Starting phenix.real_space_refine on Thu Jun 26 13:08:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpa_32680/06_2025/7wpa_32680_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpa_32680/06_2025/7wpa_32680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wpa_32680/06_2025/7wpa_32680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpa_32680/06_2025/7wpa_32680.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpa_32680/06_2025/7wpa_32680_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpa_32680/06_2025/7wpa_32680_neut.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30444 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8329 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 56, 'TRANS': 1004} Chain breaks: 6 Chain: "B" Number of atoms: 8329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8329 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 56, 'TRANS': 1004} Chain breaks: 6 Chain: "C" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8297 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 56, 'TRANS': 1000} Chain breaks: 8 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 18.67, per 1000 atoms: 0.61 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: 7.48 Conformation dependent library (CDL) restraints added in 4.0 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: 4.18 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: 13.25 Time building geometry restraints manager: 8.86 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 \ 1144 or resid 1301 through 1306)) selection = (chain 'B' and (resid 17 through 42 or resid 44 through 401 or resid 403 through \ 1144 or resid 1301 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: 7.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.440 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 70.630 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31229 Z= 0.221 Angle : 0.789 21.374 42567 Z= 0.460 Chirality : 0.051 0.591 4879 Planarity : 0.006 0.075 5421 Dihedral : 13.934 85.564 11932 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.001 TRP D 461 HIS 0.005 0.000 HIS D 535 PHE 0.025 0.001 PHE C 152 TYR 0.014 0.001 TYR D 385 ARG 0.003 0.000 ARG C 844 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 33) link_NAG-ASN : angle 1.92163 ( 99) link_BETA1-4 : bond 0.00863 ( 12) link_BETA1-4 : angle 3.00871 ( 36) hydrogen bonds : bond 0.23282 ( 870) hydrogen bonds : angle 9.18288 ( 2466) SS BOND : bond 0.00244 ( 23) SS BOND : angle 1.15031 ( 46) covalent geometry : bond 0.00393 (31161) covalent geometry : angle 0.77973 (42386) *********************** 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 : 3.130 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: 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: 0.4419 (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 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: 0.6522 (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: 0.8319 (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: 0.6909 (m-30) REVERT: A 1028 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7456 (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: 0.6309 (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: 0.7630 (m-80) REVERT: B 393 TYR cc_start: 0.6917 (m-10) cc_final: 0.5690 (m-10) REVERT: B 395 ASP cc_start: 0.7773 (m-30) cc_final: 0.7571 (m-30) REVERT: B 448 TYR cc_start: 0.7668 (m-10) cc_final: 0.7428 (m-10) REVERT: B 512 PHE cc_start: 0.6524 (m-80) cc_final: 0.6113 (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: 0.6785 (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: 0.7089 (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: 0.5180 (tp30) REVERT: C 127 LYS cc_start: 0.7331 (mtpp) cc_final: 0.7127 (mtpp) REVERT: C 263 TYR cc_start: 0.7597 (m-80) cc_final: 0.7267 (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: 0.8034 (mmmm) REVERT: C 561 GLN cc_start: 0.6853 (tp-100) cc_final: 0.6514 (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: 0.5518 (t80) REVERT: C 816 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7149 (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: 0.7730 (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: 0.4206 (m-40) REVERT: D 75 GLU cc_start: 0.6012 (pm20) cc_final: 0.5753 (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: 0.4422 (tttp) 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: 0.6188 (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: 1.4357 time to fit residues: 1420.1585 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 : 4.378 ------------------------------------------------------------------------------- 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 317 optimal weight: 8.9990 chunk 284 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 219 optimal weight: 0.0670 chunk 341 optimal weight: 0.4980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 132 GLN A 191 ASN A 311 GLN A 318 GLN A 357 ASN A 391 ASN A 406 GLN A 447 ASN A 474 ASN A 478 ASN A 771 GLN A 910 GLN A 952 ASN A 999 GLN A1002 GLN A1033 GLN A1051 GLN A1139 GLN B 215 GLN B 340 ASN B 411 GLN B 419 ASN B 478 ASN B 537 ASN B 553 ASN B 850 GLN B 946 GLN B 952 ASN B 999 GLN B1008 GLN B1020 ASN B1033 GLN B1068 GLN B1103 GLN C 97 ASN C 123 ASN C 268 GLN C 340 ASN C 411 GLN C 447 ASN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 ASN C 577 GLN C 774 ASN C 821 ASN C 932 GLN C 946 GLN C 962 GLN C 999 GLN C1020 ASN C1061 HIS D 61 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 340 GLN D 437 ASN D 472 GLN D 505 HIS D 522 GLN D 524 GLN D 578 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.187303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139327 restraints weight = 43187.504| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.33 r_work: 0.3585 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31229 Z= 0.174 Angle : 0.614 11.068 42567 Z= 0.313 Chirality : 0.045 0.217 4879 Planarity : 0.005 0.056 5421 Dihedral : 5.514 57.752 5012 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.26 % Allowed : 14.33 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.12), residues: 3726 helix: -1.69 (0.15), residues: 876 sheet: -0.99 (0.19), residues: 648 loop : -2.42 (0.11), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 433 HIS 0.005 0.001 HIS C1045 PHE 0.023 0.002 PHE A 84 TYR 0.027 0.002 TYR C 901 ARG 0.008 0.001 ARG A 506 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 33) link_NAG-ASN : angle 2.02253 ( 99) link_BETA1-4 : bond 0.00496 ( 12) link_BETA1-4 : angle 1.79860 ( 36) hydrogen bonds : bond 0.03880 ( 870) hydrogen bonds : angle 5.88019 ( 2466) SS BOND : bond 0.00962 ( 23) SS BOND : angle 1.98833 ( 46) covalent geometry : bond 0.00397 (31161) covalent geometry : angle 0.60176 (42386) *********************** 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 813 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 705 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.7841 (m) cc_final: 0.7558 (t) REVERT: A 127 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7702 (mtmm) REVERT: A 151 GLU cc_start: 0.0340 (OUTLIER) cc_final: -0.1100 (pp20) REVERT: A 152 PHE cc_start: 0.4507 (OUTLIER) cc_final: 0.4190 (p90) REVERT: A 185 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.7975 (mtm-85) REVERT: A 344 PHE cc_start: 0.7225 (m-80) cc_final: 0.5939 (m-10) REVERT: A 393 TYR cc_start: 0.8390 (m-80) cc_final: 0.8007 (m-80) REVERT: A 450 TYR cc_start: 0.7585 (p90) cc_final: 0.7350 (p90) REVERT: A 507 VAL cc_start: 0.8115 (t) cc_final: 0.7874 (m) REVERT: A 593 SER cc_start: 0.8838 (p) cc_final: 0.8634 (m) REVERT: A 600 ASN cc_start: 0.8230 (t0) cc_final: 0.7811 (t0) REVERT: A 616 GLU cc_start: 0.7876 (pm20) cc_final: 0.7558 (pm20) REVERT: A 808 LYS cc_start: 0.7555 (mtmt) cc_final: 0.7124 (mttt) REVERT: A 817 ASP cc_start: 0.8021 (m-30) cc_final: 0.7691 (m-30) REVERT: A 1002 GLN cc_start: 0.8359 (tp40) cc_final: 0.8119 (mm-40) REVERT: A 1016 ARG cc_start: 0.8270 (ttm170) cc_final: 0.7944 (ttp-170) REVERT: B 34 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7532 (mpt90) REVERT: B 201 LYS cc_start: 0.8055 (tttt) cc_final: 0.7679 (tttt) REVERT: B 304 THR cc_start: 0.8328 (p) cc_final: 0.8068 (t) REVERT: B 323 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8180 (pt) REVERT: B 439 ASP