Starting phenix.real_space_refine on Thu Mar 5 17:29:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fet_31563/03_2026/7fet_31563.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fet_31563/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7fet_31563/03_2026/7fet_31563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fet_31563/03_2026/7fet_31563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fet_31563/03_2026/7fet_31563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fet_31563/03_2026/7fet_31563.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 24 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 dihedrals: 27 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.41, 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: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 4.49 Time building geometry restraints manager: 2.65 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 - 24.93: 14276 24.93 - 49.85: 719 49.85 - 74.78: 112 74.78 - 99.70: 38 99.70 - 124.63: 9 Dihedral angle restraints: 15154 sinusoidal: 6422 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 15151 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.700 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 15.260 124.629 9416 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 covalent geometry : bond 0.00631 (24553) covalent geometry : angle 0.81820 (33408) SS BOND : bond 0.00470 ( 38) SS BOND : angle 2.09665 ( 76) hydrogen bonds : bond 0.22124 ( 689) hydrogen bonds : angle 8.73914 ( 1911) Misc. bond : bond 0.00153 ( 1) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 2.08680 ( 27) link_NAG-ASN : bond 0.00652 ( 32) link_NAG-ASN : angle 3.06080 ( 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 : 0.778 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: 0.1525 time to fit residues: 67.8404 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 : 0.714 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3830 r_free = 0.3830 target = 0.121278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086874 restraints weight = 51664.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089653 restraints weight = 27406.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091420 restraints weight = 18354.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.092609 restraints weight = 14189.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093336 restraints weight = 11960.002| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24633 Z= 0.148 Angle : 0.704 12.870 33607 Z= 0.359 Chirality : 0.049 0.421 3928 Planarity : 0.005 0.069 4270 Dihedral : 10.131 114.457 4065 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.44 % Favored : 89.49 % Rotamer: Outliers : 0.88 % Allowed : 7.55 % Favored : 91.57 % 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: 0.21 (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 0.008 0.001 ARG C 454 TYR 0.018 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 covalent geometry : bond 0.00334 (24553) covalent geometry : angle 0.68529 (33408) SS BOND : bond 0.00448 ( 38) SS BOND : angle 1.69596 ( 76) hydrogen bonds : bond 0.05162 ( 689) hydrogen bonds : angle 6.24302 ( 1911) Misc. bond : bond 0.00075 ( 1) link_BETA1-4 : bond 0.00420 ( 9) link_BETA1-4 : angle 1.84106 ( 27) link_NAG-ASN : bond 0.00924 ( 32) link_NAG-ASN : angle 2.65643 ( 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 : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8220 (m-90) cc_final: 0.7572 (m-90) REVERT: A 200 TYR cc_start: 0.7092 (m-80) cc_final: 0.6802 (m-80) REVERT: A 797 PHE cc_start: 0.7724 (m-80) cc_final: 0.7469 (m-10) REVERT: A 900 MET cc_start: 0.8220 (mtp) cc_final: 0.7790 (mtp) REVERT: A 959 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8632 (tt) REVERT: A 994 ASP cc_start: 0.7691 (t70) cc_final: 0.7414 (t0) REVERT: A 1005 GLN cc_start: 0.8731 (tp40) cc_final: 0.8412 (tp40) REVERT: B 104 TRP cc_start: 0.7972 (m-90) cc_final: 0.7654 (m-90) REVERT: B 493 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 779 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8253 (tm-30) REVERT: B 1005 GLN cc_start: 0.8465 (tp40) cc_final: 0.8102 (tp40) REVERT: C 346 ARG cc_start: 0.8612 (ptm-80) cc_final: 0.8241 (ptm-80) REVERT: C 424 LYS cc_start: 0.7850 (tppp) cc_final: 0.6991 (ttmm) REVERT: C 515 PHE cc_start: 0.8268 (m-10) cc_final: 0.7896 (m-10) REVERT: C 737 ASP cc_start: 0.8023 (t0) cc_final: 0.7818 (t70) REVERT: C 773 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7532 (tt0) REVERT: C 870 ILE cc_start: 0.9270 (mm) cc_final: 0.9033 (mt) REVERT: C 1050 MET cc_start: 0.7835 (mtp) cc_final: 0.7632 (mtp) outliers start: 23 outliers final: 11 residues processed: 205 average time/residue: 0.1451 time to fit residues: 49.0204 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 : 0.846 ------------------------------------------------------------------------------- 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: 0.8980 chunk 261 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 52 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C1106 GLN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.118735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085195 restraints weight = 51994.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089049 restraints weight = 28006.