Starting phenix.real_space_refine on Sat Jul 4 23:25:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fet_31563/07_2026/7fet_31563.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fet_31563/07_2026/7fet_31563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fet_31563/07_2026/7fet_31563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fet_31563/07_2026/7fet_31563.map" model { file = "/net/cci-nas-00/data/ceres_data/7fet_31563/07_2026/7fet_31563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fet_31563/07_2026/7fet_31563.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7fet_31563/07_2026/7fet_31563.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fet_31563/07_2026/7fet_31563.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.061 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 15318 2.51 5 N 3934 2.21 5 O 4667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24023 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7820 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 950} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7798 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 50, 'TRANS': 948} Chain breaks: 9 Chain: "C" Number of atoms: 7831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7831 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 50, 'TRANS': 952} Chain breaks: 7 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 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 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 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 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 chiralities: 2 Chain: "Q" 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 chiralities: 2 Chain: "S" 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 chiralities: 2 Chain: "U" 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 chiralities: 2 Chain: "V" 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 chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 6 Time building chain proxies: 5.52, per 1000 atoms: 0.23 Number of scatterers: 24023 At special positions: 0 Unit cell: (140.08, 129.2, 201.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 4667 8.00 N 3934 7.00 C 15318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 122 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG P 1 " - " ASN C 709 " " NAG Q 1 " - " ASN C 717 " " NAG S 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1134 " " NAG V 1 " - " ASN A 709 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 621.2 milliseconds 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5624 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 52 sheets defined 22.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.637A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.892A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.356A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.744A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.690A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.221A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 939 removed outlier: 6.721A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.514A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.552A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1032 removed outlier: 3.928A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.809A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.816A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.854A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 4.280A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 826 removed outlier: 3.642A pdb=" N LYS B 825 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 826 " --> pdb=" O PHE B 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 822 through 826' Processing helix chain 'B' and resid 866 through 880 removed outlier: 3.512A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 885 Processing helix chain 'B' and resid 886 through 889 removed outlier: 3.980A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 889' Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.604A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.520A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 965 removed outlier: 3.981A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.503A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 3.799A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.614A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.542A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.899A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.985A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.140A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.737A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.525A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.547A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.917A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 940 removed outlier: 4.448A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.613A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 4.005A pdb=" N ALA C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.285A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.629A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.917A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.514A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 119 through 120 removed outlier: 4.025A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 