cc_start: 0.7811 (m-30) cc_final: 0.7525 (m-30) REVERT: B 448 TYR cc_start: 0.7911 (m-10) cc_final: 0.7513 (m-10) REVERT: B 462 GLU cc_start: 0.7606 (pt0) cc_final: 0.7342 (pt0) REVERT: B 490 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7975 (ttm170) REVERT: B 512 PHE cc_start: 0.7788 (m-80) cc_final: 0.7525 (m-80) REVERT: B 526 LYS cc_start: 0.8407 (mmmm) cc_final: 0.8184 (mmmm) REVERT: B 667 ILE cc_start: 0.8422 (pt) cc_final: 0.8147 (pt) REVERT: B 800 SER cc_start: 0.8693 (t) cc_final: 0.8430 (p) REVERT: B 982 ASP cc_start: 0.7907 (p0) cc_final: 0.7647 (p0) REVERT: B 1016 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7959 (ttp-170) REVERT: B 1111 ILE cc_start: 0.8705 (mm) cc_final: 0.8472 (mt) REVERT: C 94 GLU cc_start: 0.6571 (tp30) cc_final: 0.5633 (tp30) REVERT: C 113 GLN cc_start: 0.7961 (mt0) cc_final: 0.7756 (mt0) REVERT: C 127 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8183 (mtpp) REVERT: C 164 GLU cc_start: 0.7720 (mp0) cc_final: 0.7506 (mp0) REVERT: C 263 TYR cc_start: 0.8456 (m-80) cc_final: 0.8079 (m-80) REVERT: C 433 TRP cc_start: 0.6458 (m100) cc_final: 0.6169 (m100) REVERT: C 561 GLN cc_start: 0.7527 (tp-100) cc_final: 0.7040 (tp-100) REVERT: C 814 PHE cc_start: 0.6786 (t80) cc_final: 0.6222 (t80) REVERT: C 816 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7535 (mt-10) REVERT: C 820 PHE cc_start: 0.8287 (m-80) cc_final: 0.7906 (m-80) REVERT: C 865 GLU cc_start: 0.7991 (mp0) cc_final: 0.7660 (mp0) REVERT: C 899 MET cc_start: 0.8708 (mmm) cc_final: 0.8483 (mmt) REVERT: C 930 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8296 (mtmm) REVERT: C 966 LYS cc_start: 0.8655 (ptpt) cc_final: 0.8434 (pttm) REVERT: C 1014 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7923 (mt-10) REVERT: C 1028 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8066 (mt-10) REVERT: C 1070 LYS cc_start: 0.8416 (tttm) cc_final: 0.8150 (mtpp) REVERT: D 37 GLU cc_start: 0.7869 (pt0) cc_final: 0.7263 (pm20) REVERT: D 42 GLN cc_start: 0.7996 (mt0) cc_final: 0.7707 (mt0) REVERT: D 51 ASN cc_start: 0.7663 (m-40) cc_final: 0.7384 (m-40) REVERT: D 64 ASN cc_start: 0.6656 (p0) cc_final: 0.4272 (m-40) REVERT: D 75 GLU cc_start: 0.6170 (pm20) cc_final: 0.5910 (pm20) REVERT: D 82 MET cc_start: 0.7746 (ptm) cc_final: 0.7305 (ppp) REVERT: D 187 LYS cc_start: 0.4774 (mttp) cc_final: 0.4361 (tttp) REVERT: D 199 TYR cc_start: 0.5715 (t80) cc_final: 0.5142 (t80) REVERT: D 249 MET cc_start: 0.0997 (mmm) cc_final: 0.0165 (mmm) REVERT: D 274 PHE cc_start: 0.6343 (p90) cc_final: 0.6026 (p90) REVERT: D 307 ILE cc_start: 0.8507 (mm) cc_final: 0.8302 (mm) REVERT: D 335 ASP cc_start: 0.3350 (t0) cc_final: 0.2864 (t70) REVERT: D 375 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7158 (mm-30) REVERT: D 380 GLN cc_start: 0.7042 (tp-100) cc_final: 0.6727 (tp-100) REVERT: D 381 TYR cc_start: 0.7263 (t80) cc_final: 0.7006 (t80) REVERT: D 385 TYR cc_start: 0.5883 (p90) cc_final: 0.5470 (p90) REVERT: D 398 GLU cc_start: 0.6704 (tp30) cc_final: 0.6298 (tp30) REVERT: D 488 VAL cc_start: 0.4847 (m) cc_final: 0.4588 (t) REVERT: D 579 MET cc_start: 0.2447 (tpt) cc_final: -0.0483 (pmt) outliers start: 108 outliers final: 43 residues processed: 755 average time/residue: 1.3241 time to fit residues: 1195.5838 Evaluate side-chains 696 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 648 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 167 SER Chi-restraints excluded: chain A residue 172 MET 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 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 323 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 513 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 321 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 215 optimal weight: 0.0470 chunk 58 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 76 optimal weight: 0.0060 chunk 9 optimal weight: 0.7980 chunk 319 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 overall best weight: 0.5294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 236 GLN A 560 GLN A 672 GLN A 898 GLN A1116 ASN B 113 GLN B 923 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 123 ASN C 183 ASN C 268 GLN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 ASN C 700 ASN C 962 GLN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.185015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137350 restraints weight = 43372.390| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.33 r_work: 0.3564 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 31229 Z= 0.143 Angle : 0.580 11.565 42567 Z= 0.295 Chirality : 0.044 0.182 4879 Planarity : 0.004 0.060 5421 Dihedral : 5.039 59.076 5003 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.26 % Allowed : 17.83 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.13), residues: 3726 helix: -0.93 (0.17), residues: 879 sheet: -0.67 (0.19), residues: 664 loop : -2.12 (0.12), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 328 HIS 0.004 0.001 HIS D 535 PHE 0.028 0.001 PHE A 163 TYR 0.027 0.001 TYR C 901 ARG 0.008 0.001 ARG B 352 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 33) link_NAG-ASN : angle 1.96376 ( 99) link_BETA1-4 : bond 0.00473 ( 12) link_BETA1-4 : angle 1.71594 ( 36) hydrogen bonds : bond 0.03673 ( 870) hydrogen bonds : angle 5.40292 ( 2466) SS BOND : bond 0.00742 ( 23) SS BOND : angle 2.04958 ( 46) covalent geometry : bond 0.00334 (31161) covalent geometry : angle 0.56775 (42386) *********************** 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 791 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 683 time to evaluate : 3.792 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 100 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7694 (mtp85) REVERT: A 114 SER cc_start: 0.7777 (m) cc_final: 0.7500 (t) REVERT: A 127 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7827 (mtmm) REVERT: A 151 GLU cc_start: 0.0267 (OUTLIER) cc_final: -0.0851 (pp20) REVERT: A 152 PHE cc_start: 0.4464 (OUTLIER) cc_final: 0.4180 (p90) REVERT: A 185 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.7763 (mtm-85) REVERT: A 344 PHE cc_start: 0.7448 (m-80) cc_final: 0.6327 (m-10) REVERT: A 393 TYR cc_start: 0.8416 (m-80) cc_final: 0.8123 (m-80) REVERT: A 492 TYR cc_start: 0.7132 (m-10) cc_final: 0.6892 (m-10) REVERT: A 506 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7420 (ttt180) REVERT: A 507 VAL cc_start: 0.8195 (t) cc_final: 0.7904 (m) REVERT: A 571 ASP cc_start: 0.8200 (t0) cc_final: 0.7811 (t0) REVERT: A 585 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8109 (p) REVERT: A 600 ASN cc_start: 0.8238 (t0) cc_final: 0.7834 (t0) REVERT: A 616 GLU cc_start: 0.7948 (pm20) cc_final: 0.7611 (pm20) REVERT: B 304 THR cc_start: 0.8370 (p) cc_final: 0.8120 (t) REVERT: B 400 ARG cc_start: 0.8456 (ttm170) cc_final: 0.8052 (ttt90) REVERT: B 403 GLU cc_start: 0.7715 (mp0) cc_final: 0.7252 (mm-30) REVERT: B 439 ASP cc_start: 0.7890 (m-30) cc_final: 0.7638 (m-30) REVERT: B 448 TYR cc_start: 0.7919 (m-10) cc_final: 0.7632 (m-10) REVERT: B 454 ARG cc_start: 0.8181 (tpt170) cc_final: 0.7825 (tpt90) REVERT: B 455 LYS cc_start: 0.8668 (mppt) cc_final: 0.8438 (mppt) REVERT: B 462 GLU cc_start: 0.7652 (pt0) cc_final: 0.7369 (pt0) REVERT: B 490 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7948 (ttm170) REVERT: B 526 LYS cc_start: 0.8455 (mmmm) cc_final: 0.8228 (mmmm) REVERT: B 667 ILE cc_start: 0.8426 (pt) cc_final: 0.7948 (mp) REVERT: B 800 SER cc_start: 0.8745 (t) cc_final: 0.8486 (p) REVERT: B 1016 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7955 (ttp-110) REVERT: B 1081 ASP cc_start: 0.7634 (p0) cc_final: 0.7222 (p0) REVERT: C 47 VAL cc_start: 0.8711 (p) cc_final: 0.8466 (m) REVERT: C 127 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8185 (mtpp) REVERT: C 164 GLU cc_start: 0.7627 (mp0) cc_final: 0.7417 (mp0) REVERT: C 263 TYR cc_start: 0.8465 (m-80) cc_final: 0.8027 (m-80) REVERT: C 350 TRP cc_start: 0.7944 (p-90) cc_final: 0.7444 (p-90) REVERT: C 433 TRP cc_start: 0.6569 (m100) cc_final: 0.6237 (m100) REVERT: C 561 GLN cc_start: 0.7539 (tp-100) cc_final: 0.7025 (tp-100) REVERT: C 814 PHE cc_start: 0.6810 (t80) cc_final: 0.6295 (t80) REVERT: C 816 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7455 (mt-10) REVERT: C 820 PHE cc_start: 0.8269 (m-80) cc_final: 0.7873 (m-80) REVERT: C 899 MET cc_start: 0.8667 (mmm) cc_final: 0.8437 (mmt) REVERT: C 930 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8327 (mtmm) REVERT: C 966 LYS cc_start: 0.8684 (ptpt) cc_final: 0.8409 (pttm) REVERT: C 1014 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7946 (mt-10) REVERT: C 1028 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8003 (mt-10) REVERT: D 51 ASN cc_start: 0.7729 (m-40) cc_final: 0.7438 (m-40) REVERT: D 64 ASN cc_start: 0.6636 (p0) cc_final: 0.4270 (m-40) REVERT: D 82 MET cc_start: 0.7595 (ptm) cc_final: 0.7389 (ppp) REVERT: D 249 MET cc_start: 0.1642 (mmm) cc_final: 0.0856 (mmm) REVERT: D 307 ILE cc_start: 0.8453 (mm) cc_final: 0.8231 (tp) REVERT: D 309 LYS cc_start: 0.7718 (mmpt) cc_final: 0.7233 (mmtm) REVERT: D 315 PHE cc_start: 0.7300 (m-80) cc_final: 0.6851 (m-80) REVERT: D 318 VAL cc_start: 0.5363 (p) cc_final: 0.4861 (p) REVERT: D 375 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7176 (mp0) REVERT: D 398 GLU cc_start: 0.6720 (tp30) cc_final: 0.6321 (tp30) REVERT: D 452 PHE cc_start: 0.5883 (t80) cc_final: 0.5507 (t80) REVERT: D 488 VAL cc_start: 0.4626 (m) cc_final: 0.4359 (t) REVERT: D 554 LEU cc_start: 0.5379 (pt) cc_final: 0.4846 (tp) REVERT: D 579 MET cc_start: 0.2460 (tpt) cc_final: -0.0477 (pmt) outliers start: 108 outliers final: 52 residues processed: 733 average time/residue: 1.3095 time to fit residues: 1151.8324 Evaluate side-chains 722 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 666 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 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 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 513 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 180 optimal weight: 1.9990 chunk 360 optimal weight: 0.0010 chunk 127 optimal weight: 0.5980 chunk 303 optimal weight: 1.9990 chunk 325 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 371 optimal weight: 0.0050 chunk 225 optimal weight: 3.9990 chunk 147 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 245 optimal weight: 8.9990 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 910 GLN A1116 ASN B 191 ASN B 759 GLN B 910 GLN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 113 GLN C 123 ASN C 268 GLN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 ASN C 962 GLN C1002 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.185310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.137785 restraints weight = 43583.487| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.34 r_work: 0.3567 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31229 Z= 0.119 Angle : 0.561 9.765 42567 Z= 0.282 Chirality : 0.044 0.207 4879 Planarity : 0.004 0.060 5421 Dihedral : 4.846 57.806 5003 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.35 % Allowed : 18.58 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.13), residues: 3726 helix: -0.54 (0.18), residues: 882 sheet: -0.48 (0.19), residues: 665 loop : -1.95 (0.12), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 328 HIS 0.004 0.000 HIS D 535 PHE 0.028 0.001 PHE A 163 TYR 0.027 0.001 TYR A 450 ARG 0.007 0.000 ARG C1016 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 33) link_NAG-ASN : angle 1.90433 ( 99) link_BETA1-4 : bond 0.00447 ( 12) link_BETA1-4 : angle 1.62751 ( 36) hydrogen bonds : bond 0.03313 ( 870) hydrogen bonds : angle 5.13486 ( 2466) SS BOND : bond 0.00488 ( 23) SS BOND : angle 1.57519 ( 46) covalent geometry : bond 0.00277 (31161) covalent geometry : angle 0.55024 (42386) *********************** 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 793 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 682 time to evaluate : 3.559 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: 0.8710 (OUTLIER) cc_final: 0.6946 (mmt180) REVERT: A 100 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7063 (mtp85) REVERT: A 114 SER cc_start: 0.7756 (m) cc_final: 0.7484 (t) REVERT: A 127 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7884 (mtmm) REVERT: A 151 GLU cc_start: 0.0155 (OUTLIER) cc_final: -0.0874 (pp20) REVERT: A 152 PHE cc_start: 0.4306 (OUTLIER) cc_final: 0.4054 (p90) REVERT: A 185 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8201 (mtt90) REVERT: A 344 PHE cc_start: 0.7565 (m-80) cc_final: 0.6339 (m-80) REVERT: A 495 ARG cc_start: 0.8094 (tpp-160) cc_final: 0.7823 (mmt90) REVERT: A 506 ARG cc_start: 0.7728 (mtt180) cc_final: 0.7235 (ttt180) REVERT: A 507 VAL cc_start: 0.8202 (t) cc_final: 0.7886 (m) REVERT: A 571 ASP cc_start: 0.8218 (t0) cc_final: 0.7816 (t0) REVERT: A 600 ASN cc_start: 0.8205 (t0) cc_final: 0.7815 (t0) REVERT: A 616 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: A 856 THR cc_start: 0.8618 (t) cc_final: 0.8410 (p) REVERT: B 304 THR cc_start: 0.8368 (p) cc_final: 0.8128 (t) REVERT: B 354 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7431 (tpt-90) REVERT: B 439 ASP cc_start: 0.7882 (m-30) cc_final: 0.7671 (m-30) REVERT: B 454 ARG cc_start: 0.8168 (tpt170) cc_final: 0.7795 (tpt90) REVERT: B 455 LYS cc_start: 0.8669 (mppt) cc_final: 0.8416 (mppt) REVERT: B 462 GLU cc_start: 0.7715 (pt0) cc_final: 0.7447 (pt0) REVERT: B 490 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7893 (ttm170) REVERT: B 526 LYS cc_start: 0.8448 (mmmm) cc_final: 0.8172 (mmmm) REVERT: B 667 ILE cc_start: 0.8537 (pt) cc_final: 0.8056 (mp) REVERT: B 800 SER cc_start: 0.8733 (t) cc_final: 0.8485 (p) REVERT: B 985 GLU cc_start: 0.8172 (tp30) cc_final: 0.7929 (tp30) REVERT: B 1016 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7947 (ttp-110) REVERT: B 1081 ASP cc_start: 0.7623 (p0) cc_final: 0.7239 (p0) REVERT: C 47 VAL cc_start: 0.8706 (p) cc_final: 0.8468 (m) REVERT: C 127 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8173 (mtpp) REVERT: C 203 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8243 (p) REVERT: C 263 TYR cc_start: 0.8468 (m-80) cc_final: 0.8078 (m-80) REVERT: C 350 TRP cc_start: 0.7969 (p-90) cc_final: 0.7492 (p-90) REVERT: C 433 TRP cc_start: 0.6597 (m100) cc_final: 0.6257 (m100) REVERT: C 561 GLN cc_start: 0.7506 (tp-100) cc_final: 0.6988 (tp-100) REVERT: C 814 PHE cc_start: 0.6722 (t80) cc_final: 0.6198 (t80) REVERT: C 816 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7451 (mt-10) REVERT: C 820 PHE cc_start: 0.8269 (m-80) cc_final: 0.7925 (m-80) REVERT: C 869 GLN cc_start: 0.8467 (tt0) cc_final: 0.8118 (mt0) REVERT: C 899 MET cc_start: 0.8665 (mmm) cc_final: 0.8422 (mmt) REVERT: C 930 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8265 (mtmp) REVERT: C 1002 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8204 (mm-40) REVERT: C 1014 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7873 (mt-10) REVERT: C 1028 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8059 (mt-10) REVERT: D 31 LYS cc_start: 0.8246 (tmtt) cc_final: 0.8003 (ttpp) REVERT: D 42 GLN cc_start: 0.8022 (mt0) cc_final: 0.7755 (mt0) REVERT: D 51 ASN cc_start: 0.7771 (m-40) cc_final: 0.7495 (m-40) REVERT: D 64 ASN cc_start: 0.6615 (p0) cc_final: 0.3930 (m-40) REVERT: D 82 MET cc_start: 0.7616 (ptm) cc_final: 0.7330 (ppp) REVERT: D 94 LYS cc_start: 0.7336 (tttt) cc_final: 0.6999 (mttt) REVERT: D 249 MET cc_start: 0.2391 (mmm) cc_final: 0.1559 (mmm) REVERT: D 274 PHE cc_start: 0.6256 (p90) cc_final: 0.5791 (p90) REVERT: D 313 LYS cc_start: 0.7469 (ttpp) cc_final: 0.7268 (mtmp) REVERT: D 315 PHE cc_start: 0.7296 (m-80) cc_final: 0.6628 (m-80) REVERT: D 375 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7213 (mp0) REVERT: D 398 GLU cc_start: 0.6687 (tp30) cc_final: 0.6313 (tp30) REVERT: D 452 PHE cc_start: 0.5853 (t80) cc_final: 0.5450 (t80) REVERT: D 481 LYS cc_start: 0.3454 (mtpt) cc_final: 0.3005 (mttp) REVERT: D 488 VAL cc_start: 0.4697 (m) cc_final: 0.4494 (t) REVERT: D 579 MET cc_start: 0.2444 (tpt) cc_final: -0.0397 (pmt) outliers start: 111 outliers final: 52 residues processed: 730 average time/residue: 1.4998 time to fit residues: 1342.1621 Evaluate side-chains 720 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 661 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG 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 172 MET Chi-restraints excluded: chain A residue 200 SER 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 573 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 1035 LYS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 