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7982 (ttm170) REVERT: B 512 PHE cc_start: 0.7800 (m-80) cc_final: 0.7570 (m-80) REVERT: B 526 LYS cc_start: 0.8400 (mmmm) cc_final: 0.8175 (mmmm) REVERT: B 667 ILE cc_start: 0.8423 (pt) cc_final: 0.8147 (pt) REVERT: B 800 SER cc_start: 0.8695 (t) cc_final: 0.8433 (p) REVERT: B 982 ASP cc_start: 0.7918 (p0) cc_final: 0.7663 (p0) REVERT: B 1016 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7957 (ttp-170) REVERT: B 1111 ILE cc_start: 0.8701 (mm) cc_final: 0.8470 (mt) REVERT: C 94 GLU cc_start: 0.6557 (tp30) cc_final: 0.5623 (tp30) REVERT: C 113 GLN cc_start: 0.7957 (mt0) cc_final: 0.7750 (mt0) REVERT: C 127 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8169 (mtpp) REVERT: C 164 GLU cc_start: 0.7709 (mp0) cc_final: 0.7494 (mp0) REVERT: C 263 TYR cc_start: 0.8449 (m-80) cc_final: 0.8056 (m-80) REVERT: C 433 TRP cc_start: 0.6462 (m100) cc_final: 0.6171 (m100) REVERT: C 561 GLN cc_start: 0.7526 (tp-100) cc_final: 0.7043 (tp-100) REVERT: C 814 PHE cc_start: 0.6795 (t80) cc_final: 0.6147 (t80) REVERT: C 816 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7536 (mt-10) REVERT: C 818 LEU cc_start: 0.8456 (mp) cc_final: 0.8237 (mp) REVERT: C 820 PHE cc_start: 0.8292 (m-80) cc_final: 0.7912 (m-80) REVERT: C 865 GLU cc_start: 0.8000 (mp0) cc_final: 0.7674 (mp0) REVERT: C 899 MET cc_start: 0.8716 (mmm) cc_final: 0.8493 (mmt) REVERT: C 930 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8301 (mtmm) REVERT: C 966 LYS cc_start: 0.8651 (ptpt) cc_final: 0.8428 (pttm) REVERT: C 1014 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7924 (mt-10) REVERT: C 1028 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8068 (mt-10) REVERT: C 1070 LYS cc_start: 0.8424 (tttm) cc_final: 0.8160 (mtpp) REVERT: D 37 GLU cc_start: 0.7883 (pt0) cc_final: 0.7263 (pm20) REVERT: D 51 ASN cc_start: 0.7676 (m-40) cc_final: 0.7403 (m-40) REVERT: D 64 ASN cc_start: 0.6653 (p0) cc_final: 0.4284 (m-40) REVERT: D 82 MET cc_start: 0.7738 (ptm) cc_final: 0.7305 (ppp) REVERT: D 190 MET cc_start: 0.4387 (ttp) cc_final: 0.4070 (ttt) REVERT: D 249 MET cc_start: 0.0974 (mmm) cc_final: 0.0125 (mmm) REVERT: D 274 PHE cc_start: 0.6332 (p90) cc_final: 0.6012 (p90) REVERT: D 307 ILE cc_start: 0.8509 (mm) cc_final: 0.8304 (mm) REVERT: D 335 ASP cc_start: 0.3330 (t0) cc_final: 0.2850 (t70) REVERT: D 375 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7166 (mm-30) REVERT: D 381 TYR cc_start: 0.7270 (t80) cc_final: 0.7056 (t80) REVERT: D 385 TYR cc_start: 0.5855 (p90) cc_final: 0.5455 (p90) REVERT: D 398 GLU cc_start: 0.6702 (tp30) cc_final: 0.6286 (tp30) REVERT: D 488 VAL cc_start: 0.4848 (m) cc_final: 0.4594 (t) REVERT: D 579 MET cc_start: 0.2453 (tpt) cc_final: -0.0480 (pmt) outliers start: 109 outliers final: 41 residues processed: 750 average time/residue: 0.6166 time to fit residues: 550.7444 Evaluate side-chains 699 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 653 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 513 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 234 optimal weight: 0.5980 chunk 296 optimal weight: 0.0470 chunk 157 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 250 optimal weight: 8.9990 chunk 161 optimal weight: 0.0980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 191 ASN A 236 GLN A 268 GLN A 560 GLN A 672 GLN A 781 GLN A1116 ASN B 113 GLN B 923 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 123 ASN C 268 GLN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 ASN C 700 ASN C 962 GLN C1132 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.185715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138235 restraints weight = 43628.362| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.33 r_work: 0.3572 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31229 Z= 0.131 Angle : 0.571 11.424 42567 Z= 0.290 Chirality : 0.044 0.179 4879 Planarity : 0.004 0.060 5421 Dihedral : 5.005 58.659 5003 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.17 % Allowed : 17.62 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.33 (0.13), residues: 3726 helix: -0.97 (0.17), residues: 880 sheet: -0.73 (0.19), residues: 664 loop : -2.13 (0.12), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.025 0.001 TYR C 901 PHE 0.023 0.001 PHE A 453 TRP 0.022 0.001 TRP D 48 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00305 (31161) covalent geometry : angle 0.55837 (42386) SS BOND : bond 0.00530 ( 23) SS BOND : angle 1.97271 ( 46) hydrogen bonds : bond 0.03605 ( 870) hydrogen bonds : angle 5.41473 ( 2466) link_BETA1-4 : bond 0.00348 ( 12) link_BETA1-4 : angle 1.70347 ( 36) link_NAG-ASN : bond 0.00349 ( 33) link_NAG-ASN : angle 1.92944 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 683 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.7773 (m) cc_final: 0.7496 (t) REVERT: A 151 GLU cc_start: 0.0177 (OUTLIER) cc_final: -0.0937 (pp20) REVERT: A 152 PHE cc_start: 0.4451 (OUTLIER) cc_final: 0.4167 (p90) REVERT: A 185 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.7950 (mtm-85) REVERT: A 393 TYR cc_start: 0.8405 (m-80) cc_final: 0.8117 (m-80) REVERT: A 450 TYR cc_start: 0.7495 (p90) cc_final: 0.7180 (p90) REVERT: A 492 TYR cc_start: 0.7156 (m-80) cc_final: 0.6920 (m-10) REVERT: A 507 VAL cc_start: 0.8190 (t) cc_final: 0.7908 (m) REVERT: A 571 ASP cc_start: 0.8223 (t0) cc_final: 0.7860 (t0) REVERT: A 585 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8103 (p) REVERT: A 600 ASN cc_start: 0.8227 (t0) cc_final: 0.7825 (t0) REVERT: A 616 GLU cc_start: 0.7941 (pm20) cc_final: 0.7603 (pm20) REVERT: A 1002 GLN cc_start: 0.8350 (tp40) cc_final: 0.8117 (mm-40) REVERT: B 304 THR cc_start: 0.8356 (p) cc_final: 0.8105 (t) REVERT: B 400 ARG cc_start: 0.8406 (ttm170) cc_final: 0.8115 (ttm170) REVERT: B 403 GLU cc_start: 0.7741 (mp0) cc_final: 0.7300 (mm-30) REVERT: B 439 ASP cc_start: 0.7867 (m-30) cc_final: 0.7610 (m-30) REVERT: B 448 TYR cc_start: 0.7916 (m-10) cc_final: 0.7625 (m-10) REVERT: B 454 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7792 (tpt90) REVERT: B 455 LYS cc_start: 0.8654 (mppt) cc_final: 0.8431 (mppt) REVERT: B 462 GLU cc_start: 0.7621 (pt0) cc_final: 0.7344 (pt0) REVERT: B 526 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8200 (mmmm) REVERT: B 667 ILE cc_start: 0.8379 (pt) cc_final: 0.7930 (mp) REVERT: B 800 SER cc_start: 0.8726 (t) cc_final: 0.8466 (p) REVERT: B 947 ASP cc_start: 0.8080 (m-30) cc_final: 0.7828 (m-30) REVERT: B 985 GLU cc_start: 0.8173 (tp30) cc_final: 0.7955 (tp30) REVERT: B 1016 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7950 (ttp-110) REVERT: B 1081 ASP cc_start: 0.7584 (p0) cc_final: 0.7163 (p0) REVERT: C 47 VAL cc_start: 0.8699 (p) cc_final: 0.8457 (m) REVERT: C 127 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8189 (mtpp) REVERT: C 164 GLU cc_start: 0.7629 (mp0) cc_final: 0.7422 (mp0) REVERT: C 263 TYR