Starting phenix.real_space_refine on Sun Jul 5 21:40:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpa_32680/07_2026/7wpa_32680_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpa_32680/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wpa_32680/07_2026/7wpa_32680_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpa_32680/07_2026/7wpa_32680_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wpa_32680/07_2026/7wpa_32680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpa_32680/07_2026/7wpa_32680.map" } 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-6108/lib/python3.11/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, 43 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.96, 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: 2.47 Conformation dependent library (CDL) restraints added in 1.5 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: 0.80 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: 7.06 Time building geometry restraints manager: 3.35 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: 12.900 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: 0.680 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.410 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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/Z covalent geometry : bond 0.00393 / 0.22 (31161) covalent geometry : angle 0.77973 / 0.46 (42386) SS BOND : bond 0.00244 / 0.15 ( 23) SS BOND : angle 1.15031 / 0.68 ( 46) hydrogen bonds : bond 0.23282 / 14.95 ( 870) hydrogen bonds : angle 9.18288 / 6.23 ( 2466) link_BETA1-4 : bond 0.00863 / 0.53 ( 12) link_BETA1-4 : angle 3.00871 / 1.66 ( 36) link_NAG-ASN : bond 0.00312 / 0.19 ( 33) link_NAG-ASN : angle 1.92163 / 1.18 ( 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 : 1.030 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: 0.5093 time to fit residues: 501.3243 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 : 1.112 ------------------------------------------------------------------------------- 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... 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 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 932 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 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: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.187593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139380 restraints weight = 43459.885| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.72 r_work: 0.3570 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31229 Z= 0.166 Angle : 0.607 11.608 42567 Z= 0.310 Chirality : 0.045 0.186 4879 Planarity : 0.005 0.057 5421 Dihedral : 5.525 57.352 5012 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.26 % Allowed : 14.42 % Favored : 82.32 % 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: -2.96 (0.12), residues: 3726 helix: -1.76 (0.15), residues: 871 sheet: -1.02 (0.19), residues: 657 loop : -2.45 (0.11), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 506 TYR 0.026 0.002 TYR C 901 PHE 0.022 0.001 PHE A 84 TRP 0.014 0.001 TRP A 433 HIS 0.005 0.001 HIS C1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (31161) covalent geometry : angle 0.59311 / 0.31 (42386) SS BOND : bond 0.00679 / 0.41 ( 23) SS BOND : angle 2.36316 / 1.50 ( 46) hydrogen bonds : bond 0.04379 / 2.81 ( 870) hydrogen bonds : angle 5.99303 / 4.08 ( 2466) link_BETA1-4 : bond 0.00538 / 0.30 ( 12) link_BETA1-4 : angle 1.81343 / 1.07 ( 36) link_NAG-ASN : bond 0.00797 / 0.31 ( 33) link_NAG-ASN : angle 2.03683 / 1.28 ( 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 807 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 699 time to evaluate : 0.773 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 34 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7320 (mmt180) REVERT: A 114 SER cc_start: 0.7723 (m) cc_final: 0.7403 (t) REVERT: A 151 GLU cc_start: 0.0602 (OUTLIER) cc_final: -0.0982 (pp20) REVERT: A 152 PHE cc_start: 0.4625 (OUTLIER) cc_final: 0.4297 (p90) REVERT: A 185 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7976 (mtm-85) REVERT: A 186 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: A 187 PHE cc_start: 0.8138 (m-80) cc_final: 0.7919 (m-80) REVERT: A 278 GLU cc_start: 0.7997 (pm20) cc_final: 0.7762 (pm20) REVERT: A 344 PHE cc_start: 0.7063 (m-80) cc_final: 0.5944 (m-10) REVERT: A 393 TYR cc_start: 0.8311 (m-80) cc_final: 0.7860 (m-80) REVERT: A 431 ILE cc_start: 0.8318 (mt) cc_final: 0.8109 (mp) REVERT: A 450 TYR cc_start: 0.7531 (p90) cc_final: 0.7239 (p90) REVERT: A 492 TYR cc_start: 0.7035 (m-80) cc_final: 0.6510 (m-10) REVERT: A 507 VAL cc_start: 0.7916 (t) cc_final: 0.7642 (m) REVERT: A 593 SER cc_start: 0.8711 (p) cc_final: 0.8506 (m) REVERT: A 600 ASN cc_start: 0.8048 (t0) cc_final: 0.7614 (t0) REVERT: A 616 GLU cc_start: 0.7648 (pm20) cc_final: 0.7360 (pm20) REVERT: A 808 LYS cc_start: 0.7464 (mtmt) cc_final: 0.7095 (mttt) REVERT: A 817 ASP cc_start: 0.7725 (m-30) cc_final: 0.7448 (m-30) REVERT: A 1002 GLN cc_start: 0.8031 (tp40) cc_final: 0.7800 (mm-40) REVERT: A 1016 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7691 (ttp-170) REVERT: A 1078 ILE cc_start: 0.8277 (mm) cc_final: 0.8075 (mp) REVERT: A 1122 ASN cc_start: 0.7916 (p0) cc_final: 0.7637 (p0) REVERT: B 34 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7387 (mpt90) REVERT: B 201 LYS cc_start: 0.7731 (tttt) cc_final: 0.7364 (tttt) REVERT: B 304 THR cc_start: 0.8273 (p) cc_final: 0.8016 (t) REVERT: B 439 ASP cc_start: 0.7607 (m-30) cc_final: 0.7332 (m-30) REVERT: B 448 TYR cc_start: 0.7784 (m-10) cc_final: 0.7420 (m-10) REVERT: B 462 GLU cc_start: 0.7332 (pt0) cc_final: 0.7086 (pt0) REVERT: B 490 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7702 (ttm170) REVERT: B 512 PHE cc_start: 0.7527 (m-80) cc_final: 0.7270 (m-80) REVERT: B 526 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7975 (mmmm) REVERT: B 667 ILE cc_start: 0.8380 (pt) cc_final: 0.8133 (pt) REVERT: B 800 SER cc_start: 0.8585 (t) cc_final: 0.8331 (p) REVERT: B 982 ASP cc_start: 0.7694 (p0) cc_final: 0.7450 (p0) REVERT: B 1016 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7594 (ttp-170) REVERT: C 47 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8286 (m) REVERT: C 94 GLU cc_start: 0.6356 (tp30) cc_final: 0.5472 (tp30) REVERT: C 127 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7857 (mtpp) REVERT: C 263 TYR cc_start: 0.8257 (m-80) cc_final: 0.8027 (m-80) REVERT: C 433 TRP cc_start: 0.6337 (m100) cc_final: 0.6069 (m100) REVERT: C 561 GLN cc_start: 0.7336 (tp-100) cc_final: 0.6864 (tp-100) REVERT: C 814 PHE cc_start: 0.6433 (t80) cc_final: 0.5923 (t80) REVERT: C 816 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7404 (mt-10) REVERT: C 820 PHE cc_start: 0.8152 (m-80) cc_final: 0.7774 (m-80) REVERT: C 865 GLU cc_start: 0.7745 (mp0) cc_final: 0.7412 (mp0) REVERT: C 899 MET cc_start: 0.8620 (mmm) cc_final: 0.8391 (mmt) REVERT: C 930 LYS cc_start: 0.8532 (mtpp) cc_final: 0.8234 (mtmm) REVERT: C 1014 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7470 (mt-10) REVERT: C 1028 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 1070 LYS cc_start: 0.8288 (tttm) cc_final: 0.8038 (mtpp) REVERT: D 37 GLU cc_start: 0.7842 (pt0) cc_final: 0.7219 (pm20) REVERT: D 51 ASN cc_start: 0.7678 (m-40) cc_final: 0.7399 (m-40) REVERT: D 64 ASN cc_start: 0.6600 (p0) cc_final: 0.4335 (m-40) REVERT: D 75 GLU cc_start: 0.6103 (pm20) cc_final: 0.5851 (pm20) REVERT: D 82 MET cc_start: 0.7716 (ptm) cc_final: 0.7306 (ppp) REVERT: D 190 MET cc_start: 0.4333 (ttp) cc_final: 0.4067 (ttt) REVERT: D 249 MET cc_start: 0.0938 (mmm) cc_final: 0.0090 (mmm) REVERT: D 274 PHE cc_start: 0.6306 (p90) cc_final: 0.6006 (p90) REVERT: D 307 ILE cc_start: 0.8516 (mm) cc_final: 0.8313 (mm) REVERT: D 318 VAL cc_start: 0.5369 (p) cc_final: 0.5017 (p) REVERT: D 335 ASP cc_start: 0.3207 (t0) cc_final: 0.2768 (t70) REVERT: D 375 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7149 (mm-30) REVERT: D 381 TYR cc_start: 0.7268 (t80) cc_final: 0.7058 (t80) REVERT: D 385 TYR cc_start: 0.5798 (p90) cc_final: 0.5403 (p90) REVERT: D 398 GLU cc_start: 0.6697 (tp30) cc_final: 0.6297 (tp30) REVERT: D 488 VAL cc_start: 0.4832 (m) cc_final: 0.4581 (t) REVERT: D 554 LEU cc_start: 0.5518 (pt) cc_final: 0.4958 (tp) REVERT: D 579 MET cc_start: 0.2386 (tpt) cc_final: -0.0522 (pmt) outliers start: 108 outliers final: 43 residues processed: 751 average time/residue: 0.5158 time to fit residues: 465.5383 Evaluate side-chains 694 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 644 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 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 186 GLU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 293 LEU 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 585 THR Chi-restraints excluded: chain A residue 670 SER 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 47 VAL 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: 