513 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 85 optimal weight: 1.9990 chunk 361 optimal weight: 3.9990 chunk 217 optimal weight: 0.3980 chunk 328 optimal weight: 50.0000 chunk 246 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 318 GLN A 560 GLN A 672 GLN A 910 GLN A1116 ASN B 537 ASN B 759 GLN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN C 516 HIS C 655 ASN C 700 ASN C 707 ASN C 904 ASN C 962 GLN C1132 ASN D 24 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.183526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.135725 restraints weight = 43039.681| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.32 r_work: 0.3539 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31229 Z= 0.159 Angle : 0.579 9.231 42567 Z= 0.291 Chirality : 0.045 0.242 4879 Planarity : 0.004 0.057 5421 Dihedral : 4.775 57.007 5001 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.68 % Allowed : 19.34 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3726 helix: -0.40 (0.18), residues: 883 sheet: -0.36 (0.19), residues: 665 loop : -1.85 (0.12), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 48 HIS 0.004 0.001 HIS D 535 PHE 0.029 0.001 PHE A 163 TYR 0.034 0.001 TYR A 450 ARG 0.010 0.000 ARG B 400 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 33) link_NAG-ASN : angle 1.92681 ( 99) link_BETA1-4 : bond 0.00378 ( 12) link_BETA1-4 : angle 1.62753 ( 36) hydrogen bonds : bond 0.03539 ( 870) hydrogen bonds : angle 5.07805 ( 2466) SS BOND : bond 0.00569 ( 23) SS BOND : angle 1.64267 ( 46) covalent geometry : bond 0.00378 (31161) covalent geometry : angle 0.56778 (42386) *********************** 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 790 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 668 time to evaluate : 3.501 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 34 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7023 (mmt180) REVERT: A 100 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7053 (mtp85) REVERT: A 114 SER cc_start: 0.7798 (m) cc_final: 0.7539 (t) REVERT: A 127 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7917 (mtmm) REVERT: A 151 GLU cc_start: 0.0076 (OUTLIER) cc_final: -0.1033 (pp20) REVERT: A 152 PHE cc_start: 0.4373 (OUTLIER) cc_final: 0.4092 (p90) REVERT: A 185 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.7726 (mtm-85) REVERT: A 234 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7527 (ttt-90) REVERT: A 344 PHE cc_start: 0.7661 (m-80) cc_final: 0.6802 (m-80) REVERT: A 399 ILE cc_start: 0.7762 (pt) cc_final: 0.7504 (mt) REVERT: A 507 VAL cc_start: 0.8218 (t) cc_final: 0.7886 (m) REVERT: A 571 ASP cc_start: 0.8201 (t0) cc_final: 0.7756 (t0) REVERT: A 596 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8654 (p) REVERT: A 600 ASN cc_start: 0.8168 (t0) cc_final: 0.7783 (t0) REVERT: A 616 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: B 304 THR cc_start: 0.8405 (p) cc_final: 0.8179 (t) REVERT: B 354 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7522 (tpt-90) REVERT: B 403 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7725 (mm-30) REVERT: B 439 ASP cc_start: 0.7905 (m-30) cc_final: 0.7630 (m-30) REVERT: B 448 TYR cc_start: 0.7921 (m-10) cc_final: 0.7598 (m-10) REVERT: B 454 ARG cc_start: 0.8233 (tpt170) cc_final: 0.7890 (tpp80) REVERT: B 462 GLU cc_start: 0.7770 (pt0) cc_final: 0.7515 (pt0) REVERT: B 526 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8200 (mmmm) REVERT: B 667 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8142 (mp) REVERT: B 800 SER cc_start: 0.8749 (t) cc_final: 0.8497 (p) REVERT: B 1081 ASP cc_start: 0.7659 (p0) cc_final: 0.7288 (p0) REVERT: C 47 VAL cc_start: 0.8736 (p) cc_final: 0.8495 (m) REVERT: C 52 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7713 (tm-30) REVERT: C 127 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8194 (mtpp) REVERT: C 203 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8282 (p) REVERT: C 263 TYR cc_start: 0.8468 (m-80) cc_final: 0.7963 (m-80) REVERT: C 278 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7719 (pp20) REVERT: C 350 TRP cc_start: 0.7991 (p-90) cc_final: 0.7520 (p-90) REVERT: C 433 TRP cc_start: 0.6699 (m100) cc_final: 0.6374 (m100) REVERT: C 723 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8700 (mm) REVERT: C 820 PHE cc_start: 0.8272 (m-80) cc_final: 0.7961 (m-80) REVERT: C 869 GLN cc_start: 0.8518 (tt0) cc_final: 0.8188 (mt0) REVERT: C 899 MET cc_start: 0.8704 (mmm) cc_final: 0.8460 (mmt) REVERT: C 930 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8270 (mtmp) REVERT: C 933 ASP cc_start: 0.7578 (m-30) cc_final: 0.7338 (m-30) REVERT: D 32 PHE cc_start: 0.8140 (t80) cc_final: 0.7790 (t80) REVERT: D 42 GLN cc_start: 0.8040 (mt0) cc_final: 0.7781 (mt0) REVERT: D 51 ASN cc_start: 0.7802 (m-40) cc_final: 0.7532 (m-40) REVERT: D 64 ASN cc_start: 0.6636 (p0) cc_final: 0.3962 (m-40) REVERT: D 82 MET cc_start: 0.7632 (ptm) cc_final: 0.7337 (ppp) REVERT: D 249 MET cc_start: 0.2396 (mmm) cc_final: 0.1561 (mmm) REVERT: D 274 PHE cc_start: 0.6234 (p90) cc_final: 0.5794 (p90) REVERT: D 315 PHE cc_start: 0.7379 (m-80) cc_final: 0.6426 (m-10) REVERT: D 327 PHE cc_start: 0.6288 (t80) cc_final: 0.6045 (t80) REVERT: D 383 MET cc_start: 0.6832 (ppp) cc_final: 0.6606 (mtp) REVERT: D 398 GLU cc_start: 0.6632 (tp30) cc_final: 0.6228 (tp30) REVERT: D 452 PHE cc_start: 0.5859 (t80) cc_final: 0.5453 (t80) REVERT: D 488 VAL cc_start: 0.4691 (m) cc_final: 0.4378 (t) REVERT: D 579 MET cc_start: 0.2499 (tpt) cc_final: -0.0365 (pmt) outliers start: 122 outliers final: 63 residues processed: 728 average time/residue: 1.4721 time to fit residues: 1273.2494 Evaluate side-chains 732 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 660 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain C residue 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 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 257 optimal weight: 0.0870 chunk 363 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 chunk 312 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 292 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 411 GLN A 560 GLN A 672 GLN A 910 GLN A 932 GLN A 952 ASN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN C 700 ASN C 962 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.183382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135353 restraints weight = 43075.425| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.32 r_work: 0.3535 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31229 Z= 0.160 Angle : 0.591 9.699 42567 Z= 0.297 Chirality : 0.045 0.232 4879 Planarity : 0.004 0.057 5421 Dihedral : 4.764 55.443 5001 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.35 % Allowed : 20.84 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3726 helix: -0.21 (0.18), residues: 872 sheet: -0.25 (0.19), residues: 655 loop : -1.76 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 328 HIS 0.007 0.001 HIS D 374 PHE 0.028 0.001 PHE A 163 TYR 0.031 0.001 TYR A 450 ARG 0.010 0.000 ARG C 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 33) link_NAG-ASN : angle 1.96241 ( 99) link_BETA1-4 : bond 0.00385 ( 12) link_BETA1-4 : angle 1.59926 ( 36) hydrogen bonds : bond 0.03532 ( 870) hydrogen bonds : angle 5.02250 ( 2466) SS BOND : bond 0.00524 ( 23) SS BOND : angle 1.59659 ( 46) covalent geometry : bond 0.00382 (31161) covalent geometry : angle 0.58024 (42386) *********************** 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 785 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 674 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7030 (mmt180) REVERT: A 100 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7052 (mtp85) REVERT: A 114 SER cc_start: 0.7802 (m) cc_final: 0.7545 (t) REVERT: A 127 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7976 (mtmm) REVERT: A 151 GLU cc_start: 0.0139 (OUTLIER) cc_final: -0.0984 (pp20) REVERT: A 152 PHE cc_start: 0.4268 (OUTLIER) cc_final: 0.3987 (p90) REVERT: A 185 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8148 (mtt90) REVERT: A 234 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7567 (ttt-90) REVERT: A 344 PHE cc_start: 0.7674 (m-80) cc_final: 0.6834 (m-80) REVERT: A 353 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7441 (ttpp) REVERT: A 399 