cc_start: 0.8462 (m-80) cc_final: 0.8176 (m-80) REVERT: C 350 TRP cc_start: 0.7943 (p-90) cc_final: 0.7352 (p-90) REVERT: C 433 TRP cc_start: 0.6539 (m100) cc_final: 0.6205 (m100) REVERT: C 561 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7035 (tp-100) REVERT: C 814 PHE cc_start: 0.6789 (t80) cc_final: 0.6121 (t80) REVERT: C 816 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7478 (mt-10) REVERT: C 818 LEU cc_start: 0.8432 (mp) cc_final: 0.8212 (mp) REVERT: C 820 PHE cc_start: 0.8268 (m-80) cc_final: 0.7885 (m-80) REVERT: C 865 GLU cc_start: 0.7992 (mp0) cc_final: 0.7670 (mp0) REVERT: C 899 MET cc_start: 0.8674 (mmm) cc_final: 0.8439 (mmt) REVERT: C 930 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8326 (mtmm) REVERT: C 966 LYS cc_start: 0.8673 (ptpt) cc_final: 0.8433 (pttm) REVERT: C 1028 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8021 (mt-10) REVERT: D 51 ASN cc_start: 0.7742 (m-40) cc_final: 0.7465 (m-40) REVERT: D 64 ASN cc_start: 0.6639 (p0) cc_final: 0.4239 (m-40) REVERT: D 82 MET cc_start: 0.7725 (ptm) cc_final: 0.7396 (ppp) REVERT: D 199 TYR cc_start: 0.5774 (t80) cc_final: 0.5477 (t80) REVERT: D 249 MET cc_start: 0.1635 (mmm) cc_final: 0.0827 (mmm) REVERT: D 307 ILE cc_start: 0.8464 (mm) cc_final: 0.8240 (tp) REVERT: D 309 LYS cc_start: 0.7755 (mmpt) cc_final: 0.7254 (mmtm) REVERT: D 315 PHE cc_start: 0.7319 (m-80) cc_final: 0.6877 (m-80) REVERT: D 318 VAL cc_start: 0.5305 (p) cc_final: 0.4788 (p) REVERT: D 327 PHE cc_start: 0.6965 (t80) cc_final: 0.6657 (t80) REVERT: D 375 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7136 (mp0) REVERT: D 398 GLU cc_start: 0.6724 (tp30) cc_final: 0.6324 (tp30) REVERT: D 452 PHE cc_start: 0.5905 (t80) cc_final: 0.5510 (t80) REVERT: D 488 VAL cc_start: 0.4692 (m) cc_final: 0.4428 (t) REVERT: D 554 LEU cc_start: 0.5301 (pt) cc_final: 0.4830 (tp) REVERT: D 579 MET cc_start: 0.2487 (tpt) cc_final: -0.0440 (pmt) outliers start: 105 outliers final: 54 residues processed: 732 average time/residue: 0.6047 time to fit residues: 526.0114 Evaluate side-chains 717 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 660 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 513 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 346 optimal weight: 1.9990 chunk 311 optimal weight: 0.9980 chunk 135 optimal weight: 0.0770 chunk 120 optimal weight: 3.9990 chunk 194 optimal weight: 0.2980 chunk 240 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 283 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 268 GLN A 560 GLN A 672 GLN A 781 GLN A 910 GLN A1116 ASN B 191 ASN B 759 GLN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 113 GLN C 123 ASN C 183 ASN C 268 GLN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 ASN C 962 GLN C1002 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.184937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137320 restraints weight = 43273.529| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.33 r_work: 0.3560 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31229 Z= 0.130 Angle : 0.568 10.059 42567 Z= 0.286 Chirality : 0.044 0.207 4879 Planarity : 0.004 0.060 5421 Dihedral : 4.837 57.772 5003 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.47 % Allowed : 18.40 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.98 (0.13), residues: 3726 helix: -0.59 (0.18), residues: 883 sheet: -0.54 (0.19), residues: 665 loop : -1.95 (0.12), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1016 TYR 0.024 0.001 TYR C 901 PHE 0.023 0.001 PHE B 90 TRP 0.012 0.001 TRP D 328 HIS 0.004 0.000 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00304 (31161) covalent geometry : angle 0.55668 (42386) SS BOND : bond 0.00506 ( 23) SS BOND : angle 1.63581 ( 46) hydrogen bonds : bond 0.03404 ( 870) hydrogen bonds : angle 5.15509 ( 2466) link_BETA1-4 : bond 0.00407 ( 12) link_BETA1-4 : angle 1.64165 ( 36) link_NAG-ASN : bond 0.00272 ( 33) link_NAG-ASN : angle 1.90930 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 682 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.7747 (m) cc_final: 0.7473 (t) REVERT: A 151 GLU cc_start: 0.0174 (OUTLIER) cc_final: -0.0864 (pp20) REVERT: A 152 PHE cc_start: 0.4346 (OUTLIER) cc_final: 0.4089 (p90) REVERT: A 185 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.7764 (mtm-85) REVERT: A 344 PHE cc_start: 0.7383 (m-80) cc_final: 0.6261 (m-10) REVERT: A 450 TYR cc_start: 0.7596 (p90) cc_final: 0.7305 (p90) REVERT: A 492 TYR cc_start: 0.7199 (m-80) cc_final: 0.6992 (m-10) REVERT: A 506 ARG cc_start: 0.7808 (ttt180) cc_final: 0.7289 (ttt180) REVERT: A 507 VAL cc_start: 0.8207 (t) cc_final: 0.7879 (m) REVERT: A 571 ASP cc_start: 0.8188 (t0) cc_final: 0.7768 (t0) REVERT: A 585 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8035 (p) REVERT: A 600 ASN cc_start: 0.8221 (t0) cc_final: 0.7837 (t0) REVERT: A 616 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: A 728 MET cc_start: 0.8580 (ttp) cc_final: 0.8363 (ptm) REVERT: A 856 THR cc_start: 0.8609 (t) cc_final: 0.8396 (p) REVERT: A 1002 GLN cc_start: 0.8347 (tp40) cc_final: 0.8091 (mm-40) REVERT: B 58 PHE cc_start: 0.8451 (m-10) cc_final: 0.8249 (m-10) REVERT: B 304 THR cc_start: 0.8363 (p) cc_final: 0.8118 (t) REVERT: B 439 ASP cc_start: 0.7863 (m-30) cc_final: 0.7650 (m-30) REVERT: B 454 ARG cc_start: 0.8189 (tpt170) cc_final: 0.7810 (tpt90) REVERT: B 455 LYS cc_start: 0.8668 (mppt) cc_final: 0.8414 (mppt) REVERT: B 462 GLU cc_start: 0.7709 (pt0) cc_final: 0.7439 (pt0) REVERT: B 490 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7879 (ttm170) REVERT: B 526 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8168 (mmmm) REVERT: B 657 TYR cc_start: 0.8661 (m-80) cc_final: 0.8412 (m-80) REVERT: B 667 ILE cc_start: 0.8541 (pt) cc_final: 0.8075 (mp) REVERT: B 800 SER cc_start: 0.8730 (t) cc_final: 0.8484 (p) REVERT: B 947 ASP cc_start: 0.8123 (m-30) cc_final: 0.7882 (m-30) REVERT: B 985 GLU cc_start: 0.8174 (tp30) cc_final: 0.7936 (tp30) REVERT: B 1081 ASP cc_start: 0.7605 (p0) cc_final: 0.7212 (p0) REVERT: C 47 VAL cc_start: 0.8703 (p) cc_final: 0.8465 (m) REVERT: C 127 LYS cc_start: 0.8403 (mtpp) cc_final: 0.8172 (mtpp) REVERT: C 164 GLU cc_start: 0.7667 (mp0) cc_final: 0.7465 (mp0) REVERT: C 183 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7278 (p0) REVERT: C 203 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8234 (p) REVERT: C 263 TYR cc_start: 0.8471 (m-80) cc_final: 0.7980 (m-80) REVERT: C 350 TRP cc_start: 0.7972 (p-90) cc_final: 0.7490 (p-90) REVERT: C 433 TRP cc_start: 0.6624 (m100) cc_final: 0.6255 (m100) REVERT: C 561 GLN cc_start: 0.7511 (tp-100) cc_final: 0.6991 (tp-100) REVERT: C 814 PHE cc_start: 0.6737 (t80) cc_final: 0.6040 (t80) REVERT: C 816 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7476 (mt-10) REVERT: C 818 LEU cc_start: 0.8410 (mp) cc_final: 0.8185 (mp) REVERT: C 820 PHE cc_start: 0.8275 (m-80) cc_final: 