0.7980 chunk 296 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 chunk 250 optimal weight: 9.9990 chunk 161 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 191 ASN A 236 GLN A 268 GLN A 560 GLN A 672 GLN A 781 GLN A 898 GLN A1116 ASN B 113 GLN ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN B 923 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 113 GLN C 123 ASN C 268 GLN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.184116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136348 restraints weight = 43332.195| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.34 r_work: 0.3547 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31229 Z= 0.181 Angle : 0.604 11.874 42567 Z= 0.307 Chirality : 0.045 0.193 4879 Planarity : 0.004 0.062 5421 Dihedral : 5.126 59.492 5003 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.41 % Allowed : 17.25 % Favored : 79.34 % 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: -2.34 (0.13), residues: 3726 helix: -0.98 (0.17), residues: 878 sheet: -0.70 (0.19), residues: 658 loop : -2.15 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 490 TYR 0.030 0.002 TYR C 901 PHE 0.022 0.002 PHE A 84 TRP 0.021 0.001 TRP D 48 HIS 0.007 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (31161) covalent geometry : angle 0.59048 / 0.30 (42386) SS BOND : bond 0.00922 / 0.42 ( 23) SS BOND : angle 2.18058 / 1.40 ( 46) hydrogen bonds : bond 0.03973 / 2.54 ( 870) hydrogen bonds : angle 5.45215 / 3.71 ( 2466) link_BETA1-4 : bond 0.00529 / 0.31 ( 12) link_BETA1-4 : angle 1.70891 / 1.04 ( 36) link_NAG-ASN : bond 0.00377 / 0.22 ( 33) link_NAG-ASN : angle 2.06168 / 1.29 ( 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 819 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 706 time to evaluate : 1.111 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: A 114 SER cc_start: 0.7791 (m) cc_final: 0.7519 (t) REVERT: A 151 GLU cc_start: 0.0369 (OUTLIER) cc_final: -0.0840 (pp20) REVERT: A 152 PHE cc_start: 0.4477 (OUTLIER) cc_final: 0.4182 (p90) REVERT: A 185 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.7942 (mtm-85) REVERT: A 187 PHE cc_start: 0.8411 (m-80) cc_final: 0.8181 (m-80) REVERT: A 344 PHE cc_start: 0.7539 (m-80) cc_final: 0.6138 (m-10) REVERT: A 393 TYR cc_start: 0.8399 (m-80) cc_final: 0.8089 (m-80) REVERT: A 450 TYR cc_start: 0.7566 (p90) cc_final: 0.7283 (p90) REVERT: A 492 TYR cc_start: 0.7196 (m-80) cc_final: 0.6948 (m-10) REVERT: A 507 VAL cc_start: 0.8218 (t) cc_final: 0.7897 (m) REVERT: A 571 ASP cc_start: 0.8219 (t0) cc_final: 0.7847 (t0) REVERT: A 585 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8149 (p) REVERT: A 600 ASN cc_start: 0.8252 (t0) cc_final: 0.7847 (t0) REVERT: A 616 GLU cc_start: 0.7974 (pm20) cc_final: 0.7615 (pm20) REVERT: A 856 THR cc_start: 0.8579 (t) cc_final: 0.8357 (p) REVERT: A 1002 GLN cc_start: 0.8381 (tp40) cc_final: 0.8141 (mm-40) REVERT: B 201 LYS cc_start: 0.8131 (tttt) cc_final: 0.7770 (tttt) REVERT: B 304 THR cc_start: 0.8411 (p) cc_final: 0.8139 (t) REVERT: B 321 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: B 400 ARG cc_start: 0.8416 (ttm170) cc_final: 0.8122 (ptm-80) REVERT: B 403 GLU cc_start: 0.7883 (mp0) cc_final: 0.7369 (mm-30) REVERT: B 439 ASP cc_start: 0.7899 (m-30) cc_final: 0.7622 (m-30) REVERT: B 448 TYR cc_start: 0.7924 (m-10) cc_final: 0.7563 (m-10) REVERT: B 462 GLU cc_start: 0.7753 (pt0) cc_final: 0.7487 (pt0) REVERT: B 490 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7921 (ttm170) REVERT: B 526 LYS cc_start: 0.8473 (mmmm) cc_final: 0.8214 (mmmm) REVERT: B 667 ILE cc_start: 0.8512 (pt) cc_final: 0.8135 (mp) REVERT: B 752 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7811 (mm-40) REVERT: B 800 SER cc_start: 0.8779 (t) cc_final: 0.8514 (p) REVERT: B 985 GLU cc_start: 0.8182 (tp30) cc_final: 0.7951 (tp30) REVERT: B 1016 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7973 (ttp-110) REVERT: B 1069 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: B 1081 ASP cc_start: 0.7640 (p0) cc_final: 0.7242 (p0) REVERT: C 47 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8485 (m) REVERT: C 127 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8212 (mtpp) REVERT: C 186 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7727 (mm-30) REVERT: C 263 TYR cc_start: 0.8465 (m-80) cc_final: 0.8132 (m-80) REVERT: C 350 TRP cc_start: 0.7975 (p-90) cc_final: 0.7337 (p-90) REVERT: C 433 TRP cc_start: 0.6642 (m100) cc_final: 0.6300 (m100) REVERT: C 561 GLN cc_start: 0.7525 (tp-100) cc_final: 0.7011 (tp-100) REVERT: C 814 PHE cc_start: 0.6818 (t80) cc_final: 0.6173 (t80) REVERT: C 816 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7374 (mt-10) REVERT: C 818 LEU cc_start: 0.8413 (mp) cc_final: 0.8190 (mp) REVERT: C 820 PHE cc_start: 0.8294 (m-80) cc_final: 0.7939 (m-80) REVERT: C 869 GLN cc_start: 0.8545 (tt0) cc_final: 0.8243 (mt0) REVERT: C 930 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8354 (mtmm) REVERT: C 970 ILE cc_start: 0.8662 (pt) cc_final: 0.8089 (mm) REVERT: C 1014 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7914 (mt-10) REVERT: C 1028 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8050 (mt-10) REVERT: D 51 ASN cc_start: 0.7737 (m-40) cc_final: 0.7471 (m-40) REVERT: D 64 ASN cc_start: 0.6661 (p0) cc_final: 0.4256 (m-40) REVERT: D 72 PHE cc_start: 0.7614 (t80) cc_final: 0.7006 (t80) REVERT: D 82 MET cc_start: 0.7755 (ptm) cc_final: 0.7379 (ppp) REVERT: D 199 TYR cc_start: 0.5695 (t80) cc_final: 0.5347 (t80) REVERT: D 249 MET cc_start: 0.1657 (mmm) cc_final: 0.0864 (mmm) REVERT: D 309 LYS cc_start: 0.7762 (mmpt) cc_final: 0.7264 (mmtm) REVERT: D 315 PHE cc_start: 0.7334 (m-80) cc_final: 0.6856 (m-80) REVERT: D 318 VAL cc_start: 0.5554 (p) cc_final: 0.5048 (p) REVERT: D 375 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6956 (mm-30) REVERT: D 398 GLU cc_start: 0.6674 (tp30) cc_final: 0.6274 (tp30) REVERT: D 452 PHE cc_start: 0.5890 (t80) cc_final: 0.5485 (t80) REVERT: D 488 VAL cc_start: 0.4721 (m) cc_final: 0.4454 (t) REVERT: D 554 LEU cc_start: 0.5392 (pt) cc_final: 0.4948 (tp) REVERT: D 579 MET cc_start: 0.2510 (tpt) cc_final: -0.0436 (pmt) outliers start: 113 outliers final: 55 residues processed: 756 average time/residue: 0.5566 time to fit residues: 502.1369 Evaluate side-chains 751 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 689 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 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 A residue 1133 THR 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 321 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 490 ARG 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 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 47 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 321 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 899 MET Chi-restraints excluded: chain C residue 966 LYS Chi-restraints excluded: chain C residue 976 ASP 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 76 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 316 VAL 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 513 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 346 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 313 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 283 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN A 268 GLN A 318 GLN A 331 ASN A 560 GLN A 672 GLN A 781 GLN A 910 GLN ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN B 391 ASN B 411 GLN B 537 ASN B 759 GLN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 183 ASN C 268 GLN C 700 ASN C 707 ASN C 962 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.182159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133917 restraints weight = 42982.753| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.34 r_work: 0.3510 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 31229 Z= 0.232 Angle : 0.627 10.275 42567 Z= 0.318 Chirality : 0.046 0.237 4879 Planarity : 0.004 0.062 5421 Dihedral : 5.197 58.488 5003 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.89 % Allowed : 18.46 % Favored : 77.65 % 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: -2.06 (0.13), residues: 3726 helix: -0.73 (0.17), residues: 883 sheet: -0.54 (0.19), residues: 656 loop : -1.98 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 352 TYR 0.040 0.002 TYR C 901 PHE 0.024 0.002 PHE A 84 TRP 0.012 0.001 TRP A 883 HIS 0.004 0.001 HIS C1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 (31161) covalent geometry : angle 0.61400 / 0.32 (42386) SS BOND : bond 0.00760 / 0.43 ( 23) SS BOND : angle 2.04818 / 1.39 ( 46) hydrogen bonds : bond 0.04039 / 2.59 ( 870) hydrogen bonds : angle 5.31770 / 3.61 ( 2466) link_BETA1-4 : bond 0.00371 / 0.21 ( 12) link_BETA1-4 : angle 1.69544 / 1.02 ( 36) link_NAG-ASN : bond 0.00332 / 0.18 ( 33) link_NAG-ASN : angle 2.13625 / 1.36 ( 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 835 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 