ILE cc_start: 0.7735 (pt) cc_final: 0.7483 (mt) REVERT: A 507 VAL cc_start: 0.8196 (t) cc_final: 0.7845 (m) REVERT: A 571 ASP cc_start: 0.8172 (t0) cc_final: 0.7722 (t0) REVERT: A 596 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8667 (p) REVERT: A 600 ASN cc_start: 0.8169 (t0) cc_final: 0.7724 (t0) REVERT: A 616 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: B 304 THR cc_start: 0.8419 (p) cc_final: 0.8188 (t) REVERT: B 403 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7670 (mt-10) REVERT: B 411 GLN cc_start: 0.7612 (mt0) cc_final: 0.7411 (mt0) REVERT: B 439 ASP cc_start: 0.7905 (m-30) cc_final: 0.7579 (m-30) REVERT: B 448 TYR cc_start: 0.7910 (m-10) cc_final: 0.7482 (m-10) REVERT: B 454 ARG cc_start: 0.8260 (tpt170) cc_final: 0.7878 (tpp80) REVERT: B 455 LYS cc_start: 0.8726 (mppt) cc_final: 0.8482 (mppt) REVERT: B 462 GLU cc_start: 0.7801 (pt0) cc_final: 0.7547 (pt0) REVERT: B 526 LYS cc_start: 0.8426 (mmmm) cc_final: 0.8188 (mmmm) REVERT: B 667 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8154 (mp) REVERT: B 787 LYS cc_start: 0.8375 (mttp) cc_final: 0.8064 (mttp) REVERT: B 800 SER cc_start: 0.8747 (t) cc_final: 0.8518 (p) REVERT: B 982 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7644 (p0) REVERT: B 1081 ASP cc_start: 0.7609 (p0) cc_final: 0.7252 (p0) REVERT: C 47 VAL cc_start: 0.8759 (p) cc_final: 0.8515 (m) REVERT: C 52 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7666 (tm-30) REVERT: C 53 ASP cc_start: 0.8257 (m-30) cc_final: 0.8042 (m-30) REVERT: C 94 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5615 (mp0) REVERT: C 113 GLN cc_start: 0.8065 (mm110) cc_final: 0.7650 (mm110) REVERT: C 123 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7209 (t0) REVERT: C 127 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8207 (mtpp) REVERT: C 203 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8317 (p) REVERT: C 278 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7717 (pp20) REVERT: C 350 TRP cc_start: 0.8015 (p-90) cc_final: 0.7601 (p-90) REVERT: C 433 TRP cc_start: 0.6709 (m100) cc_final: 0.6395 (m100) REVERT: C 737 MET cc_start: 0.8382 (mmm) cc_final: 0.8167 (ttp) REVERT: C 801 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8224 (mt0) REVERT: C 820 PHE cc_start: 0.8258 (m-80) cc_final: 0.7960 (m-80) REVERT: C 869 GLN cc_start: 0.8516 (tt0) cc_final: 0.8205 (mt0) REVERT: C 899 MET cc_start: 0.8688 (mmm) cc_final: 0.8437 (mmt) REVERT: C 930 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8204 (mtmm) REVERT: C 933 ASP cc_start: 0.7606 (m-30) cc_final: 0.7328 (m-30) REVERT: C 970 ILE cc_start: 0.8589 (pt) cc_final: 0.8127 (mm) REVERT: D 32 PHE cc_start: 0.8111 (t80) cc_final: 0.7697 (t80) REVERT: D 42 GLN cc_start: 0.8052 (mt0) cc_final: 0.7784 (mt0) REVERT: D 51 ASN cc_start: 0.7812 (m-40) cc_final: 0.7559 (m-40) REVERT: D 64 ASN cc_start: 0.6652 (p0) cc_final: 0.4272 (m-40) REVERT: D 82 MET cc_start: 0.7643 (ptm) cc_final: 0.7310 (ppp) REVERT: D 166 GLU cc_start: 0.5261 (pm20) cc_final: 0.4933 (pm20) REVERT: D 249 MET cc_start: 0.2782 (mmm) cc_final: 0.1949 (mmm) REVERT: D 274 PHE cc_start: 0.6228 (p90) cc_final: 0.5810 (p90) REVERT: D 309 LYS cc_start: 0.8075 (mmpt) cc_final: 0.7476 (mmpt) REVERT: D 381 TYR cc_start: 0.7199 (t80) cc_final: 0.6973 (t80) REVERT: D 398 GLU cc_start: 0.6625 (tp30) cc_final: 0.6220 (tp30) REVERT: D 452 PHE cc_start: 0.5815 (t80) cc_final: 0.5393 (t80) REVERT: D 480 MET cc_start: 0.6645 (mpm) cc_final: 0.5830 (ptp) REVERT: D 488 VAL cc_start: 0.4604 (m) cc_final: 0.4289 (t) REVERT: D 579 MET cc_start: 0.2522 (tpt) cc_final: -0.0309 (pmt) outliers start: 111 outliers final: 65 residues processed: 724 average time/residue: 1.3392 time to fit residues: 1152.3724 Evaluate side-chains 738 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 661 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 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 1133 THR Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 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 364 VAL Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 81 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 271 optimal weight: 0.0050 chunk 313 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 178 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 334 optimal weight: 20.0000 chunk 257 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 560 GLN A 910 GLN A 932 GLN A1116 ASN C 183 ASN C 641 GLN C 700 ASN C 962 GLN ** 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 = 0.4291 r_free = 0.4291 target = 0.183070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.135431 restraints weight = 42985.303| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.30 r_work: 0.3534 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31229 Z= 0.151 Angle : 0.584 9.845 42567 Z= 0.295 Chirality : 0.044 0.229 4879 Planarity : 0.004 0.056 5421 Dihedral : 4.728 53.986 5001 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.50 % Allowed : 21.27 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3726 helix: -0.03 (0.18), residues: 865 sheet: -0.26 (0.19), residues: 677 loop : -1.69 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 328 HIS 0.005 0.001 HIS D 374 PHE 0.032 0.001 PHE C 589 TYR 0.032 0.001 TYR A 450 ARG 0.010 0.000 ARG B 352 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 33) link_NAG-ASN : angle 1.95059 ( 99) link_BETA1-4 : bond 0.00365 ( 12) link_BETA1-4 : angle 1.57424 ( 36) hydrogen bonds : bond 0.03455 ( 870) hydrogen bonds : angle 4.95302 ( 2466) SS BOND : bond 0.00496 ( 23) SS BOND : angle 1.57467 ( 46) covalent geometry : bond 0.00360 (31161) covalent geometry : angle 0.57312 (42386) *********************** 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 790 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 674 time to evaluate : 3.185 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 100 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7787 (mtp85) REVERT: A 114 SER cc_start: 0.7783 (m) cc_final: 0.7527 (t) REVERT: A 127 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7951 (mtmm) REVERT: A 151 GLU cc_start: 0.0215 (OUTLIER) cc_final: -0.0926 (pp20) REVERT: A 152 PHE cc_start: 0.4281 (OUTLIER) cc_final: 0.3951 (p90) REVERT: A 185 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8137 (mtt90) REVERT: A 344 PHE cc_start: 0.7811 (m-80) cc_final: 0.7026 (m-80) REVERT: A 353 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7410 (ttpp) REVERT: A 399 ILE cc_start: 0.7740 (pt) cc_final: 0.7499 (mt) REVERT: A 400 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6621 (mtp180) REVERT: A 571 ASP cc_start: 0.8182 (t0) cc_final: 0.7671 (t0) REVERT: A 596 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8646 (p) REVERT: A 600 ASN cc_start: 0.8171 (t0) cc_final: 0.7728 (t0) REVERT: A 616 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: A 984 PRO cc_start: 0.8317 (Cg_exo) cc_final: 0.7957 (Cg_endo) REVERT: B 304 THR cc_start: 0.8430 (p) cc_final: 0.8203 (t) REVERT: B 354 ARG cc_start: 0.7763 (tpp80) cc_final: 0.7534 (tpt-90) REVERT: B 398 VAL cc_start: 0.8691 (p) cc_final: 0.8478 (t) REVERT: B 400 ARG cc_start: 0.8354 (ttm170) cc_final: 0.8105 (tpp80) REVERT: B 403 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7719 (mm-30) REVERT: B 439 ASP cc_start: 0.7925 (m-30) cc_final: 0.7661 (m-30) REVERT: B 448 TYR cc_start: 0.7924 (m-10) cc_final: 0.7572 (m-10) REVERT: B 454 ARG cc_start: 0.8263 (tpt170) cc_final: 0.7858 (tpp80) REVERT: B 455 LYS cc_start: 0.8737 (mppt) cc_final: 0.8499 (mppt) REVERT: B 462 GLU cc_start: 0.7815 (pt0) cc_final: 0.7565 (pt0) REVERT: B 526 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8182 (mmmm) REVERT: B 667 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8158 (mp) REVERT: B 800 SER cc_start: 0.8736 (t) cc_final: 0.8509 (p) REVERT: B 982 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7673 (p0) REVERT: B 1081 ASP cc_start: 0.7612 (p0) cc_final: 0.7257 (p0) REVERT: C 47 VAL cc_start: 0.8753 (p) cc_final: 0.8503 (m) REVERT: C 52 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 53 ASP cc_start: 0.8281 (m-30) cc_final: 0.8072 (m-30) REVERT: C 94 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5667 (mp0) REVERT: C 95 LYS cc_start: 0.8415 (mtpp) cc_final: 0.7926 (mtpp) REVERT: C 113 