0.7940 (m-80) REVERT: C 869 GLN cc_start: 0.8479 (tt0) cc_final: 0.8154 (mt0) REVERT: C 899 MET cc_start: 0.8666 (mmm) cc_final: 0.8436 (mmt) REVERT: C 930 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8327 (mtmm) REVERT: C 966 LYS cc_start: 0.8654 (ptpt) cc_final: 0.8370 (pttm) REVERT: C 1002 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8211 (mm-40) REVERT: C 1028 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8070 (mt-10) REVERT: D 31 LYS cc_start: 0.8236 (tmtt) cc_final: 0.7985 (tmmm) REVERT: D 32 PHE cc_start: 0.8159 (t80) cc_final: 0.7822 (t80) REVERT: D 42 GLN cc_start: 0.8015 (mt0) cc_final: 0.7757 (mt0) REVERT: D 51 ASN cc_start: 0.7746 (m-40) cc_final: 0.7479 (m-40) REVERT: D 60 GLN cc_start: 0.6403 (tm-30) cc_final: 0.5899 (tm-30) REVERT: D 64 ASN cc_start: 0.6658 (p0) cc_final: 0.3970 (m-40) REVERT: D 249 MET cc_start: 0.2397 (mmm) cc_final: 0.1568 (mmm) REVERT: D 274 PHE cc_start: 0.6263 (p90) cc_final: 0.5794 (p90) REVERT: D 315 PHE cc_start: 0.7320 (m-80) cc_final: 0.6691 (m-80) REVERT: D 332 MET cc_start: 0.5231 (OUTLIER) cc_final: 0.3180 (ppp) REVERT: D 375 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7210 (mp0) REVERT: D 380 GLN cc_start: 0.7201 (tp-100) cc_final: 0.6003 (tp-100) REVERT: D 398 GLU cc_start: 0.6678 (tp30) cc_final: 0.6292 (tp30) REVERT: D 452 PHE cc_start: 0.5864 (t80) cc_final: 0.5458 (t80) REVERT: D 554 LEU cc_start: 0.5236 (pt) cc_final: 0.4931 (tp) REVERT: D 579 MET cc_start: 0.2458 (tpt) cc_final: -0.0376 (pmt) outliers start: 115 outliers final: 59 residues processed: 733 average time/residue: 0.6258 time to fit residues: 541.8104 Evaluate side-chains 728 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 660 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 260 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 200 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.0030 chunk 114 optimal weight: 5.9990 chunk 334 optimal weight: 30.0000 chunk 64 optimal weight: 0.9990 chunk 210 optimal weight: 0.0270 overall best weight: 0.6210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 268 GLN A 318 GLN A 560 GLN A 781 GLN A 910 GLN B 318 GLN B 537 ASN B 759 GLN B 910 GLN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN C 516 HIS C 700 ASN C 707 ASN C 962 GLN D 24 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.183827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136018 restraints weight = 43201.300| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.34 r_work: 0.3543 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31229 Z= 0.155 Angle : 0.580 8.960 42567 Z= 0.292 Chirality : 0.044 0.230 4879 Planarity : 0.004 0.071 5421 Dihedral : 4.776 56.973 5001 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.26 % Allowed : 19.70 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.80 (0.13), residues: 3726 helix: -0.44 (0.18), residues: 884 sheet: -0.40 (0.19), residues: 664 loop : -1.84 (0.12), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 234 TYR 0.024 0.001 TYR C 901 PHE 0.026 0.001 PHE A 163 TRP 0.026 0.001 TRP D 328 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00369 (31161) covalent geometry : angle 0.56884 (42386) SS BOND : bond 0.00584 ( 23) SS BOND : angle 1.72429 ( 46) hydrogen bonds : bond 0.03527 ( 870) hydrogen bonds : angle 5.08352 ( 2466) link_BETA1-4 : bond 0.00419 ( 12) link_BETA1-4 : angle 1.61964 ( 36) link_NAG-ASN : bond 0.00259 ( 33) link_NAG-ASN : angle 1.95987 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 673 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.7793 (m) cc_final: 0.7533 (t) REVERT: A 151 GLU cc_start: 0.0081 (OUTLIER) cc_final: -0.1034 (pp20) REVERT: A 152 PHE cc_start: 0.4381 (OUTLIER) cc_final: 0.4098 (p90) REVERT: A 185 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.7779 (mtm-85) REVERT: A 234 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7545 (ttt-90) REVERT: A 344 PHE cc_start: 0.7461 (m-80) cc_final: 0.6199 (m-10) REVERT: A 399 ILE cc_start: 0.7536 (pt) cc_final: 0.7311 (mt) REVERT: A 450 TYR cc_start: 0.7640 (p90) cc_final: 0.7404 (p90) REVERT: A 492 TYR cc_start: 0.7270 (m-80) cc_final: 0.7055 (m-10) REVERT: A 495 ARG cc_start: 0.8080 (tpp-160) cc_final: 0.7814 (mmt90) REVERT: A 506 ARG cc_start: 0.7823 (ttt180) cc_final: 0.7345 (ttt180) REVERT: A 507 VAL cc_start: 0.8208 (t) cc_final: 0.7872 (m) REVERT: A 571 ASP cc_start: 0.8197 (t0) cc_final: 0.7757 (t0) REVERT: A 596 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8653 (p) REVERT: A 600 ASN cc_start: 0.8179 (t0) cc_final: 0.7791 (t0) REVERT: A 616 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: A 1002 GLN cc_start: 0.8366 (tp40) cc_final: 0.8045 (mm-40) REVERT: B 304 THR cc_start: 0.8398 (p) cc_final: 0.8170 (t) REVERT: B 400 ARG cc_start: 0.8380 (ttm110) cc_final: 0.8175 (ttt90) REVERT: B 403 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7613 (mt-10) REVERT: B 439 ASP cc_start: 0.7903 (m-30) cc_final: 0.7614 (m-30) REVERT: B 448 TYR cc_start: 0.7932 (m-10) cc_final: 0.7560 (m-10) REVERT: B 454 ARG cc_start: 0.8221 (tpt170) cc_final: 0.7846 (tpp80) REVERT: B 455 LYS cc_start: 0.8692 (mppt) cc_final: 0.8413 (mppt) REVERT: B 462 GLU cc_start: 0.7762 (pt0) cc_final: 0.7489 (pt0) REVERT: B 526 LYS cc_start: 0.8448 (mmmm) cc_final: 0.8197 (mmmm) REVERT: B 657 TYR cc_start: 0.8656 (m-80) cc_final: 0.8405 (m-80) REVERT: B 667 ILE cc_start: 0.8570 (pt) cc_final: 0.8141 (mp) REVERT: B 800 SER cc_start: 0.8762 (t) cc_final: 0.8514 (p) REVERT: B 822 LYS cc_start: 0.8623 (mmtm) cc_final: 0.8396 (tptm) REVERT: B 947 ASP cc_start: 0.8131 (m-30) cc_final: 0.7872 (m-30) REVERT: B 985 GLU cc_start: 0.8190 (tp30) cc_final: 0.7945 (tp30) REVERT: B 1081 ASP cc_start: 0.7588 (p0) cc_final: 0.7231 (p0) REVERT: C 47 VAL cc_start: 0.8737 (p) cc_final: 0.8492 (m) REVERT: C 52 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 127 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8209 (mtpp) REVERT: C 203 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8242 (p) REVERT: C 263 TYR cc_start: 0.8479 (m-80) cc_final: 0.7977 (m-80) REVERT: C 278 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7728 (pp20) REVERT: C 350 TRP cc_start: 0.8000 (p-90) cc_final: 0.7532 (p-90) REVERT: C 433 TRP cc_start: 0.6686 (m100) cc_final: 0.6368 (m100) REVERT: C 561 GLN cc_start: 0.7530 (tp-100) cc_final: 0.7000 (tp-100) REVERT: C 723 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8697 (mm) REVERT: C 818 LEU cc_start: 0.8405 (mp) cc_final: 0.8174 (mp) REVERT: C 820 PHE cc_start: 0.8284 (m-80) cc_final: 0.7939 (m-80) REVERT: C 869 GLN cc_start: 0.8517 (tt0) cc_final: 0.8201 (mt0) REVERT: C 899 MET cc_start: 0.8702 (mmm) cc_final: 0.8463 (mmt) REVERT: C 930 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8278 (mtmp) REVERT: C 933 ASP cc_start: 0.7554 (m-30) cc_final: 0.7312 (m-30) REVERT: C 1115 ASP cc_start: 0.7883 (m-30) cc_final: 0.7574 (m-30) REVERT: D 24 GLN cc_start: 0.7117 (mm110) cc_final: 0.6878 (mm-40) REVERT: D 31 LYS cc_start: 0.8228 (tmtt) cc_final: 0.7678 (ttmt) REVERT: D 32 PHE cc_start: 0.8132 (t80) cc_final: 0.7645 (t80) REVERT: D 42 GLN cc_start: 0.8046 (mt0) cc_final: 0.7782 (mt0) REVERT: D 51 ASN cc_start: 0.7826 (m-40) cc_final: 0.7579 (m-40) REVERT: D 64 ASN cc_start: 0.6641 (p0) cc_final: 0.3987 (m-40) REVERT: D 249 MET cc_start: 0.2409 (mmm) cc_final: 0.1583 (mmm) REVERT: D 274 PHE cc_start: 0.6250 (p90) cc_final: 0.5804 (p90) REVERT: D 313 LYS cc_start: 0.7184 (mtpm) cc_final: 0.6866 (mttp) REVERT: D 315 PHE cc_start: 0.7394 (m-80) cc_final: 0.6361 (m-10) REVERT: D 318 VAL cc_start: 0.5090 (p) cc_final: 0.4377 (t) REVERT: D 332 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.3423 (ppp) REVERT: D 381 TYR cc_start: 0.7241 (t80) cc_final: 0.6971 (t80) REVERT: D 398 GLU cc_start: 0.6634 (tp30) cc_final: 0.6234 (tp30) REVERT: D 452 PHE cc_start: 0.5866 (t80) cc_final: 0.5460 (t80) REVERT: D 579 MET cc_start: 0.2538 (tpt) cc_final: -0.0280 (pmt) outliers start: 108 outliers final: 60 residues processed: 727 average time/residue: 0.6374 time to fit residues: 548.1634 Evaluate side-chains 728 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 660 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 235 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 298 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 307 optimal weight: 1.9990 chunk 332 optimal weight: 9.9990 chunk 357 optimal weight: 7.9990 chunk 47 optimal weight: 0.1980 chunk 311 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 268 GLN A 411 GLN A 560 GLN A 672 GLN A 781 GLN A 910 GLN A 932 GLN A 952 ASN A1116 ASN B 759 GLN B 946 GLN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN C 700 ASN C 904 ASN C 962 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.182362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134547 restraints weight = 43097.125| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.32 r_work: 0.3524 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 31229 Z= 0.196 Angle : 0.608 10.345 42567 Z= 0.306 Chirality : 0.046 0.243 4879 Planarity : 0.004 0.059 5421 Dihedral : 4.896 55.975 5001 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.62 % Allowed : 20.27 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.13), residues: 3726 helix: -0.32 (0.18), residues: 883 sheet: -0.29 (0.19), residues: 654 loop : -1.76 (0.12), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 234 TYR 0.031 0.001 TYR C 901 PHE 0.026 0.002 PHE A 163 TRP 0.015 0.001 TRP A 883 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00469 (31161) covalent geometry : angle 0.59612 (42386) SS BOND : bond 0.00607 ( 23) SS BOND : angle 1.79304 ( 46) hydrogen bonds : bond 0.03782 ( 870) hydrogen bonds : angle 5.08368 ( 2466) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 1.61889 ( 36) link_NAG-ASN : bond 0.00255 ( 33) link_NAG-ASN : angle 2.03399 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 685 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.7828 (m) cc_final: 0.7567 (t) REVERT: A 151 GLU cc_start: 0.0351 (OUTLIER) cc_final: -0.0833 (pp20) REVERT: A 152 PHE cc_start: 0.4278 (OUTLIER) cc_final: 0.3962 (p90) REVERT: A 185 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.7948 (mtm-85) REVERT: A 226 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7267 (mp) REVERT: A 234 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7636 (ttt-90) REVERT: A 344 PHE cc_start: 0.7685 (m-80) cc_final: 0.6442 (m-80) REVERT: A 353 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7534 (ttpp) REVERT: A 399 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7370 (mt) REVERT: A 495 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7873 (mmt90) REVERT: A 506 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7252 (ttt180) REVERT: A 571 ASP cc_start: 0.8170 (t0) cc_final: 0.7743 (t0) REVERT: A 596 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 600 ASN cc_start: 0.8166 (t0) cc_final: 0.7714 (t0) REVERT: A 616 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: A 822 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8626 (mttp) REVERT: A 1002 GLN cc_start: 0.8395 (tp40) cc_final: 0.8124 (mm-40) REVERT: B 304 THR cc_start: 0.8417 (p) cc_final: 0.8205 (t) REVERT: B 398 VAL cc_start: 0.8725 (p) cc_final: 0.8498 (t) REVERT: B 400 ARG cc_start: 0.8401 (ttm110) cc_final: 0.8198 (ttt90) REVERT: B 403 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7770 (mm-30) REVERT: B 439 ASP cc_start: 0.7927 (m-30) cc_final: 0.7717 (m-30) REVERT: B 454 ARG cc_start: 0.8324 (tpt170) cc_final: 0.7925 (tpp80) REVERT: B 462 GLU cc_start: 0.7831 (pt0) cc_final: 0.7576 (pt0) REVERT: B 526 LYS cc_start: 0.8438 (mmmm) cc_final: 0.8205 (mmmm) REVERT: B 657 TYR cc_start: 0.8631 (m-80) cc_final: 0.8392 (m-80) REVERT: B 667 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8187 (mp) REVERT: B 701 SER cc_start: 0.8816 (t) cc_final: 0.8616 (t) REVERT: B 800 SER cc_start: 0.8758 (t) cc_final: 0.8526 (p) REVERT: B 822 LYS cc_start: 0.8671 (mmtm) cc_final: 0.8444 (tptm) REVERT: B 892 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: B 947 ASP cc_start: 0.8130 (m-30) cc_final: 0.7869 (m-30) REVERT: B 982 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7665 (p0) REVERT: B 1081 ASP cc_start: 0.7649 (p0) cc_final: 0.7295 (p0) REVERT: C 47 VAL cc_start: 0.8772 (p) cc_final: 0.8526 (m) REVERT: C 52 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 94 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5562 (mp0) REVERT: C 113 GLN cc_start: 0.8100 (mm110) cc_final: 0.7720 (mm110) REVERT: C 123 ASN cc_start: 0.7532 (t0) cc_final: 0.7166 (t0) REVERT: C 127 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8198 (mtpp) REVERT: C 203 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8358 (p) REVERT: C 263 TYR cc_start: 0.8472 (m-80) cc_final: 0.7973 (m-80) REVERT: C 278 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7683 (pp20) REVERT: C 350 TRP cc_start: 0.8084 (p-90) cc_final: 0.7673 (p-90) REVERT: C 433 TRP cc_start: 0.6740 (m100) cc_final: 0.6433 (m100) REVERT: C 737 MET cc_start: 0.8415 (mmm) cc_final: 0.8035 (tpp) REVERT: C 820 PHE cc_start: 0.8292 (m-80) cc_final: 0.7958 (m-80) REVERT: C 869 GLN cc_start: 0.8538 (tt0) cc_final: 0.8249 (mt0) REVERT: C 899 MET cc_start: 0.8658 (mmm) cc_final: 0.8412 (mmt) REVERT: C 930 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8261 (mtmm) REVERT: C 933 ASP cc_start: 0.7723 (m-30) cc_final: 0.7459 (m-30) REVERT: C 970 ILE cc_start: 0.8650 (pt) cc_final: 0.8173 (mm) REVERT: C 1007 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: C 1042 LYS cc_start: 0.8588 (tptm) cc_final: 0.8360 (mmmm) REVERT: D 24 GLN cc_start: 0.7137 (mm110) cc_final: 0.6818 (mm-40) REVERT: D 31 LYS cc_start: 0.8239 (tmtt) cc_final: 0.7711 (ttmt) REVERT: D 32 PHE