706 time to evaluate : 1.107 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: A 114 SER cc_start: 0.7828 (m) cc_final: 0.7563 (t) REVERT: A 151 GLU cc_start: 0.0521 (OUTLIER) cc_final: -0.0685 (pp20) REVERT: A 152 PHE cc_start: 0.4441 (OUTLIER) cc_final: 0.4114 (p90) REVERT: A 185 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8213 (mtm-85) REVERT: A 187 PHE cc_start: 0.8429 (m-80) cc_final: 0.8227 (m-80) REVERT: A 234 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7917 (ttm-80) REVERT: A 277 ASN cc_start: 0.7940 (p0) cc_final: 0.7738 (p0) REVERT: A 344 PHE cc_start: 0.7668 (m-80) cc_final: 0.6456 (m-80) REVERT: A 399 ILE cc_start: 0.7678 (pt) cc_final: 0.7435 (mt) REVERT: A 507 VAL cc_start: 0.8207 (t) cc_final: 0.7858 (m) REVERT: A 549 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8706 (mt) REVERT: A 571 ASP cc_start: 0.8205 (t0) cc_final: 0.7818 (t0) REVERT: A 600 ASN cc_start: 0.8248 (t0) cc_final: 0.7852 (t0) REVERT: A 616 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: A 1002 GLN cc_start: 0.8384 (tp40) cc_final: 0.8100 (mm-40) REVERT: B 34 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7698 (mpt90) REVERT: B 201 LYS cc_start: 0.8256 (tttt) cc_final: 0.7882 (tttt) REVERT: B 304 THR cc_start: 0.8419 (p) cc_final: 0.8169 (t) REVERT: B 400 ARG cc_start: 0.8370 (ttm170) cc_final: 0.7846 (ptm-80) REVERT: B 403 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: B 418 TYR cc_start: 0.8004 (m-10) cc_final: 0.7346 (m-80) REVERT: B 439 ASP cc_start: 0.7906 (m-30) cc_final: 0.7681 (m-30) REVERT: B 462 GLU cc_start: 0.7833 (pt0) cc_final: 0.7535 (pt0) REVERT: B 490 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7861 (ttm170) REVERT: B 526 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8238 (mmmm) REVERT: B 632 VAL cc_start: 0.8486 (m) cc_final: 0.8242 (t) REVERT: B 667 ILE cc_start: 0.8583 (pt) cc_final: 0.8170 (mp) REVERT: B 752 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7889 (mm-40) REVERT: B 800 SER cc_start: 0.8771 (t) cc_final: 0.8507 (p) REVERT: B 822 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8475 (tptm) REVERT: B 1081 ASP cc_start: 0.7642 (p0) cc_final: 0.7290 (p0) REVERT: C 47 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8552 (m) REVERT: C 52 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7675 (tm-30) REVERT: C 113 GLN cc_start: 0.8140 (mm110) cc_final: 0.7849 (mm110) REVERT: C 127 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8259 (mtpp) REVERT: C 186 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 263 TYR cc_start: 0.8473 (m-80) cc_final: 0.8039 (m-80) REVERT: C 350 TRP cc_start: 0.8052 (p-90) cc_final: 0.7437 (p-90) REVERT: C 433 TRP cc_start: 0.6781 (m100) cc_final: 0.6467 (m100) REVERT: C 814 PHE cc_start: 0.6832 (t80) cc_final: 0.6153 (t80) REVERT: C 816 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7563 (mt-10) REVERT: C 818 LEU cc_start: 0.8407 (mp) cc_final: 0.8145 (mp) REVERT: C 820 PHE cc_start: 0.8290 (m-80) cc_final: 0.7976 (m-80) REVERT: C 869 GLN cc_start: 0.8528 (tt0) cc_final: 0.8192 (mt0) REVERT: C 899 MET cc_start: 0.8708 (mmm) cc_final: 0.8481 (mmt) REVERT: C 930 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8341 (mtmt) REVERT: C 933 ASP cc_start: 0.7701 (m-30) cc_final: 0.7401 (m-30) REVERT: C 970 ILE cc_start: 0.8645 (pt) cc_final: 0.8159 (mm) REVERT: C 1028 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8081 (mt-10) REVERT: C 1115 ASP cc_start: 0.7927 (m-30) cc_final: 0.7505 (m-30) REVERT: D 32 PHE cc_start: 0.8144 (t80) cc_final: 0.7773 (t80) REVERT: D 37 GLU cc_start: 0.7891 (pt0) cc_final: 0.7262 (pm20) REVERT: D 42 GLN cc_start: 0.8044 (mt0) cc_final: 0.7800 (mt0) REVERT: D 51 ASN cc_start: 0.7787 (m-40) cc_final: 0.7529 (m-40) REVERT: D 64 ASN cc_start: 0.6738 (p0) cc_final: 0.4070 (m-40) REVERT: D 75 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6609 (pp20) REVERT: D 76 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7936 (tm-30) REVERT: D 82 MET cc_start: 0.7717 (ptm) cc_final: 0.7348 (ppp) REVERT: D 249 MET cc_start: 0.2080 (mmm) cc_final: 0.1267 (mmm) REVERT: D 274 PHE cc_start: 0.6282 (p90) cc_final: 0.5822 (p90) REVERT: D 313 LYS cc_start: 0.7141 (mtpm) cc_final: 0.6771 (mttt) REVERT: D 315 PHE cc_start: 0.7337 (m-80) cc_final: 0.6644 (m-10) REVERT: D 375 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6944 (mm-30) REVERT: D 380 GLN cc_start: 0.6800 (tp-100) cc_final: 0.6289 (tp-100) REVERT: D 398 GLU cc_start: 0.6639 (tp30) cc_final: 0.6238 (tp30) REVERT: D 452 PHE cc_start: 0.5861 (t80) cc_final: 0.5459 (t80) REVERT: D 488 VAL cc_start: 0.4689 (m) cc_final: 0.4419 (t) REVERT: D 554 LEU cc_start: 0.5427 (pt) cc_final: 0.4998 (tp) REVERT: D 579 MET cc_start: 0.2643 (tpt) cc_final: -0.0276 (pmt) outliers start: 129 outliers final: 68 residues processed: 763 average time/residue: 0.5987 time to fit residues: 543.9483 Evaluate side-chains 760 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 684 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP 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 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 549 LEU 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 999 GLN 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 267 LEU 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 382 THR Chi-restraints excluded: chain B residue 403 GLU 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 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 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1093 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 321 GLU 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 966 LYS Chi-restraints excluded: chain C residue 994 ILE 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 316 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 447 VAL 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: 0.4980 chunk 236 optimal weight: 1.9990 chunk 307 optimal weight: 0.5980 chunk 192 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 334 optimal weight: 30.0000 chunk 64 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN A 560 GLN A 781 GLN A 910 GLN B 191 ASN B 391 ASN B 759 GLN B 910 GLN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 215 GLN C 236 GLN C 537 ASN C 700 ASN C 962 GLN C1002 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.182258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134240 restraints weight = 43074.976| |-----------------------------------------------------------------------------| 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: 0.3354 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31229 Z= 0.177 Angle : 0.596 9.036 42567 Z= 0.301 Chirality : 0.045 0.227 4879 Planarity : 0.004 0.060 5421 Dihedral : 5.056 58.376 5003 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.98 % Allowed : 19.82 % Favored : 76.20 % 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: -1.85 (0.13), residues: 3726 helix: -0.49 (0.18), residues: 879 sheet: -0.38 (0.19), residues: 661 loop : -1.88 (0.12), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 234 TYR 0.029 0.001 TYR C 901 PHE 0.021 0.001 PHE A 84 TRP 0.012 0.001 TRP A 883 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (31161) covalent geometry : angle 0.58395 / 0.30 (42386) SS BOND : bond 0.00571 / 0.35 ( 23) SS BOND : angle 1.77999 / 1.21 ( 46) hydrogen bonds : bond 0.03723 / 2.39 ( 870) hydrogen bonds : angle 5.15688 / 3.51 ( 2466) link_BETA1-4 : bond 0.00351 / 0.21 ( 12) link_BETA1-4 : angle 1.62947 / 0.98 ( 36) link_NAG-ASN : bond 0.00272 / 0.16 ( 33) link_NAG-ASN : angle 2.07480 / 1.32 ( 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 825 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 693 time to evaluate : 1.007 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: 0.7772 (m) cc_final: 0.7511 (t) REVERT: A 151 GLU cc_start: 0.0522 (OUTLIER) cc_final: -0.0718 (pp20) REVERT: A 152 PHE cc_start: 0.4412 (OUTLIER) cc_final: 0.4097 (p90) REVERT: A 185 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8176 (mtm-85) REVERT: A 226 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7258 (mp) REVERT: A 234 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7891 (ttm-80) REVERT: A 344 PHE cc_start: 0.7771 (m-80) cc_final: 0.6642 (m-80) REVERT: A 399 ILE cc_start: 0.7635 (pt) cc_final: 0.7377 (mt) REVERT: A 571 ASP cc_start: 0.8189 (t0) cc_final: 0.7705 (t0) REVERT: A 600 ASN cc_start: 0.8228 (t0) cc_final: 0.7850 (t0) REVERT: A 616 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: A 728 MET cc_start: 0.8714 (ttp) cc_final: 0.8490 (ptm) REVERT: A 762 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7890 (mtp85) REVERT: B 54 LEU cc_start: 0.8644 (mp) cc_final: 0.8396 (mt) REVERT: B 201 LYS cc_start: 0.8180 (tttt) cc_final: 0.7828 (tttt) REVERT: B 304 THR cc_start: 0.8426 (p) cc_final: 0.8191 (t) REVERT: B 354 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7326 (tpt-90) REVERT: B 400 