142 removed outlier: 5.638A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.810A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.289A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 394 through 396 removed outlier: 3.953A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 401 removed outlier: 4.048A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.009A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.990A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A1094 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AB6, first strand: chain 'A' and resid 721 through 722 removed outlier: 6.881A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.707A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.102A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.102A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.510A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (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 119 through 121 removed outlier: 3.894A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 313 through 318 removed outlier: 7.070A pdb=" N VAL B 597 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN B 317 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 595 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.567A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.926A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 376 through 380 removed outlier: 3.901A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 551 through 554 Processing sheet with id=AD3, first strand: chain 'B' and resid 609 through 610 removed outlier: 3.818A pdb=" N VAL B 610 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.758A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.577A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.696A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1077 through 1078 removed outlier: 3.862A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 6.965A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.235A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.088A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 201 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.514A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 103 through 104 removed outlier: 4.352A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.963A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 328 removed outlier: 7.577A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AF1, first strand: chain 'C' and resid 395 through 403 removed outlier: 3.609A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.960A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.924A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.084A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.756A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 4.038A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1911 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: 4.45 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7610 1.34 - 1.46: 6015 1.46 - 1.59: 10800 1.59 - 1.71: 0 1.71 - 1.83: 128 Bond restraints: 24553 Sorted by residual: bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CA GLU B 748 " pdb=" C GLU B 748 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.41e-02 5.03e+03 7.91e+00 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.72e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" CB ARG C1107 " pdb=" CG ARG C1107 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.85e+00 ... (remaining 24548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 32455 2.16 - 4.31: 852 4.31 - 6.47: 81 6.47 - 8.63: 14 8.63 - 10.79: 6 Bond angle restraints: 33408 Sorted by residual: angle pdb=" CA GLY B 431 " pdb=" C GLY B 431 " pdb=" N CYS B 432 " ideal model delta sigma weight residual 114.23 119.55 -5.32 8.80e-01 1.29e+00 3.66e+01 angle pdb=" CA GLY B 431 " pdb=" C GLY B 431 " pdb=" O GLY B 431 " ideal model delta sigma weight residual 122.33 118.61 3.72 8.10e-01 1.52e+00 2.11e+01 angle pdb=" C ARG C 983 " pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " ideal model delta sigma weight residual 109.29 114.70 -5.41 1.51e+00 4.39e-01 1.28e+01 angle pdb=" N GLN A1010 " pdb=" CA GLN A1010 " pdb=" CB GLN A1010 " ideal model delta sigma weight residual 110.28 115.74 -5.46 1.55e+00 4.16e-01 1.24e+01 angle pdb=" N ASP A 985 " pdb=" CA ASP A 985 " pdb=" C ASP A 985 " ideal model delta sigma weight residual 109.81 117.48 -7.67 2.21e+00 2.05e-01 1.21e+01 ... (remaining 33403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12884 17.91 - 35.83: 1144 35.83 - 53.74: 186 53.74 - 71.66: 46 71.66 - 89.57: 33 Dihedral angle restraints: 14293 sinusoidal: 5561 harmonic: 8732 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 2.37 -88.37 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 1.63 -87.63 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -164.69 78.69 1 1.00e+01 1.00e-02 7.72e+01 ... (remaining 14290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3796 0.114 - 0.228: 127 0.228 - 0.342: 4 0.342 - 0.456: 0 0.456 - 0.570: 1 Chirality restraints: 3928 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.12e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3925 not shown) Planarity restraints: 4302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " -0.030 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP B 64 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 811 " -0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 812 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 812 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 812 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " 0.044 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO C 209 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.036 5.00e-02 4.00e+02 ... (remaining 4299 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 492 2.66 - 3.22: 22807 3.22 - 3.78: 33378 3.78 - 4.34: 44904 4.34 - 4.90: 75776 Nonbonded interactions: 177357 Sorted by model distance: nonbonded pdb=" OD1 ASN A 658 " pdb=" N SER A 659 " model vdw 2.102 3.120 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.149 3.040 nonbonded pdb=" O ALA B 352 " pdb=" NE ARG B 466 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR B 612 " pdb=" O ASN B 616 " model vdw 2.212 3.040 nonbonded pdb=" O SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.225 3.040 ... (remaining 177352 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 27 through 129 or resid 131 through 591 or resid 593 throu \ gh 827 or resid 855 through 1306)) selection = (chain 'B' and (resid 27 through 106 or resid 108 through 165 or (resid 166 and \ (name N or name CA or name C or name O or name CB )) or resid 167 through 1306)) \ selection = (chain 'C' and (resid 27 through 106 or resid 108 through 129 or resid 131 throu \ gh 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or \ resid 167 through 591 or resid 593 through 621 or resid 641 through 827 or resi \ d 855 through 1306)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' } 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 group one per residue 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: 5.050 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 20.450 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.006 0.069 24633 Z= 0.278 Angle : 0.840 11.129 33607 Z= 0.447 Chirality : 0.052 0.570 3928 Planarity : 0.005 0.066 4270 Dihedral : 14.191 89.569 8555 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.94 % Favored : 86.00 % Rotamer: Outliers : 0.08 % Allowed : 0.11 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.14), residues: 2949 helix: -0.29 (0.21), residues: 600 sheet: -1.90 (0.23), residues: 509 loop : -3.20 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 357 TYR 0.025 0.002 TYR A 266 PHE 0.035 0.002 PHE A 823 TRP 0.076 0.003 TRP B 64 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.28 (24553) covalent geometry : angle 0.81820 / 0.44 (33408) SS BOND : bond 0.00470 / 0.32 ( 38) SS BOND : angle 2.09665 / 1.50 ( 76) hydrogen bonds : bond 0.22124 / 14.11 ( 689) hydrogen bonds : angle 8.73914 / 5.97 ( 1911) Misc. bond : bond 0.00153 / 0.08 ( 1) link_BETA1-4 : bond 0.00439 / 0.27 ( 9) link_BETA1-4 : angle 2.08680 / 1.27 ( 27) link_NAG-ASN : bond 0.00652 / 0.42 ( 32) link_NAG-ASN : angle 3.06080 / 2.04 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.6135 (p0) cc_final: 0.5819 (m-30) REVERT: A 697 MET cc_start: 0.8259 (ptp) cc_final: 0.7987 (ptm) REVERT: A 900 MET cc_start: 0.8153 (mtp) cc_final: 0.7829 (mtp) REVERT: A 994 ASP cc_start: 0.7162 (t70) cc_final: 0.6905 (t0) REVERT: B 266 TYR cc_start: 0.8492 (m-80) cc_final: 0.8244 (m-10) REVERT: B 392 PHE cc_start: 0.7037 (m-80) cc_final: 0.6534 (m-80) REVERT: B 396 TYR cc_start: 0.7460 (m-10) cc_final: 0.7209 (m-10) REVERT: B 927 PHE cc_start: 0.9071 (t80) cc_final: 0.8761 (t80) REVERT: C 223 LEU cc_start: 0.7864 (mp) cc_final: 0.7537 (mt) REVERT: C 424 LYS cc_start: 0.8582 (tppp) cc_final: 0.8011 (ttmm) REVERT: C 804 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7475 (tm-30) REVERT: C 870 ILE cc_start: 0.9335 (mm) cc_final: 0.9124 (mt) REVERT: C 1130 ILE cc_start: 0.8691 (pt) cc_final: 0.8429 (mp) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.1444 time to fit residues: 64.4458 Evaluate side-chains 147 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 957 GLN A1011 GLN B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN C 52 GLN C 207 HIS C1106 GLN C1135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.121300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086900 restraints weight = 51667.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089677 restraints weight = 27376.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091495 restraints weight = 18339.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.092628 restraints weight = 14119.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093373 restraints weight = 11942.383| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24633 Z= 0.149 Angle : 0.703 14.920 33607 Z= 0.358 Chirality : 0.049 0.420 3928 Planarity : 0.005 0.066 4270 Dihedral : 5.674 28.506 3204 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.38 % Favored : 89.56 % Rotamer: Outliers : 0.88 % Allowed : 7.70 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.14), residues: 2949 helix: 0.22 (0.21), residues: 605 sheet: -1.68 (0.20), residues: 586 loop : -2.99 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 454 TYR 0.020 0.001 TYR B 505 PHE 0.025 0.001 PHE A 238 TRP 0.020 0.002 TRP B 104 HIS 0.003 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (24553) covalent geometry : angle 0.68342 / 0.35 (33408) SS BOND : bond 0.00458 / 0.31 ( 38) SS BOND : angle 1.68107 / 1.17 ( 76) hydrogen bonds : bond 0.05075 / 3.39 ( 689) hydrogen bonds : angle 6.22692 / 4.24 ( 1911) Misc. bond : bond 0.00046 / 0.02 ( 1) link_BETA1-4 : bond 