cc_start: 0.8091 (t80) cc_final: 0.7567 (t80) REVERT: D 42 GLN cc_start: 0.8031 (mt0) cc_final: 0.7762 (mt0) REVERT: D 51 ASN cc_start: 0.7853 (m-40) cc_final: 0.7618 (m-40) REVERT: D 64 ASN cc_start: 0.6733 (p0) cc_final: 0.4383 (m-40) REVERT: D 187 LYS cc_start: 0.4646 (tptm) cc_final: 0.4435 (tptm) REVERT: D 249 MET cc_start: 0.2409 (mmm) cc_final: 0.1590 (mmm) REVERT: D 274 PHE cc_start: 0.6226 (p90) cc_final: 0.5821 (p90) REVERT: D 313 LYS cc_start: 0.7033 (mtpm) cc_final: 0.6709 (mttp) REVERT: D 332 MET cc_start: 0.5227 (OUTLIER) cc_final: 0.3440 (ppp) REVERT: D 398 GLU cc_start: 0.6617 (tp30) cc_final: 0.6207 (tp30) REVERT: D 452 PHE cc_start: 0.5859 (t80) cc_final: 0.5431 (t80) REVERT: D 579 MET cc_start: 0.2616 (tpt) cc_final: -0.0250 (pmt) outliers start: 120 outliers final: 64 residues processed: 738 average time/residue: 0.6330 time to fit residues: 553.2645 Evaluate side-chains 750 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 671 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 364 optimal weight: 3.9990 chunk 345 optimal weight: 10.0000 chunk 342 optimal weight: 0.0670 chunk 148 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 327 optimal weight: 8.9990 chunk 331 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 203 optimal weight: 0.0980 chunk 213 optimal weight: 0.1980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 560 GLN A 910 GLN A 932 GLN B1002 GLN C 215 GLN C 236 GLN C 641 GLN C 700 ASN C 904 ASN C 962 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS D 572 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.182324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134252 restraints weight = 43106.112| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.33 r_work: 0.3516 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 31229 Z= 0.197 Angle : 0.612 9.978 42567 Z= 0.309 Chirality : 0.046 0.282 4879 Planarity : 0.004 0.057 5421 Dihedral : 4.907 53.726 5001 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.26 % Allowed : 21.51 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.13), residues: 3726 helix: -0.16 (0.18), residues: 869 sheet: -0.33 (0.19), residues: 659 loop : -1.71 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 352 TYR 0.035 0.002 TYR C 901 PHE 0.031 0.002 PHE C 589 TRP 0.018 0.001 TRP A 883 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00469 (31161) covalent geometry : angle 0.60064 (42386) SS BOND : bond 0.00605 ( 23) SS BOND : angle 1.80244 ( 46) hydrogen bonds : bond 0.03740 ( 870) hydrogen bonds : angle 5.08025 ( 2466) link_BETA1-4 : bond 0.00357 ( 12) link_BETA1-4 : angle 1.58312 ( 36) link_NAG-ASN : bond 0.00255 ( 33) link_NAG-ASN : angle 1.99002 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 674 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.7793 (m) cc_final: 0.7552 (t) REVERT: A 151 GLU cc_start: 0.0462 (OUTLIER) cc_final: -0.0699 (pp20) REVERT: A 152 PHE cc_start: 0.4337 (OUTLIER) cc_final: 0.4016 (p90) REVERT: A 185 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8098 (mtt90) REVERT: A 226 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7320 (mp) REVERT: A 234 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7893 (ttm-80) REVERT: A 344 PHE cc_start: 0.7784 (m-80) cc_final: 0.6557 (m-80) REVERT: A 353 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7511 (ttpp) REVERT: A 399 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7369 (mt) REVERT: A 506 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7316 (ttt180) REVERT: A 571 ASP cc_start: 0.8195 (t0) cc_final: 0.7662 (t0) REVERT: A 600 ASN cc_start: 0.8195 (t0) cc_final: 0.7822 (t0) REVERT: A 616 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: A 911 ASN cc_start: 0.8236 (p0) cc_final: 0.8010 (p0) REVERT: B 304 THR cc_start: 0.8438 (p) cc_final: 0.8209 (t) REVERT: B 365 LEU cc_start: 0.8226 (mt) cc_final: 0.8011 (mp) REVERT: B 398 VAL cc_start: 0.8727 (p) cc_final: 0.8519 (t) REVERT: B 418 TYR cc_start: 0.8038 (m-10) cc_final: 0.7407 (m-80) REVERT: B 439 ASP cc_start: 0.7940 (m-30) cc_final: 0.7719 (m-30) REVERT: B 462 GLU cc_start: 0.7873 (pt0) cc_final: 0.7618 (pt0) REVERT: B 526 LYS cc_start: 0.8410 (mmmm) cc_final: 0.8180 (mmmm) REVERT: B 632 VAL cc_start: 0.8516 (m) cc_final: 0.8289 (t) REVERT: B 657 TYR cc_start: 0.8636 (m-80) cc_final: 0.8336 (m-80) REVERT: B 667 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8175 (mp) REVERT: B 800 SER cc_start: 0.8744 (t) cc_final: 0.8508 (p) REVERT: B 822 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8459 (tptm) REVERT: B 892 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: B 947 ASP cc_start: 0.8138 (m-30) cc_final: 0.7873 (m-30) REVERT: B 973 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8703 (m) REVERT: B 982 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7688 (p0) REVERT: B 1081 ASP cc_start: 0.7663 (p0) cc_final: 0.7321 (p0) REVERT: C 47 VAL cc_start: 0.8775 (p) cc_final: 0.8522 (m) REVERT: C 52 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 94 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5528 (mp0) REVERT: C 113 GLN cc_start: 0.8039 (mm110) cc_final: 0.7680 (mm110) REVERT: C 127 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8181 (mtpp) REVERT: C 164 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7546 (mp0) REVERT: C 203 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8356 (p) REVERT: C 278 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7757 (pp20) REVERT: C 350 TRP cc_start: 0.8102 (p-90) cc_final: 0.7745 (p-90) REVERT: C 433 TRP cc_start: 0.6839 (m100) cc_final: 0.6515 (m100) REVERT: C 571 ASP cc_start: 0.8065 (t70) cc_final: 0.7461 (t0) REVERT: C 737 MET cc_start: 0.8477 (mmm) cc_final: 0.8107 (tpp) REVERT: C 816 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8041 (mt-10) REVERT: C 820 PHE cc_start: 0.8277 (m-80) cc_final: 0.7896 (m-80) REVERT: C 869 GLN cc_start: 0.8546 (tt0) cc_final: 0.8259 (mt0) REVERT: C 930 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8319 (mtmt) REVERT: C 933 ASP cc_start: 0.7788 (m-30) cc_final: 0.7557 (m-30) REVERT: C 970 ILE cc_start: 0.8655 (pt) cc_final: 0.8236 (mm) REVERT: C 1042 LYS cc_start: 0.8568 (tptm) cc_final: 0.8346 (mmmm) REVERT: D 24 GLN cc_start: 0.7159 (mm110) cc_final: 0.6808 (mm-40) REVERT: D 31 LYS cc_start: 0.8273 (tmtt) cc_final: 0.7737 (ttmt) REVERT: D 32 PHE cc_start: 0.8084 (t80) cc_final: 0.7577 (t80) REVERT: D 42 GLN cc_start: 0.8049 (mt0) cc_final: 0.7780 (mt0) REVERT: D 51 ASN cc_start: 0.7859 (m-40) cc_final: 0.7626 (m-40) REVERT: D 64 ASN cc_start: 0.6690 (p0) cc_final: 0.4304 (m-40) REVERT: D 249 MET cc_start: 0.2530 (mmm) cc_final: 0.1724 (mmm) REVERT: D 274 PHE cc_start: 0.6256 (p90) cc_final: 0.5888 (p90) REVERT: D 313 LYS cc_start: 0.7078 (mtpm) cc_final: 0.6755 (mttp) REVERT: D 398 GLU cc_start: 0.6637 (tp30) cc_final: 0.6229 (tp30) REVERT: D 452 PHE cc_start: 0.5889 (t80) cc_final: 0.5452 (t80) REVERT: D 480 MET cc_start: 0.6666 (mpm) cc_final: 0.5769 (ptp) REVERT: D 579 MET cc_start: 0.2687 (tpt) cc_final: -0.0220 (pmt) outliers start: 108 outliers final: 76 residues processed: 724 average time/residue: 0.6419 time to fit residues: 546.9139 Evaluate side-chains 752 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 663 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 204 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 315 optimal weight: 0.4980 chunk 368 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 285 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 910 GLN A 932 GLN A 999 GLN A1116 ASN B 202 HIS B 502 HIS B 999 GLN C 123 ASN C 183 ASN C 700 ASN C 999 GLN C1002 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.182484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134414 restraints weight = 43145.846| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.33 r_work: 0.3521 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31229 Z= 0.166 Angle : 0.603 10.336 42567 Z= 0.304 Chirality : 0.045 0.284 4879 Planarity : 0.004 0.059 5421 Dihedral : 4.835 54.014 5001 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.71 % Allowed : 21.60 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.49 (0.13), residues: 3726 helix: -0.09 (0.18), residues: 882 sheet: -0.33 (0.19), residues: 672 loop : -1.64 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 352 TYR 0.045 0.001 TYR A 450 PHE 0.033 0.001 PHE C 589 TRP 0.015 0.001 TRP A 883 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00396 (31161) covalent geometry : angle 0.59165 (42386) SS BOND : bond 0.00541 ( 23) SS BOND : angle 1.66807 ( 46) hydrogen bonds : bond 0.03595 ( 870) hydrogen bonds : angle 5.02744 ( 2466) link_BETA1-4 : bond 0.00356 ( 12) link_BETA1-4 : angle 1.56081 ( 36) link_NAG-ASN : bond 0.00344 ( 33) link_NAG-ASN : angle 2.08249 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 667 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7027 (mmt180) REVERT: A 114 SER cc_start: 0.7764 (m) cc_final: 0.7528 (t) REVERT: A 151 GLU cc_start: 0.0512 (OUTLIER) cc_final: -0.0654 (pp20) REVERT: A 152 PHE cc_start: 0.4303 (OUTLIER) cc_final: 0.3993 (p90) REVERT: A 185 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8126 (mtm-85) REVERT: A 234 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7867 (ttm-80) REVERT: A 344 PHE cc_start: 0.7823 (m-80) cc_final: 0.6596 (m-80) REVERT: A 353 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7495 (ttpp) REVERT: A 399 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7384 (mt) REVERT: A 506 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7322 (ttt180) REVERT: A 571 ASP cc_start: 0.8189 (t0) cc_final: 0.7671 (t0) REVERT: A 600 ASN cc_start: 0.8199 (t0) cc_final: 0.7827 (t0) REVERT: A 616 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: A 801 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8328 (mm110) REVERT: A 911 ASN cc_start: 0.8217 (p0) cc_final: 0.8010 (p0) REVERT: A 1002 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8161 (mm-40) REVERT: B 304 THR cc_start: 0.8442 (p) cc_final: 0.8213 (t) REVERT: B 365 LEU cc_start: 0.8239 (mt) cc_final: 0.8039 (mp) REVERT: B 398 VAL cc_start: 0.8691 (p) cc_final: 0.8487 (t) REVERT: B 418 TYR cc_start: 0.8037 (m-10) cc_final: 0.7411 (m-80) REVERT: B 439 ASP cc_start: 0.7929 (m-30) cc_final: 0.7716 (m-30) REVERT: B 462 GLU cc_start: 0.7881 (pt0) cc_final: 0.7603 (pt0) REVERT: B 526 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8191 (mmmm) REVERT: B 632 VAL cc_start: 0.8519 (m) cc_final: 0.8291 (t) REVERT: B 657 TYR cc_start: 0.8636 (m-80) cc_final: 0.8339 (m-80) REVERT: B 667 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8173 (mp) REVERT: B 800 SER cc_start: 0.8730 (t) cc_final: 0.8499 (p) REVERT: B 822 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8452 (tptm) REVERT: B 947 ASP cc_start: 0.8121 (m-30) cc_final: 0.7868 (m-30) REVERT: B 973 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8697 (m) REVERT: B 982 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7695 (p0) REVERT: B 1081 ASP cc_start: 0.7667 (p0) cc_final: 0.7316 (p0) REVERT: C 47 VAL cc_start: 0.8785 (p) cc_final: 0.8525 (m) REVERT: C 52 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7629 (tm-30) REVERT: C 94 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5696 (mp0) REVERT: C 113 GLN cc_start: 0.8030 (mm110) cc_final: 0.7638 (mm110) REVERT: C 127 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8165 (mtpp) REVERT: C 164 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7541 (mp0) REVERT: C 203 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8320 (p) REVERT: C 278 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7777 (pp20) REVERT: C 350 TRP cc_start: 0.8103 (p-90) cc_final: 0.7822 (p-90) REVERT: C 433 TRP cc_start: 0.6855 (m100) cc_final: 0.6533 (m100) REVERT: C 571 ASP cc_start: 0.8074 (t70) cc_final: 0.7497 (t0) REVERT: C 801 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8503 (mt0) REVERT: C 816 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7967 (mt-10) REVERT: C 820 PHE cc_start: 0.8277 (m-80) cc_final: 0.7935 (m-80) REVERT: C 869 GLN cc_start: 0.8544 (tt0) cc_final: 0.8284 (mt0) REVERT: C 899 MET cc_start: 0.8707 (mmm) cc_final: 0.8449 (mmt) REVERT: C 930 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8328 (mtmt) REVERT: C 933 ASP cc_start: 0.7818 (m-30) cc_final: 0.7593 (m-30) REVERT: C 970 ILE cc_start: 0.8557 (pt) cc_final: 0.8246 (mm) REVERT: C 1042 LYS cc_start: 0.8550 (tptm) cc_final: 0.8335 (mmmm) REVERT: D 24 GLN cc_start: 0.7154 (mm110) cc_final: 0.6851 (mm-40) REVERT: D 31 LYS cc_start: 0.8278 (tmtt) cc_final: 0.7742 (ttmt) REVERT: D 32 PHE cc_start: 0.8085 (t80) cc_final: 0.7571 (t80) REVERT: D 42 GLN cc_start: 0.8058 (mt0) cc_final: 0.7779 (mt0) REVERT: D 51 ASN cc_start: 0.7867 (m-40) cc_final: 0.7652 (m-40) REVERT: D 64 ASN cc_start: 0.6604 (p0) cc_final: 0.4146 (m-40) REVERT: D 249 MET cc_start: 0.2547 (mmm) cc_final: 0.1764 (mmm) REVERT: D 274 PHE cc_start: 0.6259 (p90) cc_final: 0.5918 (p90) REVERT: D 313 LYS cc_start: 0.7063 (mtpm) cc_final: 0.6817 (mttp) REVERT: D 398 GLU cc_start: 0.6642 (tp30) cc_final: 0.6241 (tp30) REVERT: D 452 PHE cc_start: 0.5808 (t80) cc_final: 0.5278 (t80) REVERT: D 455 MET cc_start: 0.4755 (OUTLIER) cc_final: 0.3675 (ppp) REVERT: D 480 MET cc_start: 0.6645 (mpm) cc_final: 0.5724 (ptp) REVERT: D 579 MET cc_start: 0.2784 (tpt) cc_final: -0.0144 (pmt) outliers start: 123 outliers final: 80 residues processed: 726 average time/residue: 0.6289 time to fit residues: 536.5388 Evaluate side-chains 752 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 659 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 238 optimal weight: 0.9990 chunk 329 optimal weight: 4.9990 chunk 246 optimal weight: 0.0060 chunk 256 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 