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7795 (ptm-80) REVERT: B 403 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: B 439 ASP cc_start: 0.7892 (m-30) cc_final: 0.7654 (m-30) REVERT: B 454 ARG cc_start: 0.8309 (tpt170) cc_final: 0.7837 (tpp80) REVERT: B 462 GLU cc_start: 0.7837 (pt0) cc_final: 0.7544 (pt0) REVERT: B 526 LYS cc_start: 0.8453 (mmmm) cc_final: 0.8224 (mmmm) REVERT: B 553 ASN cc_start: 0.7987 (t0) cc_final: 0.7547 (t0) REVERT: B 632 VAL cc_start: 0.8501 (m) cc_final: 0.8258 (t) REVERT: B 667 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8152 (mp) REVERT: B 752 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7867 (mm-40) REVERT: B 800 SER cc_start: 0.8750 (t) cc_final: 0.8499 (p) REVERT: B 822 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8471 (tptm) REVERT: B 1081 ASP cc_start: 0.7651 (p0) cc_final: 0.7301 (p0) REVERT: C 47 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8558 (m) REVERT: C 52 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7664 (tm-30) REVERT: C 94 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.5548 (mp0) REVERT: C 113 GLN cc_start: 0.8091 (mm110) cc_final: 0.7777 (mm110) REVERT: C 127 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8261 (mtpp) REVERT: C 203 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8357 (p) REVERT: C 263 TYR cc_start: 0.8465 (m-80) cc_final: 0.8099 (m-80) REVERT: C 350 TRP cc_start: 0.8104 (p-90) cc_final: 0.7606 (p-90) REVERT: C 433 TRP cc_start: 0.6781 (m100) cc_final: 0.6476 (m100) REVERT: C 571 ASP cc_start: 0.8039 (t70) cc_final: 0.7442 (t0) REVERT: C 652 TYR cc_start: 0.8841 (t80) cc_final: 0.8613 (t80) REVERT: C 816 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7524 (mt-10) REVERT: C 820 PHE cc_start: 0.8297 (m-80) cc_final: 0.7999 (m-80) REVERT: C 869 GLN cc_start: 0.8531 (tt0) cc_final: 0.8234 (mt0) REVERT: C 899 MET cc_start: 0.8634 (mmm) cc_final: 0.8364 (mmt) REVERT: C 930 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8249 (mtmm) REVERT: C 933 ASP cc_start: 0.7725 (m-30) cc_final: 0.7455 (m-30) REVERT: C 970 ILE cc_start: 0.8607 (pt) cc_final: 0.8082 (mm) REVERT: C 989 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7702 (mt0) REVERT: C 1028 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8060 (mt-10) REVERT: C 1042 LYS cc_start: 0.8572 (tptm) cc_final: 0.8334 (mmmm) REVERT: D 31 LYS cc_start: 0.8278 (tmtt) cc_final: 0.7750 (ttmt) REVERT: D 32 PHE cc_start: 0.8121 (t80) cc_final: 0.7607 (t80) REVERT: D 38 ASP cc_start: 0.7931 (t0) cc_final: 0.7389 (t0) REVERT: D 42 GLN cc_start: 0.8054 (mt0) cc_final: 0.7561 (mt0) REVERT: D 51 ASN cc_start: 0.7862 (m-40) cc_final: 0.7621 (m-40) REVERT: D 64 ASN cc_start: 0.6721 (p0) cc_final: 0.4361 (m-40) REVERT: D 82 MET cc_start: 0.7754 (ptm) cc_final: 0.7460 (ppp) REVERT: D 249 MET cc_start: 0.2405 (mmm) cc_final: 0.1558 (mmm) REVERT: D 274 PHE cc_start: 0.6262 (p90) cc_final: 0.5826 (p90) REVERT: D 313 LYS cc_start: 0.7133 (mtpm) cc_final: 0.6795 (mttp) REVERT: D 375 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7042 (mm-30) REVERT: D 380 GLN cc_start: 0.6827 (tp-100) cc_final: 0.6301 (tp-100) REVERT: D 381 TYR cc_start: 0.7244 (t80) cc_final: 0.6947 (t80) REVERT: D 398 GLU cc_start: 0.6625 (tp30) cc_final: 0.6229 (tp30) REVERT: D 452 PHE cc_start: 0.5902 (t80) cc_final: 0.5371 (t80) REVERT: D 455 MET cc_start: 0.4731 (OUTLIER) cc_final: 0.3822 (ppp) REVERT: D 488 VAL cc_start: 0.4441 (m) cc_final: 0.4147 (t) REVERT: D 553 LYS cc_start: 0.6697 (tppp) cc_final: 0.6494 (tppp) REVERT: D 554 LEU cc_start: 0.5281 (pt) cc_final: 0.5026 (tp) REVERT: D 579 MET cc_start: 0.2708 (tpt) cc_final: -0.0178 (pmt) outliers start: 132 outliers final: 73 residues processed: 749 average time/residue: 0.6017 time to fit residues: 536.5869 Evaluate side-chains 767 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 683 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP 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 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 333 CYS 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 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 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 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 34 ARG 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 354 ARG Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER 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 1063 THR Chi-restraints excluded: chain B residue 1070 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 112 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 228 ILE Chi-restraints excluded: chain C residue 278 GLU 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 695 SER 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 823 VAL Chi-restraints excluded: chain C residue 966 LYS Chi-restraints excluded: chain C residue 993 LEU 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 316 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 235 optimal weight: 0.9990 chunk 168 optimal weight: 0.0980 chunk 145 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 298 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 307 optimal weight: 0.9990 chunk 332 optimal weight: 10.0000 chunk 357 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 311 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN A 268 GLN A 411 GLN A 560 GLN A 672 GLN A 781 GLN A 910 GLN A1002 GLN A1116 ASN B 759 GLN C 537 ASN C 700 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 Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.182871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135074 restraints weight = 42986.756| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.30 r_work: 0.3529 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31229 Z= 0.144 Angle : 0.581 10.017 42567 Z= 0.292 Chirality : 0.044 0.264 4879 Planarity : 0.004 0.062 5421 Dihedral : 4.902 57.617 5003 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.13 % Allowed : 20.51 % Favored : 75.35 % 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: -1.70 (0.13), residues: 3726 helix: -0.31 (0.18), residues: 887 sheet: -0.41 (0.19), residues: 680 loop : -1.78 (0.12), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 352 TYR 0.037 0.001 TYR A 450 PHE 0.027 0.001 PHE A 163 TRP 0.012 0.001 TRP D 477 HIS 0.004 0.000 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (31161) covalent geometry : angle 0.56912 / 0.29 (42386) SS BOND : bond 0.00486 / 0.31 ( 23) SS BOND : angle 1.57744 / 1.04 ( 46) hydrogen bonds : bond 0.03457 / 2.22 ( 870) hydrogen bonds : angle 5.03298 / 3.43 ( 2466) link_BETA1-4 : bond 0.00377 / 0.22 ( 12) link_BETA1-4 : angle 1.59514 / 0.96 ( 36) link_NAG-ASN : bond 0.00258 / 0.15 ( 33) link_NAG-ASN : angle 2.08265 / 1.34 ( 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 820 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 683 time to evaluate : 1.158 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: 0.7741 (m) cc_final: 0.7481 (t) REVERT: A 151 GLU cc_start: 0.0464 (OUTLIER) cc_final: -0.0755 (pp20) REVERT: A 152 PHE cc_start: 0.4332 (OUTLIER) cc_final: 0.4000 (p90) REVERT: A 185 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.7765 (mtm-85) REVERT: A 226 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7293 (mp) REVERT: A 234 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7978 (ttm-80) REVERT: A 344 PHE cc_start: 0.7783 (m-80) cc_final: 0.6678 (m-80) REVERT: A 399 ILE cc_start: 0.7596 (pt) cc_final: 0.7350 (mt) REVERT: A 530 LEU cc_start: 0.8654 (tp) cc_final: 0.8351 (tt) REVERT: A 571 ASP cc_start: 0.8176 (t0) cc_final: 0.7674 (t0) REVERT: A 600 ASN cc_start: 0.8181 (t0) cc_final: 0.7799 (t0) REVERT: A 616 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: A 911 ASN cc_start: 0.8179 (p0) cc_final: 0.7968 (p0) REVERT: A 1002 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8102 (mm-40) REVERT: A 1026 MET cc_start: 0.8791 (tpp) cc_final: 0.8582 (ttp) REVERT: B 54 LEU cc_start: 0.8646 (mp) cc_final: 0.8402 (mt) REVERT: B 304 THR cc_start: 0.8428 (p) cc_final: 0.8199 (t) REVERT: B 403 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: B 418 TYR cc_start: 0.8026 (m-10) cc_final: 0.7392 (m-80) REVERT: B 439 ASP cc_start: 0.7909 (m-30) cc_final: 0.7680 (m-30) REVERT: B 462 GLU cc_start: 0.7803 (pt0) cc_final: 0.7557 (pt0) REVERT: B 526 LYS cc_start: 0.8444 (mmmm) cc_final: 0.8209 (mmmm) REVERT: B 553 ASN cc_start: 0.7965 (t0) cc_final: 0.7575 (t0) REVERT: B 632 VAL cc_start: 0.8511 (m) cc_final: 0.8273 (t) REVERT: B 667 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8123 (mp) REVERT: B 752 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7833 (mm-40) REVERT: B 800 SER cc_start: 0.8741 (t) cc_final: 0.8499 (p) REVERT: B 822 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8466 (tptm) REVERT: B 973 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8677 (m) REVERT: B 1081 ASP cc_start: 0.7579 (p0) cc_final: 0.7225 (p0) REVERT: C 47 