0.00694 / 0.51 ( 9) link_BETA1-4 : angle 1.66588 / 1.04 ( 27) link_NAG-ASN : bond 0.00956 / 0.49 ( 32) link_NAG-ASN : angle 2.69170 / 1.90 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8226 (m-90) cc_final: 0.7568 (m-90) REVERT: A 200 TYR cc_start: 0.7087 (m-80) cc_final: 0.6793 (m-80) REVERT: A 797 PHE cc_start: 0.7726 (m-80) cc_final: 0.7465 (m-10) REVERT: A 900 MET cc_start: 0.8221 (mtp) cc_final: 0.7790 (mtp) REVERT: A 959 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8631 (tt) REVERT: A 994 ASP cc_start: 0.7700 (t70) cc_final: 0.7422 (t0) REVERT: A 1005 GLN cc_start: 0.8737 (tp40) cc_final: 0.8416 (tp40) REVERT: B 104 TRP cc_start: 0.7977 (m-90) cc_final: 0.7644 (m-90) REVERT: B 779 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 1005 GLN cc_start: 0.8475 (tp40) cc_final: 0.8114 (tp40) REVERT: C 346 ARG cc_start: 0.8627 (ptm-80) cc_final: 0.8344 (ptm-80) REVERT: C 347 PHE cc_start: 0.6462 (m-10) cc_final: 0.5335 (m-10) REVERT: C 424 LYS cc_start: 0.7805 (tppp) cc_final: 0.6950 (ttmm) REVERT: C 515 PHE cc_start: 0.8275 (m-10) cc_final: 0.7910 (m-10) REVERT: C 737 ASP cc_start: 0.8024 (t0) cc_final: 0.7811 (t70) REVERT: C 870 ILE cc_start: 0.9259 (mm) cc_final: 0.9022 (mt) REVERT: C 1050 MET cc_start: 0.7818 (mtp) cc_final: 0.7610 (mtp) outliers start: 23 outliers final: 11 residues processed: 205 average time/residue: 0.1440 time to fit residues: 48.7554 Evaluate side-chains 153 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 770 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 66 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 151 optimal weight: 0.0870 chunk 261 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 7 optimal weight: 0.0000 chunk 253 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C1106 GLN C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.121807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087291 restraints weight = 51594.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.090058 restraints weight = 27507.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091852 restraints weight = 18450.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093011 restraints weight = 14279.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093670 restraints weight = 12091.995| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24633 Z= 0.149 Angle : 0.648 10.592 33607 Z= 0.331 Chirality : 0.047 0.357 3928 Planarity : 0.005 0.061 4270 Dihedral : 5.406 28.717 3204 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.09 % Favored : 88.84 % Rotamer: Outliers : 1.22 % Allowed : 10.60 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.15), residues: 2949 helix: 0.49 (0.21), residues: 605 sheet: -1.44 (0.21), residues: 559 loop : -2.88 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1019 TYR 0.017 0.001 TYR C1067 PHE 0.018 0.001 PHE A 238 TRP 0.024 0.002 TRP A 64 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (24553) covalent geometry : angle 0.62959 / 0.33 (33408) SS BOND : bond 0.00397 / 0.29 ( 38) SS BOND : angle 1.70607 / 1.25 ( 76) hydrogen bonds : bond 0.04830 / 3.21 ( 689) hydrogen bonds : angle 5.68395 / 3.85 ( 1911) Misc. bond : bond 0.00068 / 0.04 ( 1) link_BETA1-4 : bond 0.00508 / 0.34 ( 9) link_BETA1-4 : angle 1.67531 / 1.03 ( 27) link_NAG-ASN : bond 0.00524 / 0.35 ( 32) link_NAG-ASN : angle 2.45279 / 1.70 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.965 Fit side-chains REVERT: A 104 TRP cc_start: 0.8128 (m-90) cc_final: 0.7460 (m-90) REVERT: A 200 TYR cc_start: 0.7119 (m-80) cc_final: 0.6866 (m-80) REVERT: A 797 PHE cc_start: 0.7784 (m-80) cc_final: 0.7528 (m-10) REVERT: A 900 MET cc_start: 0.8185 (mtp) cc_final: 0.7445 (mtp) REVERT: A 959 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8658 (tt) REVERT: A 994 ASP cc_start: 0.7632 (t70) cc_final: 0.7339 (t0) REVERT: B 104 TRP cc_start: 0.8257 (m-90) cc_final: 0.7870 (m-90) REVERT: B 392 PHE cc_start: 0.6796 (m-80) cc_final: 0.6328 (m-80) REVERT: B 740 MET cc_start: 0.8614 (tpp) cc_final: 0.8269 (tpt) REVERT: B 1005 GLN cc_start: 0.8633 (tp40) cc_final: 0.8313 (tp40) REVERT: C 346 ARG cc_start: 0.8547 (ptm-80) cc_final: 0.8304 (ptm-80) REVERT: C 347 PHE cc_start: 0.6354 (m-10) cc_final: 0.5390 (m-10) REVERT: C 424 LYS cc_start: 0.8151 (tppp) cc_final: 0.7506 (ttmm) REVERT: C 515 PHE cc_start: 0.8419 (m-10) cc_final: 0.8077 (m-10) REVERT: C 773 GLU cc_start: 0.7751 (tt0) cc_final: 0.7269 (tt0) outliers start: 32 outliers final: 18 residues processed: 175 average time/residue: 0.1555 time to fit residues: 44.7716 Evaluate side-chains 145 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 19 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 493 GLN ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.120115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.085457 restraints weight = 51687.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.088116 restraints weight = 27758.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089858 restraints weight = 18846.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090970 restraints weight = 14686.