GLN cc_start: 0.8003 (mm110) cc_final: 0.7605 (mm110) REVERT: C 123 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.7194 (t0) REVERT: C 127 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8189 (mtpp) REVERT: C 203 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8306 (p) REVERT: C 278 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7753 (pp20) REVERT: C 350 TRP cc_start: 0.8044 (p-90) cc_final: 0.7704 (p-90) REVERT: C 433 TRP cc_start: 0.6708 (m100) cc_final: 0.6406 (m100) REVERT: C 571 ASP cc_start: 0.8048 (t70) cc_final: 0.7459 (t0) REVERT: C 737 MET cc_start: 0.8468 (mmm) cc_final: 0.8056 (tpp) REVERT: C 801 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8167 (mt0) REVERT: C 820 PHE cc_start: 0.8259 (m-80) cc_final: 0.7896 (m-80) REVERT: C 869 GLN cc_start: 0.8520 (tt0) cc_final: 0.8206 (mt0) REVERT: C 899 MET cc_start: 0.8677 (mmm) cc_final: 0.8432 (mmt) REVERT: C 930 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8319 (mtmt) REVERT: C 933 ASP cc_start: 0.7696 (m-30) cc_final: 0.7460 (m-30) REVERT: C 970 ILE cc_start: 0.8640 (pt) cc_final: 0.8201 (mm) REVERT: C 1042 LYS cc_start: 0.8556 (tptm) cc_final: 0.8334 (mmmm) REVERT: D 32 PHE cc_start: 0.8111 (t80) cc_final: 0.7692 (t80) REVERT: D 42 GLN cc_start: 0.8054 (mt0) cc_final: 0.7781 (mt0) REVERT: D 51 ASN cc_start: 0.7857 (m-40) cc_final: 0.7618 (m-40) REVERT: D 64 ASN cc_start: 0.6676 (p0) cc_final: 0.4275 (m-40) REVERT: D 82 MET cc_start: 0.7687 (ptm) cc_final: 0.7358 (ppp) REVERT: D 166 GLU cc_start: 0.5037 (pm20) cc_final: 0.4719 (pm20) REVERT: D 187 LYS cc_start: 0.4558 (tptm) cc_final: 0.3943 (tppp) REVERT: D 213 ASP cc_start: 0.7042 (t0) cc_final: 0.6740 (t0) REVERT: D 249 MET cc_start: 0.2790 (mmm) cc_final: 0.1935 (mmm) REVERT: D 274 PHE cc_start: 0.6241 (p90) cc_final: 0.5867 (p90) REVERT: D 341 LYS cc_start: 0.6934 (mtmm) cc_final: 0.6699 (mppt) REVERT: D 398 GLU cc_start: 0.6639 (tp30) cc_final: 0.6238 (tp30) REVERT: D 452 PHE cc_start: 0.5882 (t80) cc_final: 0.5451 (t80) REVERT: D 481 LYS cc_start: 0.2890 (mtmt) cc_final: 0.1807 (mttp) REVERT: D 488 VAL cc_start: 0.4589 (m) cc_final: 0.4299 (t) REVERT: D 553 LYS cc_start: 0.6743 (tppp) cc_final: 0.6246 (mppt) REVERT: D 579 MET cc_start: 0.2595 (tpt) cc_final: -0.0237 (pmt) outliers start: 116 outliers final: 67 residues processed: 728 average time/residue: 1.3351 time to fit residues: 1152.8668 Evaluate side-chains 735 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 656 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 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 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 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 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 61 ASN 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 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 320 THR 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 732 SER Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain 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 364 VAL Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 233 optimal weight: 0.8980 chunk 280 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 305 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 249 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 560 GLN A 655 ASN A 781 GLN A 910 GLN A1116 ASN B 411 GLN B 999 GLN C 30 ASN C 183 ASN C 700 ASN C1002 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.182031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134183 restraints weight = 43244.560| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.32 r_work: 0.3518 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31229 Z= 0.195 Angle : 0.614 10.379 42567 Z= 0.309 Chirality : 0.046 0.247 4879 Planarity : 0.004 0.060 5421 Dihedral : 4.811 53.837 5001 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.20 % Allowed : 22.14 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3726 helix: -0.04 (0.18), residues: 870 sheet: -0.23 (0.19), residues: 666 loop : -1.69 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 883 HIS 0.004 0.001 HIS D 535 PHE 0.033 0.002 PHE C 589 TYR 0.036 0.002 TYR C 901 ARG 0.008 0.001 ARG B 352 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 33) link_NAG-ASN : angle 2.09629 ( 99) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.56676 ( 36) hydrogen bonds : bond 0.03703 ( 870) hydrogen bonds : angle 5.01867 ( 2466) SS BOND : bond 0.00580 ( 23) SS BOND : angle 1.75994 ( 46) covalent geometry : bond 0.00467 (31161) covalent geometry : angle 0.60271 (42386) *********************** 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 779 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 673 time to evaluate : 3.223 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: 0.7789 (m) cc_final: 0.7532 (t) REVERT: A 127 LYS cc_start: 0.8382 (mtpt) cc_final: 0.8017 (mtmm) REVERT: A 151 GLU cc_start: 0.0402 (OUTLIER) cc_final: -0.0762 (pp20) REVERT: A 152 PHE cc_start: 0.4291 (OUTLIER) cc_final: 0.3967 (p90) REVERT: A 185 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8155 (mtm-85) REVERT: A 234 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7918 (ttm-80) REVERT: A 344 PHE cc_start: 0.7887 (m-80) cc_final: 0.7097 (m-80) REVERT: A 353 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7526 (ttpp) REVERT: A 399 ILE cc_start: 0.7771 (pt) cc_final: 0.7545 (mt) REVERT: A 400 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6765 (mtp180) REVERT: A 571 ASP cc_start: 0.8212 (t0) cc_final: 0.7692 (t0) REVERT: A 600 ASN cc_start: 0.8172 (t0) cc_final: 0.7724 (t0) REVERT: A 616 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: A 984 PRO cc_start: 0.8340 (Cg_exo) cc_final: 0.8007 (Cg_endo) REVERT: B 304 THR cc_start: 0.8447 (p) cc_final: 0.8220 (t) REVERT: B 365 LEU cc_start: 0.8227 (mt) cc_final: 0.8024 (mp) REVERT: B 400 ARG cc_start: 0.8327 (ttm170) cc_final: 0.8062 (ttm170) REVERT: B 403 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7774 (mm-30) REVERT: B 439 ASP cc_start: 0.7928 (m-30) cc_final: 0.7728 (m-30) REVERT: B 454 ARG cc_start: 0.8333 (tpt170) cc_final: 0.7890 (tpt90) REVERT: B 455 LYS cc_start: 0.8754 (mppt) cc_final: 0.8486 (mppt) REVERT: B 462 GLU cc_start: 0.7844 (pt0) cc_final: 0.7588 (pt0) REVERT: B 502 HIS cc_start: 0.8088 (m-70) cc_final: 0.7859 (t-90) REVERT: B 526 LYS cc_start: 0.8414 (mmmm) cc_final: 0.8187 (mmmm) REVERT: B 632 VAL cc_start: 0.8486 (m) cc_final: 0.8255 (t) REVERT: B 667 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8177 (mp) REVERT: B 800 SER cc_start: 0.8741 (t) cc_final: 0.8505 (p) REVERT: B 982 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7666 (p0) REVERT: B 1081 ASP cc_start: 0.7679 (p0) cc_final: 0.7335 (p0) REVERT: C 47 VAL cc_start: 0.8759 (p) cc_final: 0.8508 (m) REVERT: C 52 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7657 (tm-30) REVERT: C 94 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5643 (mp0) REVERT: C 113 GLN cc_start: 0.8033 (mm110) cc_final: 0.7619 (mm110) REVERT: C 123 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.7131 (t0) REVERT: C 127 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8188 (mtpp) REVERT: C 203 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8339 (p) REVERT: C 234 ARG cc_start: 0.8372 (mtp85) cc_final: 0.8170 (mtp85) REVERT: C 263 TYR cc_start: 0.8484 (m-80) cc_final: 0.8104 (m-80) REVERT: C 278 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7749 (pp20) REVERT: C 350 TRP cc_start: 0.8085 (p-90) cc_final: 0.7809 (p-90) REVERT: C 433 TRP cc_start: 0.6810 (m100) cc_final: 0.6488 (m100) REVERT: C 571 ASP cc_start: 0.8071 (t70) cc_final: 0.7468 (t0) REVERT: C 737 MET cc_start: 0.8524 (mmm) cc_final: 0.8168 (tpp) REVERT: C 801 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8180 (mt0) REVERT: C 820 PHE cc_start: 0.8288 (m-80) cc_final: 0.7953 (m-80) REVERT: C 869 GLN cc_start: 0.8535 (tt0) cc_final: 0.8221 (mt0) REVERT: C 899 MET cc_start: 0.8621 (mmm) cc_final: 0.8381 (mmt) REVERT: C 930 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8310 (mtmt) REVERT: C 933 ASP cc_start: 0.7829 (m-30) cc_final: 0.7625 (m-30) REVERT: C 970 ILE cc_start: 0.8666 (pt) cc_final: 0.8225 (mm) REVERT: C 1042 LYS cc_start: 0.8562 (tptm) cc_final: 0.8342 (mmmm) REVERT: D 32 PHE cc_start: 0.8111 (t80) cc_final: 0.7701 (t80) REVERT: D 41 TYR cc_start: 0.7907 (t80) cc_final: 0.7433 (t80) REVERT: D 42 GLN cc_start: 0.8058 (mt0) cc_final: 0.7778 (mt0) REVERT: D 51 ASN cc_start: 0.7864 (m-40) cc_final: 0.7630 (m-40) REVERT: D 64 ASN cc_start: 0.6647 (p0) cc_final: 0.4234 (m-40) REVERT: D 82 MET cc_start: 0.7738 (ptm) cc_final: 0.7400 (ppp) REVERT: D 166 GLU cc_start: 0.5179 (pm20) cc_final: 0.4890 (pm20) REVERT: D 187 LYS cc_start: 0.4294 (tptm) cc_final: 0.3247 (tmtt) REVERT: D 213 ASP cc_start: 0.7098 (t0) cc_final: 0.6798 (t0) REVERT: D 249 MET cc_start: 0.2538 (mmm) cc_final: 0.1750 (mmm) REVERT: D 274 PHE cc_start: 0.6250 (p90) cc_final: 0.5905 (p90) REVERT: D 398 GLU cc_start: 0.6632 (tp30) cc_final: 0.6224 (tp30) REVERT: D 452 PHE cc_start: 0.5789 (t80) cc_final: 0.5347 (t80) REVERT: D 480 MET cc_start: 0.6553 (mmm) cc_final: 0.5778 (ptp) REVERT: D 481 LYS cc_start: 0.3010 (mtmt) cc_final: 0.1829 (mttp) REVERT: D 488 VAL cc_start: 0.4570 (m) cc_final: 0.4280 (t) REVERT: D 579 MET cc_start: 0.2664 (tpt) cc_final: -0.0208 (pmt) outliers start: 106 outliers final: 73 residues processed: 726 average time/residue: 1.3857 time to fit residues: 1200.1446 Evaluate side-chains 739 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 655 time to evaluate : 3.118 ------------------------------------------------------------------------------- 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 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 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 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 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 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 320 THR 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 702 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1047 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 57 optimal weight: 2.9990 chunk 366 optimal weight: 0.1980 chunk 81 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 chunk 340 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 560 GLN A 655 ASN A 869 GLN A 910 GLN A 975 ASN B 962 GLN B1002 GLN C 30 ASN C 700 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 572 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.183355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135688 restraints weight = 43072.230| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.30 r_work: 0.3542 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31229 Z= 0.123 Angle : 0.583 10.174 42567 Z= 0.293 Chirality : 0.044 0.272 4879 Planarity : 0.004 0.058 5421 Dihedral : 4.636 54.383 5001 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.78 % Allowed : 23.05 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3726 helix: 0.21 (0.19), residues: 858 sheet: -0.22 (0.19), residues: 678 loop : -1.62 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 48 HIS 0.005 0.000 HIS D 374 PHE 0.034 0.001 PHE C 589 TYR 0.028 0.001 TYR A 450 ARG 0.010 0.000 ARG B 352 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 33) link_NAG-ASN : angle 1.90122 ( 99) link_BETA1-4 : bond 0.00387 ( 12) link_BETA1-4 : angle 1.52757 ( 36) hydrogen bonds : bond 0.03234 ( 870) hydrogen bonds : angle 4.88928 ( 2466) SS BOND : bond 0.00478 ( 23) SS BOND : angle 1.43116 ( 46) covalent geometry : bond 0.00294 (31161) covalent geometry : angle 0.57317 (42386) *********************** 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 758 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 666 time to evaluate : 3.148 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: A 114 SER cc_start: 0.7717 (m) cc_final: 0.7466 (t) REVERT: A 151 GLU cc_start: 0.0346 (OUTLIER) cc_final: -0.0793 (pp20) REVERT: A 152 PHE cc_start: 0.4221 (OUTLIER) cc_final: 0.3906 (p90) REVERT: A 185 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8152 (mtt90) REVERT: A 344 PHE cc_start: 0.7876 (m-80) cc_final: 0.7068 (m-80) REVERT: A 353 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7423 (ttpp) REVERT: A 400 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6785 (mtp180) REVERT: A 571 ASP cc_start: 0.8157 (t0) cc_final: 0.7607 (t0) REVERT: A 596 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 600 ASN cc_start: 0.8146 (t0) cc_final: 0.7715 (t0) REVERT: A 616 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: A 822 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8503 (mtpt) REVERT: A 984 PRO cc_start: 0.8317 (Cg_exo) cc_final: 0.7956 (Cg_endo) REVERT: B 304 THR cc_start: 0.8450 (p) cc_final: 0.8228 (t) REVERT: B 365 LEU cc_start: 0.8260 (mt) cc_final: 0.8055 (mp) REVERT: B 400 ARG cc_start: 0.8305 (ttm170) cc_final: 0.8019 (ttm170) REVERT: B 403 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7678 (mt-10) REVERT: B 439 ASP cc_start: 0.7895 (m-30) cc_final: 0.7667 (m-30) REVERT: B 454 ARG cc_start: 0.8231 (tpt170) cc_final: 0.7891 (tpt90) REVERT: B 455 LYS cc_start: 0.8716 (mppt) cc_final: 0.8489 (mppt) REVERT: B 462 GLU cc_start: 0.7795 (pt0) cc_final: 0.7545 (pt0) REVERT: B 526 LYS cc_start: 0.8393 (mmmm) cc_final: 0.8156 (mmmm) REVERT: B 632 VAL cc_start: 0.8478 (m) cc_final: 0.8234 (t) REVERT: B 667 ILE cc_start: 0.8553 (pt) cc_final: 0.8133 (mp) REVERT: B 800 SER cc_start: 0.8708 (t) cc_final: 0.8491 (p) REVERT: B 982 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7705 (p0) REVERT: B 1081 ASP cc_start: 0.7599 (p0) cc_final: 0.7249 (p0) REVERT: C 52 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7632 (tm-30) REVERT: C 94 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5653 (mp0) REVERT: C 113 GLN cc_start: 0.7948 (mm110) cc_final: 0.7544 (mm110) REVERT: C 127 LYS cc_start: 0.8441 (mtpp) cc_final: 0.8145 (mtpp) REVERT: C 183 ASN cc_start: 0.7455 (p0) cc_final: 0.7237 (p0) REVERT: C 203 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8315 (p) REVERT: C 278 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7731 (pp20) REVERT: C 350 TRP cc_start: 0.8049 (p-90) cc_final: 0.7819 (p-90) REVERT: C 433 TRP cc_start: 0.6742 (m100) cc_final: 0.6424 (m100) REVERT: C 571 ASP cc_start: 0.8086 (t70) cc_final: 0.7508 (t0) REVERT: C 737 MET cc_start: 0.8473 (mmm) cc_final: 0.8036 (tpp) REVERT: C 801 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8249 (mt0) REVERT: C 820 PHE cc_start: 0.8235 (m-80) cc_final: 0.7882 (m-80) REVERT: C 869 GLN cc_start: 0.8505 (tt0) cc_final: 0.8198 (mt0) REVERT: C 930 LYS cc_start: 0.8552 (mtpp) cc_final: 0.8310 (mtmt) REVERT: C 933 ASP cc_start: 0.7814 (m-30) cc_final: 0.7600 (m-30) REVERT: C 970 ILE cc_start: 0.8640 (pt) cc_final: 0.8198 (mm) REVERT: C 1042 LYS cc_start: 0.8550 (tptm) cc_final: 0.8339 (mmmm) REVERT: D 32 PHE cc_start: 0.8088 (t80) cc_final: 0.7661 (t80) REVERT: D 42 GLN cc_start: 0.8055 (mt0) cc_final: 0.7758 (mt0) REVERT: D 51 ASN cc_start: 0.7850 (m-40) cc_final: 0.7632 (m-40) REVERT: D 64 ASN cc_start: 0.6582 (p0) cc_final: 0.4059 (m-40) REVERT: D 82 MET cc_start: 0.7770 (ptm) cc_final: 0.7429 (ppp) REVERT: D 166 GLU cc_start: 0.5213 (pm20) cc_final: 0.4924 (pm20) REVERT: D 187 LYS cc_start: 0.4069 (tptm) cc_final: 0.3371 (tppp) REVERT: D 249 MET cc_start: 0.2458 (mmm) cc_final: 0.1638 (mmm) REVERT: D 274 PHE cc_start: 0.6241 (p90) cc_final: 0.5906 (p90) REVERT: D 398 GLU cc_start: 0.6638 (tp30) cc_final: 0.6230 (tp30) REVERT: D 452 PHE cc_start: 0.5685 (t80) cc_final: 0.5215 (t80) REVERT: D 481 LYS cc_start: 0.3033 (mtmt) cc_final: 0.1987 (mttp) REVERT: D 488 VAL cc_start: 0.4570 (m) cc_final: 0.4278 (t) REVERT: D 579 MET cc_start: 0.2507 (tpt) cc_final: -0.0252 (pmt) outliers start: 92 outliers final: 63 residues processed: 710 average time/residue: 1.3525 time to fit residues: 1137.6658 Evaluate side-chains 725 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 652 time to evaluate : 3.086 ------------------------------------------------------------------------------- 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 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 824 THR 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 1071 ASN Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 822 LYS Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 536 VAL 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 732 SER Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain 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 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 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 228 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 364 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 0.0470 chunk 234 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 332 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 268 GLN A 560 GLN A 655 ASN A 869 GLN A 910 GLN A1116 ASN B 502 HIS B 954 GLN B1002 GLN C 30 ASN C 700 ASN ** 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 = 0.4284 r_free = 0.4284 target = 0.182614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134851 restraints weight = 43155.560| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.32 r_work: 0.3527 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31229 Z= 0.164 Angle : 0.605 10.526 42567 Z= 0.306 Chirality : 0.045 0.262 4879 Planarity : 0.004 0.060 5421 Dihedral : 4.684 54.180 5001 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.59 % Allowed : 23.