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8544 (m) REVERT: C 52 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7651 (tm-30) REVERT: C 94 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5589 (mp0) REVERT: C 113 GLN cc_start: 0.8069 (mm110) cc_final: 0.7742 (mm110) REVERT: C 127 LYS cc_start: 0.8478 (mtpp) cc_final: 0.8212 (mtpp) REVERT: C 203 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8347 (p) REVERT: C 234 ARG cc_start: 0.8410 (mtm110) cc_final: 0.7901 (mtp85) REVERT: C 278 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7749 (pp20) REVERT: C 350 TRP cc_start: 0.8118 (p-90) cc_final: 0.7642 (p-90) REVERT: C 433 TRP cc_start: 0.6796 (m100) cc_final: 0.6487 (m100) REVERT: C 530 LEU cc_start: 0.8552 (tp) cc_final: 0.8277 (tt) REVERT: C 571 ASP cc_start: 0.8045 (t70) cc_final: 0.7453 (t0) REVERT: C 820 PHE cc_start: 0.8273 (m-80) cc_final: 0.7941 (m-80) REVERT: C 869 GLN cc_start: 0.8516 (tt0) cc_final: 0.8228 (mt0) REVERT: C 899 MET cc_start: 0.8650 (mmm) cc_final: 0.8405 (mmt) REVERT: C 930 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8249 (mtmm) REVERT: C 933 ASP cc_start: 0.7737 (m-30) cc_final: 0.7487 (m-30) REVERT: C 970 ILE cc_start: 0.8598 (pt) cc_final: 0.8118 (mm) REVERT: C 989 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7719 (mt0) REVERT: C 1042 LYS cc_start: 0.8553 (tptm) cc_final: 0.8329 (mmmm) REVERT: D 31 LYS cc_start: 0.8254 (tmtt) cc_final: 0.7710 (ttmt) REVERT: D 32 PHE cc_start: 0.8063 (t80) cc_final: 0.7532 (t80) REVERT: D 42 GLN cc_start: 0.8062 (mt0) cc_final: 0.7797 (mt0) REVERT: D 51 ASN cc_start: 0.7879 (m-40) cc_final: 0.7640 (m-40) REVERT: D 64 ASN cc_start: 0.6721 (p0) cc_final: 0.4354 (m-40) REVERT: D 82 MET cc_start: 0.7776 (ptm) cc_final: 0.7467 (ppp) REVERT: D 187 LYS cc_start: 0.4713 (tptm) cc_final: 0.4487 (tptm) REVERT: D 213 ASP cc_start: 0.7046 (t0) cc_final: 0.6739 (t0) REVERT: D 249 MET cc_start: 0.2437 (mmm) cc_final: 0.1603 (mmm) REVERT: D 274 PHE cc_start: 0.6235 (p90) cc_final: 0.5830 (p90) REVERT: D 398 GLU cc_start: 0.6622 (tp30) cc_final: 0.6225 (tp30) REVERT: D 452 PHE cc_start: 0.5856 (t80) cc_final: 0.5315 (t80) REVERT: D 455 MET cc_start: 0.4734 (OUTLIER) cc_final: 0.3598 (ppp) REVERT: D 480 MET cc_start: 0.6623 (mpm) cc_final: 0.5760 (ptp) REVERT: D 488 VAL cc_start: 0.4497 (m) cc_final: 0.4197 (t) REVERT: D 554 LEU cc_start: 0.5241 (pt) cc_final: 0.5005 (tp) REVERT: D 579 MET cc_start: 0.2768 (tpt) cc_final: -0.0134 (pmt) outliers start: 137 outliers final: 77 residues processed: 746 average time/residue: 0.6172 time to fit residues: 547.9107 Evaluate side-chains 758 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 668 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 226 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 333 CYS 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 585 THR 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 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 1002 GLN 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 1141 GLU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 36 VAL 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 403 GLU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER 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 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1070 LYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 GLU 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 228 ILE Chi-restraints excluded: chain C residue 278 GLU 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 897 MET Chi-restraints excluded: chain C residue 966 LYS Chi-restraints excluded: chain C residue 994 ILE 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 76 GLN 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 316 VAL Chi-restraints excluded: chain D residue 364 VAL 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 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: 6.9990 chunk 345 optimal weight: 0.8980 chunk 342 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 253 optimal weight: 20.0000 chunk 327 optimal weight: 2.9990 chunk 331 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 213 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN A 560 GLN A 898 GLN A 910 GLN A 952 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 ASN C 700 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.181764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133851 restraints weight = 43139.206| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.32 r_work: 0.3516 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31229 Z= 0.181 Angle : 0.597 8.895 42567 Z= 0.301 Chirality : 0.045 0.428 4879 Planarity : 0.004 0.060 5421 Dihedral : 4.958 55.124 5001 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.98 % Allowed : 21.12 % Favored : 74.90 % 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: -1.61 (0.13), residues: 3726 helix: -0.24 (0.18), residues: 889 sheet: -0.29 (0.19), residues: 665 loop : -1.74 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 352 TYR 0.034 0.001 TYR A 450 PHE 0.026 0.001 PHE A 163 TRP 0.014 0.001 TRP A 883 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (31161) covalent geometry : angle 0.58471 / 0.30 (42386) SS BOND : bond 0.00544 / 0.35 ( 23) SS BOND : angle 1.69555 / 1.13 ( 46) hydrogen bonds : bond 0.03633 / 2.33 ( 870) hydrogen bonds : angle 5.04909 / 3.44 ( 2466) link_BETA1-4 : bond 0.00364 / 0.21 ( 12) link_BETA1-4 : angle 1.58895 / 0.95 ( 36) link_NAG-ASN : bond 0.00402 / 0.28 ( 33) link_NAG-ASN : angle 2.09676 / 1.38 ( 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 804 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 672 time to evaluate : 1.021 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: 0.7773 (m) cc_final: 0.7526 (t) REVERT: A 151 GLU cc_start: 0.0513 (OUTLIER) cc_final: -0.0720 (pp20) REVERT: A 152 PHE cc_start: 0.4256 (OUTLIER) cc_final: 0.3914 (p90) REVERT: A 185 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.7747 (mtm-85) REVERT: A 226 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7300 (mp) REVERT: A 234 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7956 (ttm-80) REVERT: A 344 PHE cc_start: 0.7822 (m-80) cc_final: 0.6749 (m-80) REVERT: A 399 ILE cc_start: 0.7642 (pt) cc_final: 0.7407 (mt) REVERT: A 530 LEU cc_start: 0.8687 (tp) cc_final: 0.8333 (tt) REVERT: A 571 ASP cc_start: 0.8192 (t0) cc_final: 0.7687 (t0) REVERT: A 600 ASN cc_start: 0.8199 (t0) cc_final: 0.7823 (t0) REVERT: A 616 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: A 911 ASN cc_start: 0.8234 (p0) cc_final: 0.8031 (p0) REVERT: A 1002 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8081 (mm-40) REVERT: B 54 LEU cc_start: 0.8644 (mp) cc_final: 0.8405 (mt) REVERT: B 304 THR cc_start: 0.8447 (p) cc_final: 0.8218 (t) REVERT: B 418 TYR cc_start: 0.8042 (m-10) cc_final: 0.7431 (m-80) REVERT: B 439 ASP cc_start: 0.7902 (m-30) cc_final: 0.7668 (m-30) REVERT: B 462 GLU cc_start: 0.7812 (pt0) cc_final: 0.7581 (pt0) REVERT: B 526 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8219 (mmmm) REVERT: B 553 ASN cc_start: 0.8001 (t0) cc_final: 0.7612 (t0) REVERT: B 577 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7207 (mt0) REVERT: B 632 VAL cc_start: 0.8510 (m) cc_final: 0.8279 (t) REVERT: B 667 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8170 (mp) REVERT: B 752 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7871 (mm-40) REVERT: B 800 SER cc_start: 0.8746 (t) cc_final: 0.8500 (p) REVERT: B 822 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8466 (tptm) REVERT: B 973 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8670 (m) REVERT: B 1081 ASP cc_start: 0.7676 (p0) cc_final: 0.7319 (p0) REVERT: C 30 ASN cc_start: 0.8243 (t0) cc_final: 0.8039 (t0) REVERT: C 47 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8537 (m) REVERT: C 52 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7635 (tm-30) REVERT: C 94 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5566 (mp0) REVERT: C 95 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7882 (mtpp) REVERT: C 113 GLN cc_start: 0.8093 (mm110) cc_final: 0.7767 (mm110) REVERT: C 127 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8211 (mtpp) REVERT: C 203 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8366 (p) REVERT: C 234 ARG cc_start: 0.8427 (mtm110) cc_final: 0.7874 (mtp85) REVERT: C 263 TYR cc_start: 0.8475 (m-80) cc_final: 0.8133 (m-80) REVERT: C 278 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7772 (pp20) REVERT: C 350 TRP cc_start: 0.8143 (p-90) cc_final: 0.7731 (p-90) REVERT: C 433 TRP cc_start: 0.6865 (m100) cc_final: 0.6535 (m100) REVERT: C 571 ASP cc_start: 0.8071 (t70) cc_final: 0.7491 (t0) REVERT: C 737 MET cc_start: 0.8532 (tpp) cc_final: 0.8218 (ttp) REVERT: C 801 GLN cc_start: 0.8839 (mm-40) cc_final: 0.7894 (mt0) REVERT: C 820 PHE cc_start: 0.8271 (m-80) cc_final: 0.7918 (m-80) REVERT: C 869 GLN cc_start: 0.8542 (tt0) cc_final: 0.8250 (mt0) REVERT: C 899 MET cc_start: 0.8652 (mmm) cc_final: 0.8402 (mmt) REVERT: C 930 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8306 (mtmt) REVERT: C 933 ASP cc_start: 0.7829 (m-30) cc_final: 0.7577 (m-30) REVERT: C 970 ILE cc_start: 0.8601 (pt) cc_final: 0.8108 (mm) REVERT: C 989 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7685 (mt0) REVERT: C 992 ARG cc_start: 0.8661 (ttm-80) cc_final: 0.8441 (ttm170) REVERT: C 1042 LYS cc_start: 0.8542 (tptm) cc_final: 0.8321 (mmmm) REVERT: D 31 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7724 (ttmt) REVERT: D 32 PHE cc_start: 0.8044 (t80) cc_final: 0.7518 (t80) REVERT: D 42 GLN cc_start: 0.8056 (mt0) cc_final: 0.7794 (mt0) REVERT: D 51 ASN cc_start: 0.7878 (m-40) cc_final: 0.7640 (m-40) REVERT: D 64 ASN cc_start: 0.6635 (p0) cc_final: 0.4203 (m-40) REVERT: D 82 MET cc_start: 0.7808 (ptm) cc_final: 0.7472 (ppp) REVERT: D 213 ASP cc_start: 0.7053 (t0) cc_final: 0.6749 (t0) REVERT: D 249 MET cc_start: 0.2412 (mmm) cc_final: 0.1598 (mmm) REVERT: D 274 PHE cc_start: 0.6249 (p90) cc_final: 0.5863 (p90) REVERT: D 398 GLU cc_start: 0.6627 (tp30) cc_final: 0.6239 (tp30) REVERT: D 452 PHE cc_start: 0.5884 (t80) cc_final: 0.5353 (t80) REVERT: D 455 MET cc_start: 0.4706 (OUTLIER) cc_final: 0.3745 (ppp) REVERT: D 488 VAL cc_start: 0.4470 (m) cc_final: 0.4129 (t) REVERT: D 554 LEU cc_start: 0.5211 (pt) cc_final: 0.4992 (tp) REVERT: D 579 MET cc_start: 0.2757 (tpt) cc_final: -0.0166 (pmt) outliers start: 132 outliers final: 87 residues processed: 735 average time/residue: 0.6283 time to fit residues: 549.6620 Evaluate side-chains 767 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 667 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 999 GLN 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 34 ARG Chi-restraints excluded: chain B residue 36 VAL 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 403 GLU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 530 LEU 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 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1093 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 47 VAL 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 228 ILE Chi-restraints excluded: chain C residue 278 GLU 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 897 MET Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 966 LYS Chi-restraints excluded: chain C residue 993 LEU 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 76 GLN 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 187 LYS 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 Chi-restraints excluded: chain D residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 204 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 315 optimal weight: 0.8980 chunk 368 optimal weight: 0.5980 chunk 210 optimal weight: 0.0570 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 285 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 672 GLN A 898 GLN A 910 GLN A1116 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 ASN C 700 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.182614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134498 restraints weight = 43129.385| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.34 r_work: 0.3528 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31229 Z= 0.138 Angle : 0.584 10.330 42567 Z= 0.294 Chirality : 0.045 0.368 4879 Planarity : 0.004 0.061 5421 Dihedral : 4.851 54.253 5001 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.53 % Allowed : 22.11 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.50 (0.13), residues: 3726 helix: -0.09 (0.18), residues: 889 sheet: -0.26 (0.19), residues: 671 loop : -1.69 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 352 TYR 0.037 0.001 TYR A 450 PHE 0.026 0.001 PHE A 163 TRP 0.011 0.001 TRP A 883 HIS 0.004 0.000 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (31161) covalent geometry : angle 0.57284 / 0.29 (42386) SS BOND : bond 0.00464 / 0.30 ( 23) SS BOND : angle 1.51136 / 1.01 ( 46) hydrogen bonds : bond 0.03378 / 2.17 ( 870) hydrogen bonds : angle 4.95555 / 3.38 ( 2466) link_BETA1-4 : bond 0.00386 / 0.21 ( 12) link_BETA1-4 : angle 1.57436 / 0.94 ( 36) link_NAG-ASN : bond 0.00273 / 0.16 ( 33) link_NAG-ASN : angle 2.08762 / 1.38 ( 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 802 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 685 time to evaluate : 1.071 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: 0.7735 (m) cc_final: 0.7481 (t) REVERT: A 151 GLU cc_start: 0.0459 (OUTLIER) cc_final: -0.0664 (pp20) REVERT: A 152 PHE cc_start: 0.4277 (OUTLIER) cc_final: 0.3931 (p90) REVERT: A 185 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.7781 (mtm-85) REVERT: A 226 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7267 (mp) REVERT: A 234 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7921 (ttm-80) REVERT: A 277 ASN cc_start: 0.7929 (p0) cc_final: 0.7691 (p0) REVERT: A 344 PHE cc_start: 0.7806 (m-80) cc_final: 0.6781 (m-80) REVERT: A 400 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6297 (mtp180) REVERT: A 571 ASP cc_start: 0.8175 (t0) cc_final: 0.7643 (t0) REVERT: A 600 ASN cc_start: 0.8174 (t0) cc_final: 0.7793 (t0) REVERT: A 616 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: A 911 ASN cc_start: 0.8238 (p0) cc_final: 0.8012 (p0) REVERT: A 984 PRO cc_start: 0.8345 (Cg_exo) cc_final: 0.8012 (Cg_endo) REVERT: A 1002 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8116 (mm-40) REVERT: B 304 THR cc_start: 0.8436 (p) cc_final: 0.8212 (t) REVERT: B 323 ILE cc_start: 0.8470 (mp) cc_final: 0.8269 (pt) REVERT: B 403 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: B 418 TYR cc_start: 0.8046 (m-10) cc_final: 0.7464 (m-80) REVERT: B 439 ASP cc_start: 0.7882 (m-30) cc_final: 0.7653 (m-30) REVERT: B 462 GLU cc_start: 0.7786 (pt0) cc_final: 0.7523 (pt0) REVERT: B 502 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7561 (t-90) REVERT: B 526 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8207 (mmmm) REVERT: B 553 ASN cc_start: 0.7952 (t0) cc_final: 0.7588 (t0) REVERT: B 577 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7770 (mp10) REVERT: B 632 VAL cc_start: 0.8503 (m) cc_final: 0.8273 (t) REVERT: B 667 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8158 (mp) REVERT: B 752 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7844 (mm-40) REVERT: B 800 SER cc_start: 0.8731 (t) cc_final: 0.8497 (p) REVERT: B 822 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8469 (tptm) REVERT: B 973 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8672 (m) REVERT: B 1081 ASP cc_start: 0.7595 (p0) cc_final: 0.7243 (p0) REVERT: C 47 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8537 (m) REVERT: C 52 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7649 (tm-30) REVERT: C 94 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5306 (mp0) REVERT: C 113 GLN cc_start: 0.8053 (mm110) cc_final: 0.7742 (mm110) REVERT: C 127 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8194 (mtpp) REVERT: C 203 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8306 (p) REVERT: C 234 ARG cc_start: 0.8408 (mtm110) cc_final: 0.7879 (mtp85) REVERT: C 263 TYR cc_start: 0.8478 (m-80) cc_final: 0.8129 (m-80) REVERT: C 278 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7719 (pp20) REVERT: C 350 TRP cc_start: 0.8138 (p-90) cc_final: 0.7732 (p-90) REVERT: C 433 TRP cc_start: 0.6858 (m100) cc_final: 0.6523 (m100) REVERT: C 571 ASP cc_start: 0.8084 (t70) cc_final: 0.7509 (t0) REVERT: C 737 MET cc_start: 0.8530 (tpp) cc_final: 0.8218 (ttp) REVERT: C 820 PHE cc_start: 0.8225 (m-80) cc_final: 0.7844 (m-80) REVERT: C 869 GLN cc_start: 0.8532 (tt0) cc_final: 0.8245 (mt0) REVERT: C 899 MET cc_start: 0.8631 (mmm) cc_final: 0.8389 (mmt) REVERT: C 930 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8302 (mtmt) REVERT: C 933 ASP cc_start: 0.7602 (m-30) cc_final: 0.7368 (m-30) REVERT: C 970 ILE cc_start: 0.8599 (pt) cc_final: 0.8254 (mm) REVERT: C 990 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7944 (tt) REVERT: C 1042 LYS cc_start: 0.8537 (tptm) cc_final: 0.8327 (mmmm) REVERT: D 24 GLN cc_start: 0.7116 (mm110) cc_final: 0.6818 (mm-40) REVERT: D 31 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7758 (ttmt) REVERT: D 42 GLN cc_start: 0.8059 (mt0) cc_final: 0.7798 (mt0) REVERT: D 51 ASN cc_start: 0.7852 (m-40) cc_final: 0.7639 (m-40) REVERT: D 64 ASN cc_start: 0.6564 (p0) cc_final: 0.4071 (m-40) REVERT: D 82 MET cc_start: 0.7839 (ptm) cc_final: 0.7487 (ppp) REVERT: D 213 ASP cc_start: 0.7047 (t0) cc_final: 0.6753 (t0) REVERT: D 249 MET cc_start: 0.2542 (mmm) cc_final: 0.1750 (mmm) REVERT: D 274 PHE cc_start: 0.6243 (p90) cc_final: 0.5892 (p90) REVERT: D 373 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.7013 (m170) REVERT: D 398 GLU cc_start: 0.6606 (tp30) cc_final: 0.6210 (tp30) REVERT: D 452 PHE cc_start: 0.5614 (t80) cc_final: 0.5101 (t80) REVERT: D 455 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.3577 (ppp) REVERT: D 480 MET cc_start: 0.6614 (mmm) cc_final: 0.5783 (ptp) REVERT: D 579 MET cc_start: 0.2727 (tpt) cc_final: -0.0226 (pmt) outliers start: 117 outliers final: 78 residues processed: 745 average time/residue: 0.5865 time to fit residues: 519.6596 Evaluate side-chains 775 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 680 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 226 LEU 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 400 ARG Chi-restraints excluded: chain A residue 450 TYR 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 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 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1042 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 19 THR Chi-restraints excluded: chain B residue 36 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 403 GLU 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 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 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 47 VAL 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 228 ILE Chi-restraints excluded: chain C residue 239 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 897 MET Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 966 LYS Chi-restraints excluded: chain C residue 990 ILE 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 76 GLN Chi-restraints excluded: chain D residue 81 GLN 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 373 HIS 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: 0.8980 chunk 329 optimal weight: 0.1980 chunk 246 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 137 optimal weight: 0.1980 chunk 202 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 869 GLN A 898 GLN A 910 GLN A 932 GLN A 962 GLN A1116 ASN C 537 ASN C 700 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.182969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135059 restraints weight = 42953.606| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.32 r_work: 0.3520 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31229 Z= 0.161 Angle : 0.605 11.359 42567 Z= 0.305 Chirality : 0.045 0.296 4879 Planarity : 0.004 0.063 5421 Dihedral : 4.807 54.244 5001 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.41 % Allowed : 22.44 % Favored : 74.15 % 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: -1.40 (0.13), residues: 3726 helix: 0.02 (0.18), residues: 878 sheet: -0.21 (0.19), residues: 671 loop : -1.63 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 352 TYR 0.052 0.002 TYR D 199 PHE 0.025 0.001 PHE A 163 TRP 0.015 0.001 TRP A 883 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (31161) covalent geometry : angle 0.59474 / 0.30 (42386) SS BOND : bond 0.00499 / 0.32 ( 23) SS BOND : angle 1.59335 / 1.07 ( 46) hydrogen bonds : bond 0.03515 / 2.25 ( 870) hydrogen bonds : angle 4.95758 / 3.37 ( 2466) link_BETA1-4 : bond 0.00397 / 0.23 ( 12) link_BETA1-4 : angle 1.55559 / 0.94 ( 36) link_NAG-ASN : bond 0.00252 / 0.15 ( 33) link_NAG-ASN : angle 1.99508 / 1.29 ( 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 812 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 699 time to evaluate : 1.024 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: 0.7738 (m) cc_final: 0.7498 (t) REVERT: A 185 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.7776 (mtm-85) REVERT: A 226 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7295 (mp) REVERT: A 234 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7923 (ttm-80) REVERT: A 344 PHE cc_start: 0.7797 (m-80) cc_final: 0.6852 (m-80) REVERT: A 400 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.5804 (mtp180) REVERT: A 571 ASP cc_start: 0.8194 (t0) cc_final: 0.7643 (t0) REVERT: A 600 ASN cc_start: 0.8184 (t0) cc_final: 0.7808 (t0) REVERT: A 616 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: A 984 PRO cc_start: 0.8342 (Cg_exo) cc_final: 0.7986 (Cg_endo) REVERT: B 304 THR cc_start: 0.8450 (p) cc_final: 0.8224 (t) REVERT: B 323 ILE cc_start: 0.8497 (mp) cc_final: 0.8247 (pt) REVERT: B 398 VAL cc_start: 0.8701 (p) cc_final: 0.8476 (t) REVERT: B 403 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: B 418 TYR cc_start: 0.8042 (m-10) cc_final: 0.7451 (m-80) REVERT: B 439 ASP cc_start: 0.7847 (m-30) cc_final: 0.7623 (m-30) REVERT: B 462 GLU cc_start: 0.7799 (pt0) cc_final: 0.7550 (pt0) REVERT: B 526 LYS cc_start: 0.8441 (mmmm) cc_final: 0.8200 (mmmm) REVERT: B 553 ASN cc_start: 0.8007 (t0) cc_final: 0.7674 (t0) REVERT: B 632 VAL cc_start: 0.8472 (m) cc_final: 0.8247 (t) REVERT: B 667 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8184 (mp) REVERT: B 752 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7854 (mm-40) REVERT: B 800 SER cc_start: 0.8736 (t) cc_final: 0.8494 (p) REVERT: B 973 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8660 (m) REVERT: B 1081 ASP cc_start: 0.7631 (p0) cc_final: 0.7281 (p0) REVERT: C 30 ASN cc_start: 0.8047 (t0) cc_final: 0.7795 (t0) REVERT: C 47 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8532 (m) REVERT: C 52 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 94 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5288 (mp0) REVERT: C 113 GLN cc_start: 0.8057 (mm110) cc_final: 0.7766 (mm110) REVERT: C 127 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8197 (mtpp) REVERT: C 203 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8376 (p) REVERT: C 263 TYR cc_start: 0.8479 (m-80) cc_final: 0.8132 (m-80) REVERT: C 278 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7716 (pp20) REVERT: C 350 TRP cc_start: 0.8139 (p-90) cc_final: 0.7817 (p-90) REVERT: C 433 TRP cc_start: 0.6908 (m100) cc_final: 0.6569 (m100) REVERT: C 530 LEU cc_start: 0.8633 (tp) cc_final: 0.8428 (tp) REVERT: C 571 ASP cc_start: 0.8079 (t70) cc_final: 0.7471 (t0) REVERT: C 737 MET cc_start: 0.8549 (tpp) cc_final: 0.8207 (ttp) REVERT: C 820 PHE cc_start: 0.8262 (m-80) cc_final: 0.7903 (m-80) REVERT: C 869 GLN cc_start: 0.8538 (tt0) cc_final: 0.8233 (mt0) REVERT: C 930 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8264 (mtmt) REVERT: C 933 ASP cc_start: 0.7673 (m-30) cc_final: 0.7455 (m-30) REVERT: C 970 ILE cc_start: 0.8583 (pt) cc_final: 0.8274 (mm) REVERT: C 990 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7892 (tt) REVERT: C 1042 LYS cc_start: 0.8521 (tptm) cc_final: 0.8312 (mmmm) REVERT: D 31 LYS cc_start: 0.8279 (tmtt) cc_final: 0.7775 (ttmt) REVERT: D 41 TYR cc_start: 0.7865 (t80) cc_final: 0.7433 (t80) REVERT: D 42 GLN cc_start: 0.8066 (mt0) cc_final: 0.7799 (mt0) REVERT: D 51 ASN cc_start: 0.7850 (m-40) cc_final: 0.7642 (m-40) REVERT: D 64 ASN cc_start: 0.6561 (p0) cc_final: 0.4027 (m-40) REVERT: D 82 MET cc_start: 0.7875 (ptm) cc_final: 0.7519 (ppp) REVERT: D 213 ASP cc_start: 0.7094 (t0) cc_final: 0.6810 (t0) REVERT: D 249 MET cc_start: 0.2443 (mmm) cc_final: 0.1665 (mmm) REVERT: D 274 PHE cc_start: 0.6249 (p90) cc_final: 0.5915 (p90) REVERT: D 313 LYS cc_start: 0.7059 (mtmp) cc_final: 0.6723 (mttp) REVERT: D 373 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.7042 (m170) REVERT: D 398 GLU cc_start: 0.6610 (tp30) cc_final: 0.6210 (tp30) REVERT: D 452 PHE cc_start: 0.5668 (t80) cc_final: 0.5235 (t80) REVERT: D 481 LYS cc_start: 0.3251 (mtpt) cc_final: 0.2631 (mttp) REVERT: D 488 VAL cc_start: 0.4433 (m) cc_final: 0.4105 (t) REVERT: D 579 MET cc_start: 0.2793 (tpt) cc_final: -0.0183 (pmt) outliers start: 113 outliers final: 81 residues processed: 759 average time/residue: 0.5534 time to fit residues: 500.0382 Evaluate side-chains 773 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 680 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 450 TYR 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 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 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 1042 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 19 THR Chi-restraints excluded: chain B residue 36 VAL 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 396 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER 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 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 47 VAL 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 228 ILE Chi-restraints excluded: chain C residue 278 GLU 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 897 MET Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 966 LYS Chi-restraints excluded: chain C residue 990 ILE Chi-restraints excluded: chain C residue 994 ILE 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 76 GLN Chi-restraints excluded: chain D residue 81 GLN 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 373 HIS 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 321 optimal weight: 0.3980 chunk 244 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 chunk 79 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 330 optimal weight: 6.9990 chunk 284 optimal weight: 0.4980 chunk 224 optimal weight: 0.9980 chunk 365 optimal weight: 8.