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091661 restraints weight = 12502.728| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24633 Z= 0.198 Angle : 0.674 10.314 33607 Z= 0.344 Chirality : 0.047 0.346 3928 Planarity : 0.005 0.059 4270 Dihedral : 5.401 29.288 3204 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.60 % Favored : 88.34 % Rotamer: Outliers : 2.10 % Allowed : 12.81 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.15), residues: 2949 helix: 0.57 (0.22), residues: 602 sheet: -1.33 (0.20), residues: 629 loop : -2.87 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.018 0.001 TYR C1067 PHE 0.023 0.002 PHE A1121 TRP 0.035 0.002 TRP A 64 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (24553) covalent geometry : angle 0.65506 / 0.34 (33408) SS BOND : bond 0.00508 / 0.37 ( 38) SS BOND : angle 1.73790 / 1.25 ( 76) hydrogen bonds : bond 0.04958 / 3.28 ( 689) hydrogen bonds : angle 5.54218 / 3.75 ( 1911) Misc. bond : bond 0.00079 / 0.04 ( 1) link_BETA1-4 : bond 0.00471 / 0.31 ( 9) link_BETA1-4 : angle 1.73755 / 1.06 ( 27) link_NAG-ASN : bond 0.00525 / 0.34 ( 32) link_NAG-ASN : angle 2.52045 / 1.75 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 133 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8087 (m-90) cc_final: 0.7415 (m-90) REVERT: A 568 ASP cc_start: 0.7702 (t0) cc_final: 0.7376 (t0) REVERT: A 797 PHE cc_start: 0.7769 (m-80) cc_final: 0.7542 (m-10) REVERT: A 900 MET cc_start: 0.8258 (mtp) cc_final: 0.7558 (mtp) REVERT: A 959 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8733 (tt) REVERT: A 994 ASP cc_start: 0.7732 (t70) cc_final: 0.7415 (t0) REVERT: A 1005 GLN cc_start: 0.8826 (tp40) cc_final: 0.8524 (tp40) REVERT: B 104 TRP cc_start: 0.8363 (m-90) cc_final: 0.7955 (m-90) REVERT: B 392 PHE cc_start: 0.6986 (m-80) cc_final: 0.6448 (m-80) REVERT: B 696 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8452 (t) REVERT: B 740 MET cc_start: 0.8737 (tpp) cc_final: 0.8394 (tpt) REVERT: B 902 MET cc_start: 0.8953 (tpp) cc_final: 0.8651 (tpp) REVERT: B 1005 GLN cc_start: 0.8768 (tp40) cc_final: 0.8453 (tp40) REVERT: C 102 ARG cc_start: 0.6407 (mtt90) cc_final: 0.6164 (mtt90) REVERT: C 346 ARG cc_start: 0.8570 (ptm-80) cc_final: 0.8252 (ptm-80) REVERT: C 347 PHE cc_start: 0.6249 (m-10) cc_final: 0.5527 (m-10) REVERT: C 424 LYS cc_start: 0.8191 (tppp) cc_final: 0.7442 (ttmm) REVERT: C 515 PHE cc_start: 0.8509 (m-10) cc_final: 0.8213 (m-10) REVERT: C 902 MET cc_start: 0.8897 (tpp) cc_final: 0.8406 (tpt) outliers start: 55 outliers final: 33 residues processed: 184 average time/residue: 0.1491 time to fit residues: 45.7317 Evaluate side-chains 155 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.119699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084941 restraints weight = 51767.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.087608 restraints weight = 27780.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.089331 restraints weight = 18871.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090447 restraints weight = 14707.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091166 restraints weight = 12528.793| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24633 Z= 0.198 Angle : 0.668 10.253 33607 Z= 0.340 Chirality : 0.047 0.341 3928 Planarity : 0.005 0.060 4270 Dihedral : 5.373 29.886 3204 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.66 % Favored : 88.27 % Rotamer: Outliers : 2.29 % Allowed : 14.49 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.15), residues: 2949 helix: 0.59 (0.22), residues: 609 sheet: -1.30 (0.20), residues: 623 loop : -2.82 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.031 0.001 TYR C 423 PHE 0.022 0.002 PHE A1121 TRP 0.042 0.002 TRP A 64 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (24553) covalent geometry : angle 0.64800 / 0.34 (33408) SS BOND : bond 0.00450 / 0.33 ( 38) SS BOND : angle 1.86487 / 1.36 ( 76) hydrogen bonds : bond 0.04928 / 3.25 ( 689) hydrogen bonds : angle 5.45522 / 3.69 ( 1911) Misc. bond : bond 0.00075 / 0.04 ( 1) link_BETA1-4 : bond 0.00444 / 0.30 ( 9) link_BETA1-4 : angle 1.79695 / 1.09 ( 27) link_NAG-ASN : bond 0.00526 / 0.35 ( 32) link_NAG-ASN : angle 2.50864 / 1.74 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 123 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.7995 (t) REVERT: A 568 ASP cc_start: 0.7791 (t0) cc_final: 0.7435 (t0) REVERT: A 580 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: A 900 MET cc_start: 0.8291 (mtp) cc_final: 0.7625 (mtp) REVERT: A 959 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8742 (tt) REVERT: A 994 ASP cc_start: 0.7774 (t70) cc_final: 0.7442 (t0) REVERT: B 104 TRP cc_start: 0.8405 (m-90) cc_final: 0.7952 (m-90) REVERT: B 392 PHE cc_start: 0.7021 (m-80) cc_final: 0.6448 (m-80) REVERT: B 394 ASN cc_start: 0.6367 (t0) cc_final: 0.6001 (t0) REVERT: B 696 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8456 (t) REVERT: B 740 MET cc_start: 0.8706 (tpp) cc_final: 0.8424 (tpt) REVERT: B 902 MET cc_start: 0.8981 (tpp) cc_final: 0.8661 (tpp) REVERT: C 346 ARG cc_start: 0.8549 (ptm-80) cc_final: 0.8243 (ptm-80) REVERT: C 347 PHE cc_start: 0.6356 (m-10) cc_final: 0.5524 (m-10) REVERT: C 424 LYS cc_start: 0.8302 (tppp) cc_final: 0.7728 (ttmm) REVERT: C 515 PHE cc_start: 0.8539 (m-10) cc_final: 0.8226 (m-10) REVERT: C 902 MET cc_start: 0.8949 (tpp) cc_final: 0.8536 (tpt) REVERT: C 1050 MET cc_start: 0.7734 (mtp) cc_final: 0.7380 (mtp) outliers start: 60 outliers final: 38 residues processed: 178 average time/residue: 0.1483 time to fit residues: 44.0779 Evaluate side-chains 159 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 295 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 266 optimal weight: 0.4980 chunk 279 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.120624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.086449 restraints weight = 51904.