chunk 349 optimal weight: 0.9990 chunk 279 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 910 GLN A 932 GLN A 975 ASN A 999 GLN B 502 HIS B 748 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 183 ASN C 700 ASN C 999 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.182135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134406 restraints weight = 43070.985| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.32 r_work: 0.3517 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31229 Z= 0.177 Angle : 0.619 10.492 42567 Z= 0.312 Chirality : 0.046 0.292 4879 Planarity : 0.004 0.057 5421 Dihedral : 4.827 54.105 5001 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.32 % Allowed : 22.44 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 3726 helix: 0.03 (0.18), residues: 867 sheet: -0.37 (0.19), residues: 683 loop : -1.62 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 352 TYR 0.037 0.001 TYR A 450 PHE 0.035 0.001 PHE C 589 TRP 0.017 0.001 TRP A 883 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00423 (31161) covalent geometry : angle 0.60828 (42386) SS BOND : bond 0.00560 ( 23) SS BOND : angle 1.69209 ( 46) hydrogen bonds : bond 0.03638 ( 870) hydrogen bonds : angle 5.02591 ( 2466) link_BETA1-4 : bond 0.00468 ( 12) link_BETA1-4 : angle 1.55963 ( 36) link_NAG-ASN : bond 0.00234 ( 33) link_NAG-ASN : angle 1.98523 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 671 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7039 (mmt180) REVERT: A 114 SER cc_start: 0.7764 (m) cc_final: 0.7506 (t) REVERT: A 151 GLU cc_start: 0.0643 (OUTLIER) cc_final: -0.0532 (pp20) REVERT: A 152 PHE cc_start: 0.4270 (OUTLIER) cc_final: 0.3950 (p90) REVERT: A 185 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.8130 (mtm-85) REVERT: A 226 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7373 (mp) REVERT: A 344 PHE cc_start: 0.7855 (m-80) cc_final: 0.6627 (m-80) REVERT: A 353 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7563 (ttpp) REVERT: A 399 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7401 (mt) REVERT: A 506 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7327 (ttt180) REVERT: A 571 ASP cc_start: 0.8204 (t0) cc_final: 0.7662 (t0) REVERT: A 600 ASN cc_start: 0.8195 (t0) cc_final: 0.7826 (t0) REVERT: A 616 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: A 911 ASN cc_start: 0.8241 (p0) cc_final: 0.8035 (p0) REVERT: A 984 PRO cc_start: 0.8358 (Cg_exo) cc_final: 0.8025 (Cg_endo) REVERT: A 1002 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8176 (mm-40) REVERT: B 304 THR cc_start: 0.8450 (p) cc_final: 0.8218 (t) REVERT: B 365 LEU cc_start: 0.8306 (mt) cc_final: 0.8104 (mp) REVERT: B 418 TYR cc_start: 0.8039 (m-10) cc_final: 0.7409 (m-80) REVERT: B 439 ASP cc_start: 0.7943 (m-30) cc_final: 0.7725 (m-30) REVERT: B 462 GLU cc_start: 0.7861 (pt0) cc_final: 0.7592 (pt0) REVERT: B 526 LYS cc_start: 0.8417 (mmmm) cc_final: 0.8184 (mmmm) REVERT: B 577 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7183 (mt0) REVERT: B 632 VAL cc_start: 0.8519 (m) cc_final: 0.8295 (t) REVERT: B 657 TYR cc_start: 0.8650 (m-80) cc_final: 0.8363 (m-80) REVERT: B 667 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8176 (mp) REVERT: B 800 SER cc_start: 0.8742 (t) cc_final: 0.8510 (p) REVERT: B 822 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8457 (tptm) REVERT: B 947 ASP cc_start: 0.8123 (m-30) cc_final: 0.7861 (m-30) REVERT: B 954 GLN cc_start: 0.8329 (tt0) cc_final: 0.8102 (tt0) REVERT: B 973 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8700 (m) REVERT: B 982 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7685 (p0) REVERT: B 1081 ASP cc_start: 0.7694 (p0) cc_final: 0.7333 (p0) REVERT: C 30 ASN cc_start: 0.8044 (t0) cc_final: 0.7817 (t0) REVERT: C 47 VAL cc_start: 0.8773 (p) cc_final: 0.8513 (m) REVERT: C 52 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7641 (tm-30) REVERT: C 94 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5278 (mp0) REVERT: C 113 GLN cc_start: 0.8031 (mm110) cc_final: 0.7629 (mm110) REVERT: C 127 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8163 (mtpp) REVERT: C 164 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7501 (mp0) REVERT: C 203 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8344 (p) REVERT: C 278 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7757 (pp20) REVERT: C 350 TRP cc_start: 0.8117 (p-90) cc_final: 0.7845 (p-90) REVERT: C 433 TRP cc_start: 0.6890 (m100) cc_final: 0.6564 (m100) REVERT: C 571 ASP cc_start: 0.8077 (t70) cc_final: 0.7489 (t0) REVERT: C 801 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8512 (mt0) REVERT: C 816 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7973 (mt-10) REVERT: C 820 PHE cc_start: 0.8288 (m-80) cc_final: 0.7939 (m-80) REVERT: C 869 GLN cc_start: 0.8540 (tt0) cc_final: 0.8238 (mt0) REVERT: C 930 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8324 (mtmt) REVERT: C 970 ILE cc_start: 0.8524 (pt) cc_final: 0.8281 (mm) REVERT: C 1042 LYS cc_start: 0.8550 (tptm) cc_final: 0.8337 (mmmm) REVERT: D 24 GLN cc_start: 0.7123 (mm110) cc_final: 0.6835 (mm-40) REVERT: D 32 PHE cc_start: 0.8065 (t80) cc_final: 0.7707 (t80) REVERT: D 41 TYR cc_start: 0.7894 (t80) cc_final: 0.7436 (t80) REVERT: D 42 GLN cc_start: 0.8059 (mt0) cc_final: 0.7780 (mt0) REVERT: D 51 ASN cc_start: 0.7828 (m-40) cc_final: 0.7625 (m-40) REVERT: D 64 ASN cc_start: 0.6598 (p0) cc_final: 0.4116 (m-40) REVERT: D 249 MET cc_start: 0.2503 (mmm) cc_final: 0.1717 (mmm) REVERT: D 274 PHE cc_start: 0.6262 (p90) cc_final: 0.6013 (p90) REVERT: D 313 LYS cc_start: 0.7071 (mtpm) cc_final: 0.6856 (mttp) REVERT: D 398 GLU cc_start: 0.6625 (tp30) cc_final: 0.6221 (tp30) REVERT: D 455 MET cc_start: 0.4783 (OUTLIER) cc_final: 0.3781 (ppp) REVERT: D 480 MET cc_start: 0.6550 (mpm) cc_final: 0.5673 (ptp) REVERT: D 579 MET cc_start: 0.2784 (tpt) cc_final: -0.0205 (pmt) outliers start: 110 outliers final: 82 residues processed: 722 average time/residue: 0.6310 time to fit residues: 538.1657 Evaluate side-chains 764 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 667 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 321 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 172 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 330 optimal weight: 9.9990 chunk 284 optimal weight: 0.1980 chunk 224 optimal weight: 0.8980 chunk 365 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 869 GLN A 910 GLN A1116 ASN B 502 HIS C 700 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.182214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134343 restraints weight = 42914.914| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.33 r_work: 0.3519 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31229 Z= 0.170 Angle : 0.624 10.800 42567 Z= 0.314 Chirality : 0.046 0.276 4879 Planarity : 0.004 0.059 5421 Dihedral : 