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.089493 restraints weight = 16092.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090066 restraints weight = 13581.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090281 restraints weight = 12827.411| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24633 Z= 0.182 Angle : 0.683 10.237 33607 Z= 0.347 Chirality : 0.048 0.374 3928 Planarity : 0.005 0.061 4270 Dihedral : 8.996 111.999 4065 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.53 % Favored : 88.40 % Rotamer: Outliers : 1.45 % Allowed : 11.29 % Favored : 87.26 % 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: -2.70 (0.15), residues: 2949 helix: 0.40 (0.21), residues: 605 sheet: -1.36 (0.20), residues: 609 loop : -2.93 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1107 TYR 0.019 0.002 TYR C 351 PHE 0.020 0.002 PHE A1121 TRP 0.025 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00425 (24553) covalent geometry : angle 0.66320 (33408) SS BOND : bond 0.00401 ( 38) SS BOND : angle 1.80671 ( 76) hydrogen bonds : bond 0.05104 ( 689) hydrogen bonds : angle 5.68899 ( 1911) Misc. bond : bond 0.00082 ( 1) link_BETA1-4 : bond 0.00411 ( 9) link_BETA1-4 : angle 1.95092 ( 27) link_NAG-ASN : bond 0.00548 ( 32) link_NAG-ASN : angle 2.53942 ( 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 184 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8127 (m-90) cc_final: 0.7449 (m-90) REVERT: A 797 PHE cc_start: 0.7788 (m-80) cc_final: 0.7527 (m-10) REVERT: A 902 MET cc_start: 0.9104 (tpp) cc_final: 0.8853 (tpt) REVERT: A 959 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8708 (tt) REVERT: A 994 ASP cc_start: 0.7672 (t70) cc_final: 0.7372 (t0) REVERT: B 104 TRP cc_start: 0.8333 (m-90) cc_final: 0.7996 (m-90) REVERT: B 392 PHE cc_start: 0.6812 (m-80) cc_final: 0.6367 (m-80) REVERT: B 740 MET cc_start: 0.8659 (tpp) cc_final: 0.8329 (tpt) REVERT: B 902 MET cc_start: 0.8929 (tpp) cc_final: 0.8647 (tpp) REVERT: B 1005 GLN cc_start: 0.8746 (tp40) cc_final: 0.8447 (tp40) REVERT: C 346 ARG cc_start: 0.8604 (ptm-80) cc_final: 0.8320 (ptm-80) REVERT: C 347 PHE cc_start: 0.6282 (m-10) cc_final: 0.5300 (m-10) REVERT: C 424 LYS cc_start: 0.8017 (tppp) cc_final: 0.7289 (ttmm) REVERT: C 515 PHE cc_start: 0.8427 (m-10) cc_final: 0.8147 (m-10) outliers start: 38 outliers final: 21 residues processed: 180 average time/residue: 0.1502 time to fit residues: 44.2244 Evaluate side-chains 148 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 320 VAL 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 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: 3.9990 chunk 185 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 97 optimal weight: 0.0570 chunk 222 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 493 GLN ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3802 r_free = 0.3802 target = 0.120481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.086109 restraints weight = 51660.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088765 restraints weight = 27733.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090519 restraints weight = 18811.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091609 restraints weight = 14616.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.092337 restraints weight = 12449.993| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24633 Z= 0.163 Angle : 0.656 10.205 33607 Z= 0.333 Chirality : 0.047 0.370 3928 Planarity : 0.005 0.060 4270 Dihedral : 8.421 112.801 4065 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.75 % Favored : 89.18 % Rotamer: Outliers : 2.10 % Allowed : 12.97 % Favored : 84.94 % 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: 0.65 (0.22), residues: 602 sheet: -1.23 (0.21), residues: 595 loop : -2.84 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1107 TYR 0.027 0.001 TYR C 423 PHE 0.019 0.001 PHE A1121 TRP 0.037 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00379 (24553) covalent geometry : angle 0.63772 (33408) SS BOND : bond 0.00415 ( 38) SS BOND : angle 1.62020 ( 76) hydrogen bonds : bond 0.04738 ( 689) hydrogen bonds : angle 5.46288 ( 1911) Misc. bond : bond 0.00055 ( 1) link_BETA1-4 : bond 0.00405 ( 9) link_BETA1-4 : angle 1.91202 ( 27) link_NAG-ASN : bond 0.00540 ( 32) link_NAG-ASN : angle 2.47249 ( 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 190 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 135 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 ASP cc_start: 0.7594 (t0) cc_final: 0.7340 (t0) REVERT: A 797 PHE cc_start: 0.7721 (m-80) cc_final: 0.7479 (m-10) REVERT: A 900 MET cc_start: 0.8325 (mtm) cc_final: 0.8053 (mtp) REVERT: A 902 MET cc_start: 0.9060 (tpp) cc_final: 0.8789 (tpt) REVERT: A 959 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8723 (tt) REVERT: A 994 ASP cc_start: 0.7624 (t70) cc_final: 0.7300 (t0) REVERT: A 1005 GLN cc_start: 0.8782 (tp40) cc_final: 0.8488 (tp40) REVERT: B 104 TRP cc_start: 0.8356 (m-90) cc_final: 0.7992 (m-90) REVERT: B 392 PHE cc_start: 0.6965 (m-80) cc_final: 0.6437 (m-80) REVERT: B 740 MET cc_start: 0.8698 (tpp) cc_final: 0.8362 (tpt) REVERT: B 902 MET cc_start: 0.8937 (tpp) cc_final: 0.8616 (tpp) REVERT: B 1005 GLN cc_start: 0.8742 (tp40) cc_final: 0.8437 (tp40) REVERT: C 346 ARG cc_start: 