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.090858 restraints weight = 27810.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091268 restraints weight = 15150.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091715 restraints weight = 12989.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.091841 restraints weight = 12597.679| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24633 Z= 0.144 Angle : 0.629 10.361 33607 Z= 0.320 Chirality : 0.046 0.354 3928 Planarity : 0.005 0.060 4270 Dihedral : 5.162 30.047 3204 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.55 % Favored : 89.39 % Rotamer: Outliers : 2.67 % Allowed : 14.84 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.15), residues: 2949 helix: 0.73 (0.22), residues: 614 sheet: -1.30 (0.20), residues: 631 loop : -2.75 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1107 TYR 0.032 0.001 TYR C 423 PHE 0.016 0.001 PHE A 238 TRP 0.029 0.002 TRP A 64 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (24553) covalent geometry : angle 0.60981 / 0.32 (33408) SS BOND : bond 0.00335 / 0.24 ( 38) SS BOND : angle 1.72300 / 1.24 ( 76) hydrogen bonds : bond 0.04515 / 2.99 ( 689) hydrogen bonds : angle 5.23017 / 3.55 ( 1911) Misc. bond : bond 0.00041 / 0.02 ( 1) link_BETA1-4 : bond 0.00460 / 0.31 ( 9) link_BETA1-4 : angle 1.70032 / 1.04 ( 27) link_NAG-ASN : bond 0.00509 / 0.33 ( 32) link_NAG-ASN : angle 2.42140 / 1.67 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 127 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.7965 (t) REVERT: A 580 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6858 (mp10) REVERT: A 900 MET cc_start: 0.8153 (mtp) cc_final: 0.7494 (mtp) REVERT: A 934 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8922 (tp) REVERT: A 959 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8736 (tt) REVERT: A 994 ASP cc_start: 0.7625 (t70) cc_final: 0.7275 (t0) REVERT: A 1005 GLN cc_start: 0.8787 (tp40) cc_final: 0.8517 (tp40) REVERT: B 104 TRP cc_start: 0.8355 (m-90) cc_final: 0.7967 (m-90) REVERT: B 392 PHE cc_start: 0.6986 (m-80) cc_final: 0.6448 (m-80) REVERT: B 394 ASN cc_start: 0.6203 (t0) cc_final: 0.5922 (t0) REVERT: B 432 CYS cc_start: 0.4673 (OUTLIER) cc_final: 0.4462 (p) REVERT: B 433 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8089 (p) REVERT: B 696 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8423 (t) REVERT: B 740 MET cc_start: 0.8643 (tpp) cc_final: 0.8363 (tpt) REVERT: B 886 TRP cc_start: 0.8068 (OUTLIER) cc_final: 0.7861 (m-90) REVERT: C 102 ARG cc_start: 0.6463 (mtt90) cc_final: 0.6073 (mtt90) REVERT: C 346 ARG cc_start: 0.8572 (ptm-80) cc_final: 0.8250 (ptm-80) REVERT: C 347 PHE cc_start: 0.6637 (m-10) cc_final: 0.5896 (m-10) REVERT: C 424 LYS cc_start: 0.8171 (tppp) cc_final: 0.7755 (ttmm) REVERT: C 515 PHE cc_start: 0.8522 (m-10) cc_final: 0.8175 (m-10) REVERT: C 568 ASP cc_start: 0.7577 (p0) cc_final: 0.7267 (p0) REVERT: C 740 MET cc_start: 0.8651 (mmm) cc_final: 0.8370 (tpp) outliers start: 70 outliers final: 45 residues processed: 189 average time/residue: 0.1475 time to fit residues: 46.8328 Evaluate side-chains 169 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 218 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 270 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084295 restraints weight = 52084.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.086925 restraints weight = 28003.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088641 restraints weight = 19052.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089704 restraints weight = 14893.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.090403 restraints weight = 12735.289| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24633 Z= 0.199 Angle : 0.676 11.955 33607 Z= 0.343 Chirality : 0.047 0.339 3928 Planarity : 0.005 0.059 4270 Dihedral : 5.253 29.715 3204 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.83 % Favored : 88.10 % Rotamer: Outliers : 2.59 % Allowed : 15.56 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.15), residues: 2949 helix: 0.70 (0.22), residues: 612 sheet: -1.43 (0.20), residues: 665 loop : -2.75 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.024 0.001 TYR C 423 PHE 0.025 0.002 PHE A1121 TRP 0.025 0.002 TRP A 64 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (24553) covalent geometry : angle 0.65708 / 0.34 (33408) SS BOND : bond 0.00386 / 0.28 ( 38) SS BOND : angle 1.78626 / 1.28 ( 76) hydrogen bonds : bond 0.04893 / 3.23 ( 689) hydrogen bonds : angle 5.31614 / 3.60 ( 1911) Misc. bond : bond 0.00069 / 0.04 ( 1) link_BETA1-4 : bond 0.00442 / 0.29 ( 9) link_BETA1-4 : angle 1.79614 / 1.09 ( 27) link_NAG-ASN : bond 0.00526 / 0.34 ( 32) link_NAG-ASN : angle 2.48979 / 1.73 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 117 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8041 (t) REVERT: A 580 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7026 (mp10) REVERT: A 873 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: A 900 MET cc_start: 0.8331 (mtp) cc_final: 0.7682 (mtp) REVERT: A 934 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8943 (tp) REVERT: A 959 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8728 (tt) REVERT: A 994 ASP cc_start: 0.7744 (t70) cc_final: 0.7391 (t0) REVERT: B 349 SER cc_start: 0.3627 (OUTLIER) cc_final: 0.3352 (m) REVERT: B 394 ASN cc_start: 0.6246 (t0) cc_final: 0.5967 (t0) REVERT: B 696 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8491 (t) REVERT: B 740 MET cc_start: 0.8700 (tpp) cc_final: 0.8467 (tpp) REVERT: C 346 ARG cc_start: 0.8599 (ptm-80) cc_final: 0.8248 (ptm-80) REVERT: C 347 PHE cc_start: 0.6318 (m-10) cc_final: 0.5614 (m-10) REVERT: C 424 LYS cc_start: 0.8473 (tppp) cc_final: 0.7953 (ttmm) REVERT: C 515 PHE cc_start: 0.8573 (m-10) cc_final: 0.8266 (m-10) outliers start: 68 outliers final: 52 residues processed: 179 average time/residue: 0.1536 time to fit residues: 46.0214 Evaluate side-chains 173 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 114 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 58 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 236 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 245 optimal weight: 0.0050 chunk 141 optimal weight: 0.3980 chunk 198 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 201 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.121056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.086949 restraints weight = 51674.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091330 restraints weight = 27866.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091690 restraints weight = 15212.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.092148 restraints weight = 13205.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.092291 restraints weight = 12497.444| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24633 Z= 0.118 Angle : 0.622 10.455 33607 Z= 0.316 Chirality : 0.046 0.360 3928 Planarity : 0.005 0.061 4270 Dihedral : 5.049 30.128 3204 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.70 % Favored : 90.23 % Rotamer: Outliers : 2.14 % Allowed : 16.36 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.15), residues: 2949 helix: 0.91 (0.22), residues: 612 sheet: -1.22 (0.20), residues: 633 loop : -2.69 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.019 0.001 TYR C 423 PHE 0.015 0.001 PHE A 238 TRP 0.022 0.002 TRP A 64 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (24553) covalent geometry : angle 0.60322 / 0.31 (33408) SS BOND : bond 0.00408 / 0.28 ( 38) SS BOND : angle 1.68556 / 1.24 ( 76) hydrogen bonds : bond 0.04330 / 2.88 ( 689) hydrogen bonds : angle 5.10489 / 3.47 ( 1911) Misc. bond : bond 0.00026 / 0.01 ( 1) link_BETA1-4 : bond 0.00502 / 0.34 ( 9) link_BETA1-4 : angle 1.66620 / 1.02 ( 27) link_NAG-ASN : bond 0.00509 / 0.34 ( 32) link_NAG-ASN : angle 2.37300 / 1.64 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 131 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.7988 (t) REVERT: A 580 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.6907 (mp10) REVERT: A 900 MET cc_start: 0.8119 (mtp) cc_final: 0.7471 (mtp) REVERT: A 934 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8826 (tp) REVERT: A 959 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8704 (tt) REVERT: A 994 ASP cc_start: 0.7592 (t70) cc_final: 0.7224 (t0) REVERT: B 104 TRP cc_start: 0.8364 (m-90) cc_final: 0.8030 (m-90) REVERT: B 349 SER cc_start: 0.3374 (OUTLIER) cc_final: 0.3132 (m) REVERT: B 394 ASN cc_start: 0.6181 (t0) cc_final: 0.5905 (t0) REVERT: B 433 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.7980 (p) REVERT: B 740 MET cc_start: 0.8599 (tpp) cc_final: 0.8381 (tpp) REVERT: C 346 ARG cc_start: 0.8610 (ptm-80) cc_final: 0.8248 (ptm-80) REVERT: C 347 PHE cc_start: 0.6583 (m-10) cc_final: 0.5895 (m-10) REVERT: C 424 LYS cc_start: 0.8380 (tppp) cc_final: 0.7943 (ttmm) REVERT: C 515 PHE cc_start: 0.8521 (m-10) cc_final: 0.8228 (m-10) REVERT: C 902 MET cc_start: 0.8819 (tpp) cc_final: 0.8526 (tpt) outliers start: 56 outliers final: 42 residues processed: 180 average time/residue: 0.1537 time to fit residues: 45.8517 Evaluate side-chains 170 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 16 optimal weight: 0.8980 chunk 289 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 248 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086771 restraints weight = 51758.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089481 restraints weight = 27477.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091219 restraints weight = 18508.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.092352 restraints weight = 14399.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093091 restraints weight = 12215.020| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24633 Z= 0.122 Angle : 0.613 10.107 33607 Z= 0.311 Chirality : 0.045 0.348 3928 Planarity : 0.004 0.059 4270 Dihedral : 4.896 29.650 3204 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.55 % Favored : 89.39 % Rotamer: Outliers : 2.25 % Allowed : 16.55 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.15), residues: 2949 helix: 1.08 (0.22), residues: 609 sheet: -1.23 (0.20), residues: 650 loop : -2.64 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.023 0.001 TYR C 423 PHE 0.014 0.001 PHE A 238 TRP 0.022 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (24553) covalent geometry : angle 0.59602 / 0.31 (33408) SS BOND : bond 0.00327 / 0.23 ( 38) SS BOND : angle 1.59428 / 1.17 ( 76) hydrogen bonds : bond 0.04129 / 2.75 ( 689) hydrogen bonds : angle 4.98699 / 3.39 ( 1911) Misc. bond : bond 0.00036 / 0.02 ( 1) link_BETA1-4 : bond 0.00479 / 0.33 ( 9) link_BETA1-4 : angle 1.56815 / 0.96 ( 27) link_NAG-ASN : bond 0.00505 / 0.33 ( 32) link_NAG-ASN : angle 2.31797 / 1.61 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 124 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8009 (t) REVERT: A 568 