4.789 54.144 5001 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.35 % Allowed : 22.71 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 3726 helix: 0.10 (0.18), residues: 861 sheet: -0.34 (0.19), residues: 672 loop : -1.58 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 400 TYR 0.046 0.002 TYR A 450 PHE 0.035 0.001 PHE C 589 TRP 0.022 0.001 TRP D 478 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00409 (31161) covalent geometry : angle 0.61347 (42386) SS BOND : bond 0.00541 ( 23) SS BOND : angle 1.67748 ( 46) hydrogen bonds : bond 0.03587 ( 870) hydrogen bonds : angle 5.01313 ( 2466) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 1.53088 ( 36) link_NAG-ASN : bond 0.00246 ( 33) link_NAG-ASN : angle 2.00325 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 676 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7029 (mmt180) REVERT: A 114 SER cc_start: 0.7740 (m) cc_final: 0.7476 (t) REVERT: A 185 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: A 226 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7392 (mp) REVERT: A 277 ASN cc_start: 0.7937 (p0) cc_final: 0.7724 (p0) REVERT: A 344 PHE cc_start: 0.7854 (m-80) cc_final: 0.6626 (m-80) REVERT: A 353 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7556 (ttpp) REVERT: A 506 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7331 (ttt180) REVERT: A 571 ASP cc_start: 0.8209 (t0) cc_final: 0.7642 (t0) REVERT: A 600 ASN cc_start: 0.8195 (t0) cc_final: 0.7830 (t0) REVERT: A 616 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: A 984 PRO cc_start: 0.8345 (Cg_exo) cc_final: 0.8004 (Cg_endo) REVERT: B 304 THR cc_start: 0.8455 (p) cc_final: 0.8219 (t) REVERT: B 365 LEU cc_start: 0.8326 (mt) cc_final: 0.8126 (mp) REVERT: B 418 TYR cc_start: 0.8042 (m-10) cc_final: 0.7405 (m-80) REVERT: B 439 ASP cc_start: 0.7921 (m-30) cc_final: 0.7694 (m-30) REVERT: B 462 GLU cc_start: 0.7859 (pt0) cc_final: 0.7594 (pt0) REVERT: B 526 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8194 (mmmm) REVERT: B 553 ASN cc_start: 0.8070 (m-40) cc_final: 0.7770 (t0) REVERT: B 632 VAL cc_start: 0.8519 (m) cc_final: 0.8303 (t) REVERT: B 657 TYR cc_start: 0.8655 (m-80) cc_final: 0.8367 (m-80) REVERT: B 667 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8177 (mp) REVERT: B 800 SER cc_start: 0.8737 (t) cc_final: 0.8504 (p) REVERT: B 822 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8446 (tptm) REVERT: B 947 ASP cc_start: 0.8130 (m-30) cc_final: 0.7870 (m-30) REVERT: B 954 GLN cc_start: 0.8335 (tt0) cc_final: 0.8112 (tt0) REVERT: B 973 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8691 (m) REVERT: B 982 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7688 (p0) REVERT: B 1081 ASP cc_start: 0.7715 (p0) cc_final: 0.7362 (p0) REVERT: C 30 ASN cc_start: 0.8058 (t0) cc_final: 0.7822 (t0) REVERT: C 52 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7675 (tm-30) REVERT: C 94 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5204 (mp0) REVERT: C 113 GLN cc_start: 0.8035 (mm110) cc_final: 0.7640 (mm110) REVERT: C 127 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8144 (mtpp) REVERT: C 164 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7508 (mp0) REVERT: C 203 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 278 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: C 350 TRP cc_start: 0.8117 (p-90) cc_final: 0.7874 (p-90) REVERT: C 433 TRP cc_start: 0.6884 (m100) cc_final: 0.6563 (m100) REVERT: C 571 ASP cc_start: 0.8099 (t70) cc_final: 0.7499 (t0) REVERT: C 801 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8505 (mt0) REVERT: C 816 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7978 (mt-10) REVERT: C 820 PHE cc_start: 0.8276 (m-80) cc_final: 0.7915 (m-80) REVERT: C 869 GLN cc_start: 0.8544 (tt0) cc_final: 0.8243 (mt0) REVERT: C 930 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8340 (mtmt) REVERT: C 966 LYS cc_start: 0.8672 (ptpp) cc_final: 0.8227 (mtmt) REVERT: C 970 ILE cc_start: 0.8507 (pt) cc_final: 0.8272 (mm) REVERT: C 1042 LYS cc_start: 0.8552 (tptm) cc_final: 0.8342 (mmmm) REVERT: D 24 GLN cc_start: 0.7091 (mm110) cc_final: 0.6795 (mm-40) REVERT: D 32 PHE cc_start: 0.8078 (t80) cc_final: 0.7679 (t80) REVERT: D 42 GLN cc_start: 0.8070 (mt0) cc_final: 0.7780 (mt0) REVERT: D 51 ASN cc_start: 0.7871 (m-40) cc_final: 0.7667 (m-40) REVERT: D 64 ASN cc_start: 0.6567 (p0) cc_final: 0.3970 (m-40) REVERT: D 249 MET cc_start: 0.2458 (mmm) cc_final: 0.1677 (mmm) REVERT: D 274 PHE cc_start: 0.6197 (p90) cc_final: 0.5892 (p90) REVERT: D 398 GLU cc_start: 0.6619 (tp30) cc_final: 0.6214 (tp30) REVERT: D 480 MET cc_start: 0.6546 (mpm) cc_final: 0.5712 (ptp) REVERT: D 579 MET cc_start: 0.2814 (tpt) cc_final: -0.0177 (pmt) outliers start: 111 outliers final: 85 residues processed: 732 average time/residue: 0.6268 time to fit residues: 544.4546 Evaluate side-chains 758 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 663 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 301 optimal weight: 0.0270 chunk 312 optimal weight: 0.5980 chunk 360 optimal weight: 5.9990 chunk 252 optimal weight: 0.0870 chunk 319 optimal weight: 0.9990 chunk 169 optimal weight: 0.1980 chunk 356 optimal weight: 10.0000 chunk 85 optimal weight: 0.1980 chunk 112 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 76 optimal weight: 0.0070 overall best weight: 0.1034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 502 HIS A 560 GLN A 869 GLN A 910 GLN A 962 GLN A 999 GLN A1116 ASN B 202 HIS B 502 HIS ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 700 ASN C 904 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.184499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137112 restraints weight = 43205.675| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.31 r_work: 0.3562 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31229 Z= 0.104 Angle : 0.595 10.598 42567 Z= 0.300 Chirality : 0.044 0.273 4879 Planarity : 0.004 0.097 5421 Dihedral : 4.491 54.713 4996 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.50 % Allowed : 23.62 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.14), residues: 3726 helix: 0.32 (0.19), residues: 860 sheet: -0.31 (0.19), residues: 691 loop : -1.51 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 400 TYR 0.051 0.001 TYR D 199 PHE 0.035 0.001 PHE C 589 TRP 0.022 0.001 TRP D 478 HIS 0.028 0.001 HIS B 502 Details of bonding type rmsd covalent geometry : bond 0.00239 (31161) covalent geometry : angle 0.58632 (42386) SS BOND : bond 0.00399 ( 23) SS BOND : angle 1.29744 ( 46) hydrogen bonds : bond 0.03048 ( 870) hydrogen bonds : angle 4.80223 ( 2466) link_BETA1-4 : bond 0.00390 ( 12) link_BETA1-4 : angle 1.48538 ( 36) link_NAG-ASN : bond 0.00277 ( 33) link_NAG-ASN : angle 1.84684 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15351.52 seconds wall clock time: 260 minutes 34.75 seconds (15634.75 seconds total)