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3726 helix: 0.21 (0.18), residues: 865 sheet: -0.20 (0.19), residues: 667 loop : -1.59 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 883 HIS 0.004 0.001 HIS D 535 PHE 0.034 0.001 PHE C 589 TYR 0.032 0.001 TYR C 901 ARG 0.010 0.001 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 33) link_NAG-ASN : angle 1.98117 ( 99) link_BETA1-4 : bond 0.00383 ( 12) link_BETA1-4 : angle 1.52276 ( 36) hydrogen bonds : bond 0.03526 ( 870) hydrogen bonds : angle 4.92612 ( 2466) SS BOND : bond 0.00516 ( 23) SS BOND : angle 1.59887 ( 46) covalent geometry : bond 0.00395 (31161) covalent geometry : angle 0.59468 (42386) ********************** 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 758 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 672 time to evaluate : 3.483 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: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7412 (m-30) cc_final: 0.7161 (t70) REVERT: A 114 SER cc_start: 0.7748 (m) cc_final: 0.7502 (t) REVERT: A 185 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8140 (mtt90) REVERT: A 234 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7965 (ttp80) REVERT: A 344 PHE cc_start: 0.7912 (m-80) cc_final: 0.7128 (m-80) REVERT: A 353 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7531 (ttpp) REVERT: A 400 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6859 (mtp180) REVERT: A 568 ASP cc_start: 0.7387 (p0) cc_final: 0.7111 (p0) REVERT: A 571 ASP cc_start: 0.8163 (t0) cc_final: 0.7615 (t0) REVERT: A 600 ASN cc_start: 0.8166 (t0) cc_final: 0.7732 (t0) REVERT: A 616 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: A 984 PRO cc_start: 0.8337 (Cg_exo) cc_final: 0.7973 (Cg_endo) REVERT: B 304 THR cc_start: 0.8465 (p) cc_final: 0.8228 (t) REVERT: B 365 LEU cc_start: 0.8285 (mt) cc_final: 0.8081 (mp) REVERT: B 403 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7705 (mt-10) REVERT: B 439 ASP cc_start: 0.7883 (m-30) cc_final: 0.7657 (m-30) REVERT: B 454 ARG cc_start: 0.8309 (tpt170) cc_final: 0.7913 (tpt90) REVERT: B 455 LYS cc_start: 0.8729 (mppt) cc_final: 0.8470 (mppt) REVERT: B 462 GLU cc_start: 0.7828 (pt0) cc_final: 0.7567 (pt0) REVERT: B 526 LYS cc_start: 0.8406 (mmmm) cc_final: 0.8172 (mmmm) REVERT: B 553 ASN cc_start: 0.8050 (m-40) cc_final: 0.7773 (t0) REVERT: B 632 VAL cc_start: 0.8485 (m) cc_final: 0.8253 (t) REVERT: B 667 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8182 (mp) REVERT: B 800 SER cc_start: 0.8721 (t) cc_final: 0.8494 (p) REVERT: B 982 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7688 (p0) REVERT: B 1081 ASP cc_start: 0.7652 (p0) cc_final: 0.7303 (p0) REVERT: C 47 VAL cc_start: 0.8772 (p) cc_final: 0.8514 (m) REVERT: C 52 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7654 (tm-30) REVERT: C 94 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5539 (mp0) REVERT: C 113 GLN cc_start: 0.7994 (mm110) cc_final: 0.7610 (mm110) REVERT: C 127 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8146 (mtpp) REVERT: C 203 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8351 (p) REVERT: C 278 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7737 (pp20) REVERT: C 350 TRP cc_start: 0.8071 (p-90) cc_final: 0.7840 (p-90) REVERT: C 433 TRP cc_start: 0.6822 (m100) cc_final: 0.6508 (m100) REVERT: C 571 ASP cc_start: 0.8099 (t70) cc_final: 0.7487 (t0) REVERT: C 801 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8244 (mt0) REVERT: C 820 PHE cc_start: 0.8258 (m-80) cc_final: 0.7918 (m-80) REVERT: C 869 GLN cc_start: 0.8543 (tt0) cc_final: 0.8226 (mt0) REVERT: C 930 LYS cc_start: 0.8564 (mtpp) cc_final: 0.8294 (mtmt) REVERT: C 933 ASP cc_start: 0.7873 (m-30) cc_final: 0.7667 (m-30) REVERT: C 966 LYS cc_start: 0.8651 (ptpp) cc_final: 0.8223 (mtmt) REVERT: C 970 ILE cc_start: 0.8681 (pt) cc_final: 0.8304 (mm) REVERT: C 1042 LYS cc_start: 0.8548 (tptm) cc_final: 0.8341 (mmmm) REVERT: D 32 PHE cc_start: 0.8078 (t80) cc_final: 0.7646 (t80) REVERT: D 41 TYR cc_start: 0.7887 (t80) cc_final: 0.7457 (t80) REVERT: D 42 GLN cc_start: 0.8033 (mt0) cc_final: 0.7740 (mt0) REVERT: D 64 ASN cc_start: 0.6547 (p0) cc_final: 0.4043 (m-40) REVERT: D 82 MET cc_start: 0.7812 (ptm) cc_final: 0.7465 (ppp) REVERT: D 127 TYR cc_start: 0.6300 (t80) cc_final: 0.4915 (t80) REVERT: D 187 LYS cc_start: 0.3888 (tptm) cc_final: 0.2788 (tmtt) REVERT: D 249 MET cc_start: 0.2454 (mmm) cc_final: 0.1684 (mmm) REVERT: D 274 PHE cc_start: 0.6244 (p90) cc_final: 0.5918 (p90) REVERT: D 385 TYR cc_start: 0.5838 (p90) cc_final: 0.4599 (p90) REVERT: D 398 GLU cc_start: 0.6612 (tp30) cc_final: 0.6211 (tp30) REVERT: D 452 PHE cc_start: 0.5622 (t80) cc_final: 0.5117 (t80) REVERT: D 579 MET cc_start: 0.2577 (tpt) cc_final: -0.0238 (pmt) outliers start: 86 outliers final: 66 residues processed: 717 average time/residue: 1.6166 time to fit residues: 1392.6041 Evaluate side-chains 729 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 655 time to evaluate : 3.125 ------------------------------------------------------------------------------- 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 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 822 LYS Chi-restraints excluded: chain B residue 892 GLN Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1042 LYS Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1138 LEU 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 203 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 536 VAL 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 732 SER Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain 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 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 55 optimal weight: 0.6980 chunk 282 optimal weight: 0.8980 chunk 183 optimal weight: 0.4980 chunk 136 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 337 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 237 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 560 GLN A 869 GLN A 910 GLN A1116 ASN B 502 HIS B 748 ASN B 954 GLN B1002 GLN C 30 ASN C 183 ASN C 700 ASN D 51 ASN D 53 ASN D 58 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.134998 restraints weight = 43079.521| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.32 r_work: 0.3525 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31229 Z= 0.170 Angle : 0.622 11.028 42567 Z= 0.315 Chirality : 0.046 0.269 4879 Planarity : 0.004 0.059 5421 Dihedral : 4.641 54.140 4996 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.87 % Allowed : 23.17 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3726 helix: 0.21 (0.19), residues: 860 sheet: -0.16 (0.19), residues: 662 loop : -1.57 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 478 HIS 0.003 0.001 HIS D 374 PHE 0.036 0.001 PHE C 589 TYR 0.036 0.001 TYR C 901 ARG 0.010 0.001 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 33) link_NAG-ASN : angle 1.94035 ( 99) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 1.50315 ( 36) hydrogen bonds : bond 0.03558 ( 870) hydrogen bonds : angle 4.93088 ( 2466) SS BOND : bond 0.00528 ( 23) SS BOND : angle 1.68857 ( 46) covalent geometry : bond 0.00408 (31161) covalent geometry : angle 0.61237 (42386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33828.25 seconds wall clock time: 581 minutes 40.21 seconds (34900.21 seconds total)