ASP cc_start: 0.7714 (t0) cc_final: 0.7409 (t0) REVERT: A 580 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: A 873 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: A 900 MET cc_start: 0.8154 (mtp) cc_final: 0.7542 (mtp) REVERT: A 934 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8817 (tp) REVERT: A 959 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8693 (tt) REVERT: A 994 ASP cc_start: 0.7571 (t70) cc_final: 0.7201 (t0) REVERT: A 1005 GLN cc_start: 0.8779 (tp40) cc_final: 0.8531 (tp40) REVERT: B 104 TRP cc_start: 0.8378 (m-90) cc_final: 0.8035 (m-90) REVERT: B 433 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 347 PHE cc_start: 0.6722 (m-10) cc_final: 0.6066 (m-10) REVERT: C 515 PHE cc_start: 0.8404 (m-10) cc_final: 0.8128 (m-10) REVERT: C 902 MET cc_start: 0.8819 (tpp) cc_final: 0.8555 (tpt) outliers start: 59 outliers final: 43 residues processed: 175 average time/residue: 0.1459 time to fit residues: 42.6650 Evaluate side-chains 168 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 119 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 191 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 246 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.086121 restraints weight = 52063.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088809 restraints weight = 27707.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090541 restraints weight = 18757.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.091614 restraints weight = 14623.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.092386 restraints weight = 12476.113| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24633 Z= 0.139 Angle : 0.620 10.034 33607 Z= 0.314 Chirality : 0.046 0.358 3928 Planarity : 0.005 0.060 4270 Dihedral : 4.904 29.346 3204 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.27 % Favored : 89.66 % Rotamer: Outliers : 2.06 % Allowed : 16.93 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.15), residues: 2949 helix: 1.07 (0.22), residues: 609 sheet: -1.25 (0.20), residues: 656 loop : -2.62 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.017 0.001 TYR B 501 PHE 0.016 0.001 PHE A1121 TRP 0.020 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (24553) covalent geometry : angle 0.60302 / 0.31 (33408) SS BOND : bond 0.00412 / 0.30 ( 38) SS BOND : angle 1.56497 / 1.14 ( 76) hydrogen bonds : bond 0.04231 / 2.82 ( 689) hydrogen bonds : angle 5.01820 / 3.42 ( 1911) Misc. bond : bond 0.00044 / 0.02 ( 1) link_BETA1-4 : bond 0.00463 / 0.32 ( 9) link_BETA1-4 : angle 1.59096 / 0.97 ( 27) link_NAG-ASN : bond 0.00497 / 0.33 ( 32) link_NAG-ASN : angle 2.34176 / 1.62 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8022 (t) REVERT: A 568 ASP cc_start: 0.7534 (t0) cc_final: 0.7212 (t0) REVERT: A 580 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6972 (mp10) REVERT: A 873 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: A 900 MET cc_start: 0.8192 (mtp) cc_final: 0.7556 (mtp) REVERT: A 959 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8717 (tt) REVERT: A 994 ASP cc_start: 0.7626 (t70) cc_final: 0.7349 (t0) REVERT: A 1005 GLN cc_start: 0.8797 (tp40) cc_final: 0.8547 (tp40) REVERT: B 104 TRP cc_start: 0.8422 (m-90) cc_final: 0.8055 (m-90) REVERT: B 433 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8131 (p) REVERT: C 515 PHE cc_start: 0.8442 (m-10) cc_final: 0.8183 (m-10) REVERT: C 902 MET cc_start: 0.8856 (tpp) cc_final: 0.8558 (tpt) outliers start: 54 outliers final: 44 residues processed: 171 average time/residue: 0.1368 time to fit residues: 38.8692 Evaluate side-chains 173 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 11 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 297 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 268 optimal weight: 0.0770 chunk 94 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.121862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.087230 restraints weight = 51782.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.089979 restraints weight = 27531.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.091750 restraints weight = 18514.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092879 restraints weight = 14374.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.093603 restraints weight = 12224.922| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24633 Z= 0.117 Angle : 0.607 10.004 33607 Z= 0.307 Chirality : 0.045 0.350 3928 Planarity : 0.004 0.059 4270 Dihedral : 4.813 29.395 3204 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.80 % Favored : 90.13 % Rotamer: Outliers : 2.02 % Allowed : 17.09 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.15), residues: 2949 helix: 1.17 (0.22), residues: 609 sheet: -1.16 (0.20), residues: 653 loop : -2.58 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.019 0.001 TYR B 501 PHE 0.015 0.001 PHE C 347 TRP 0.021 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (24553) covalent geometry : angle 0.59022 / 0.30 (33408) SS BOND : bond 0.00376 / 0.27 ( 38) SS BOND : angle 1.55992 / 1.12 ( 76) hydrogen bonds : bond 0.04011 / 2.67 ( 689) hydrogen bonds : angle 4.94996 / 3.38 ( 1911) Misc. bond : bond 0.00027 / 0.01 ( 1) link_BETA1-4 : bond 0.00489 / 0.34 ( 9) link_BETA1-4 : angle 1.54483 / 0.95 ( 27) link_NAG-ASN : bond 0.00502 / 0.33 ( 32) link_NAG-ASN : angle 2.27813 / 1.58 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3847.35 seconds wall clock time: 67 minutes 29.09 seconds (4049.09 seconds total)