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 869 GLN A 898 GLN A 910 GLN A 932 GLN A 962 GLN A 975 ASN A1116 ASN B 748 ASN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 ASN C 700 ASN ** C 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.182893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135420 restraints weight = 42980.453| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.29 r_work: 0.3529 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31229 Z= 0.151 Angle : 0.615 12.481 42567 Z= 0.309 Chirality : 0.045 0.300 4879 Planarity : 0.004 0.062 5421 Dihedral : 4.694 54.206 4996 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.17 % Allowed : 22.78 % Favored : 74.06 % 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: -1.33 (0.13), residues: 3726 helix: 0.19 (0.19), residues: 853 sheet: -0.24 (0.19), residues: 675 loop : -1.59 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 352 TYR 0.031 0.001 TYR A 450 PHE 0.025 0.001 PHE A 163 TRP 0.019 0.001 TRP D 478 HIS 0.004 0.000 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (31161) covalent geometry : angle 0.60508 / 0.31 (42386) SS BOND : bond 0.00518 / 0.31 ( 23) SS BOND : angle 1.65798 / 1.06 ( 46) hydrogen bonds : bond 0.03446 / 2.21 ( 870) hydrogen bonds : angle 4.92832 / 3.36 ( 2466) link_BETA1-4 : bond 0.00386 / 0.22 ( 12) link_BETA1-4 : angle 1.53401 / 0.92 ( 36) link_NAG-ASN : bond 0.00257 / 0.16 ( 33) link_NAG-ASN : angle 1.96466 / 1.26 ( 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 796 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 691 time to evaluate : 1.046 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: 0.7736 (m) cc_final: 0.7466 (t) REVERT: A 167 SER cc_start: 0.8125 (p) cc_final: 0.7850 (t) REVERT: A 185 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.7776 (mtm-85) REVERT: A 226 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7278 (mp) REVERT: A 234 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7890 (ttm-80) REVERT: A 344 PHE cc_start: 0.7813 (m-80) cc_final: 0.6891 (m-80) REVERT: A 400 ARG cc_start: 0.6052 (OUTLIER) cc_final: 0.5773 (mtp180) REVERT: A 571 ASP cc_start: 0.8190 (t0) cc_final: 0.7638 (t0) REVERT: A 600 ASN cc_start: 0.8172 (t0) cc_final: 0.7797 (t0) REVERT: A 616 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: A 984 PRO cc_start: 0.8323 (Cg_exo) cc_final: 0.7962 (Cg_endo) REVERT: B 301 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8562 (mttp) REVERT: B 304 THR cc_start: 0.8449 (p) cc_final: 0.8220 (t) REVERT: B 323 ILE cc_start: 0.8498 (mp) cc_final: 0.8252 (pt) REVERT: B 398 VAL cc_start: 0.8701 (p) cc_final: 0.8475 (t) REVERT: B 403 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: B 418 TYR cc_start: 0.8044 (m-10) cc_final: 0.7453 (m-80) REVERT: B 439 ASP cc_start: 0.7827 (m-30) cc_final: 0.7596 (m-30) REVERT: B 462 GLU cc_start: 0.7795 (pt0) cc_final: 0.7549 (pt0) REVERT: B 526 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8184 (mmmm) REVERT: B 553 ASN cc_start: 0.7958 (t0) cc_final: 0.7635 (t0) REVERT: B 632 VAL cc_start: 0.8483 (m) cc_final: 0.8261 (t) REVERT: B 667 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 752 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7860 (mm-40) REVERT: B 800 SER cc_start: 0.8726 (t) cc_final: 0.8488 (p) REVERT: B 973 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8651 (m) REVERT: B 1081 ASP cc_start: 0.7621 (p0) cc_final: 0.7267 (p0) REVERT: C 47 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8536 (m) REVERT: C 52 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 94 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5550 (mp0) REVERT: C 113 GLN cc_start: 0.8045 (mm110) cc_final: 0.7749 (mm110) REVERT: C 127 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8195 (mtpp) REVERT: C 203 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8364 (p) REVERT: C 234 ARG cc_start: 0.8420 (mtm110) cc_final: 0.7955 (mtp85) REVERT: C 263 TYR cc_start: 0.8477 (m-80) cc_final: 0.8126 (m-80) REVERT: C 278 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7689 (pp20) REVERT: C 350 TRP cc_start: 0.8147 (p-90) cc_final: 0.7828 (p-90) REVERT: C 433 TRP cc_start: 0.6889 (m100) cc_final: 0.6561 (m100) REVERT: C 571 ASP cc_start: 0.8082 (t70) cc_final: 0.7484 (t0) REVERT: C 737 MET cc_start: 0.8558 (tpp) cc_final: 0.8197 (ttp) REVERT: C 820 PHE cc_start: 0.8222 (m-80) cc_final: 0.7855 (m-80) REVERT: C 869 GLN cc_start: 0.8532 (tt0) cc_final: 0.8262 (mt0) REVERT: C 930 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8264 (mtmt) REVERT: C 933 ASP cc_start: 0.7612 (m-30) cc_final: 0.7365 (m-30) REVERT: C 970 ILE cc_start: 0.8593 (pt) cc_final: 0.8255 (mm) REVERT: C 990 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7978 (tt) REVERT: C 1042 LYS cc_start: 0.8516 (tptm) cc_final: 0.8307 (mmmm) REVERT: D 31 LYS cc_start: 0.8298 (tmtt) cc_final: 0.7788 (ttmt) REVERT: D 38 ASP cc_start: 0.7937 (t0) cc_final: 0.7464 (t0) REVERT: D 41 TYR cc_start: 0.7890 (t80) cc_final: 0.7460 (t80) REVERT: D 42 GLN cc_start: 0.8065 (mt0) cc_final: 0.7565 (mt0) REVERT: D 51 ASN cc_start: 0.7861 (m-40) cc_final: 0.7653 (m-40) REVERT: D 64 ASN cc_start: 0.6528 (p0) cc_final: 0.3922 (m-40) REVERT: D 82 MET cc_start: 0.7884 (ptm) cc_final: 0.7535 (ppp) REVERT: D 213 ASP cc_start: 0.7095 (t0) cc_final: 0.6817 (t0) REVERT: D 249 MET cc_start: 0.2459 (mmm) cc_final: 0.1684 (mmm) REVERT: D 274 PHE cc_start: 0.6246 (p90) cc_final: 0.5919 (p90) REVERT: D 373 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.7079 (m170) REVERT: D 398 GLU cc_start: 0.6604 (tp30) cc_final: 0.6210 (tp30) REVERT: D 452 PHE cc_start: 0.5612 (t80) cc_final: 0.5127 (t80) REVERT: D 480 MET cc_start: 0.6423 (mpm) cc_final: 0.5568 (ptp) REVERT: D 488 VAL cc_start: 0.4455 (m) cc_final: 0.4134 (t) REVERT: D 579 MET cc_start: 0.2797 (tpt) cc_final: -0.0170 (pmt) outliers start: 105 outliers final: 80 residues processed: 746 average time/residue: 0.5685 time to fit residues: 507.3702 Evaluate side-chains 772 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 679 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 450 TYR 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 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 702 VAL Chi-restraints excluded: chain A residue 762 ARG 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 1042 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 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 301 LYS 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 396 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER 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 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 47 VAL 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 228 ILE Chi-restraints excluded: chain C residue 278 GLU 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 965 SER Chi-restraints excluded: chain C residue 966 LYS Chi-restraints excluded: chain C residue 990 ILE 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 76 GLN Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 373 HIS 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: 2.9990 chunk 312 optimal weight: 0.5980 chunk 360 optimal weight: 0.3980 chunk 252 optimal weight: 0.0670 chunk 319 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 356 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 255 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN A 502 HIS A 560 GLN A 869 GLN A 910 GLN A1116 ASN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN C 537 ASN C 700 ASN C 904 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.182929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135412 restraints weight = 43114.813| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.32 r_work: 0.3534 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31229 Z= 0.137 Angle : 0.604 11.124 42567 Z= 0.303 Chirality : 0.045 0.239 4879 Planarity : 0.004 0.063 5421 Dihedral : 4.605 54.605 4996 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.11 % Allowed : 22.96 % Favored : 73.94 % 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: -1.27 (0.13), residues: 3726 helix: 0.25 (0.19), residues: 855 sheet: -0.25 (0.19), residues: 672 loop : -1.53 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 352 TYR 0.040 0.001 TYR D 199 PHE 0.025 0.001 PHE A 163 TRP 0.018 0.001 TRP D 478 HIS 0.004 0.000 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (31161) covalent geometry : angle 0.59368 / 0.30 (42386) SS BOND : bond 0.00501 / 0.29 ( 23) SS BOND : angle 1.60339 / 1.03 ( 46) hydrogen bonds : bond 0.03334 / 2.15 ( 870) hydrogen bonds : angle 4.87704 / 3.32 ( 2466) link_BETA1-4 : bond 0.00392 / 0.23 ( 12) link_BETA1-4 : angle 1.50644 / 0.91 ( 36) link_NAG-ASN : bond 0.00228 / 0.14 ( 33) link_NAG-ASN : angle 1.93111 / 1.23 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14385.59 seconds wall clock time: 244 minutes 46.62 seconds (14686.62 seconds total)