0.8551 (ptm-80) cc_final: 0.8248 (ptm-80) REVERT: C 347 PHE cc_start: 0.6272 (m-10) cc_final: 0.5439 (m-10) REVERT: C 424 LYS cc_start: 0.8287 (tppp) cc_final: 0.7717 (ttmm) REVERT: C 515 PHE cc_start: 0.8492 (m-10) cc_final: 0.8196 (m-10) REVERT: C 902 MET cc_start: 0.8868 (tpp) cc_final: 0.8458 (tpt) outliers start: 55 outliers final: 33 residues processed: 184 average time/residue: 0.1439 time to fit residues: 43.8618 Evaluate side-chains 153 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL 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 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 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 918 GLU 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 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 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: 3.9990 chunk 110 optimal weight: 0.0040 chunk 198 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3813 r_free = 0.3813 target = 0.121606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.086860 restraints weight = 51408.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.089572 restraints weight = 27490.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.091319 restraints weight = 18584.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.092438 restraints weight = 14468.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.093147 restraints weight = 12323.367| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24633 Z= 0.134 Angle : 0.629 9.762 33607 Z= 0.318 Chirality : 0.046 0.373 3928 Planarity : 0.005 0.059 4270 Dihedral : 7.910 112.651 4065 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.58 % Favored : 89.35 % Rotamer: Outliers : 2.29 % Allowed : 14.23 % Favored : 83.49 % 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: -2.34 (0.15), residues: 2949 helix: 0.86 (0.22), residues: 601 sheet: -1.18 (0.21), residues: 603 loop : -2.73 (0.13), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1107 TYR 0.030 0.001 TYR C 423 PHE 0.019 0.001 PHE C 220 TRP 0.044 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00309 (24553) covalent geometry : angle 0.61042 (33408) SS BOND : bond 0.00401 ( 38) SS BOND : angle 1.58309 ( 76) hydrogen bonds : bond 0.04396 ( 689) hydrogen bonds : angle 5.24553 ( 1911) Misc. bond : bond 0.00043 ( 1) link_BETA1-4 : bond 0.00432 ( 9) link_BETA1-4 : angle 1.86658 ( 27) link_NAG-ASN : bond 0.00525 ( 32) link_NAG-ASN : angle 2.38838 ( 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 195 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7110 (m-80) cc_final: 0.6633 (m-80) REVERT: A 227 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7937 (t) REVERT: A 568 ASP cc_start: 0.7750 (t0) cc_final: 0.7384 (t0) REVERT: A 580 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: A 697 MET cc_start: 0.8888 (ptm) cc_final: 0.8680 (ptm) REVERT: A 797 PHE cc_start: 0.7678 (m-80) cc_final: 0.7460 (m-10) REVERT: A 900 MET cc_start: 0.8331 (mtm) cc_final: 0.7924 (mtp) REVERT: A 959 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8711 (tt) REVERT: A 994 ASP cc_start: 0.7569 (t70) cc_final: 0.7229 (t0) REVERT: A 1005 GLN cc_start: 0.8733 (tp40) cc_final: 0.8437 (tp40) REVERT: B 104 TRP cc_start: 0.8338 (m-90) cc_final: 0.7905 (m-90) REVERT: B 392 PHE cc_start: 0.6957 (m-80) cc_final: 0.6416 (m-80) REVERT: B 394 ASN cc_start: 0.6285 (t0) cc_final: 0.5975 (t0) REVERT: B 433 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8228 (p) REVERT: B 740 MET cc_start: 0.8642 (tpp) cc_final: 0.8347 (tpt) REVERT: B 1050 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7801 (mtm) REVERT: C 346 ARG cc_start: 0.8544 (ptm-80) cc_final: 0.8307 (ptm-80) REVERT: C 347 PHE cc_start: 0.6248 (m-10) cc_final: 0.5337 (m-10) REVERT: C 424 LYS cc_start: 0.8264 (tppp) cc_final: 0.7761 (ttmm) REVERT: C 515 PHE cc_start: 0.8505 (m-10) cc_final: 0.8209 (m-10) REVERT: C 902 MET cc_start: 0.8819 (tpp) cc_final: 0.8520 (tpt) REVERT: C 1050 MET cc_start: 0.7626 (mtp) cc_final: 0.7286 (mtp) outliers start: 60 outliers final: 40 residues processed: 188 average time/residue: 0.1403 time to fit residues: 43.9204 Evaluate side-chains 167 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 42 VAL Chi-restraints excluded: chain B residue 51 THR 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 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET 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 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 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: 1.9990 chunk 2 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 148 optimal weight: 0.3980 chunk 143 optimal weight: 7.9990 chunk 266 optimal weight: 0.0070 chunk 279 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3804 r_free = 0.3804 target = 0.120611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085906 restraints weight = 51807.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088629 restraints weight = 27497.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090358 restraints weight = 18496.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.091450 restraints weight = 14415.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092175 restraints weight = 12285.293| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24633 Z= 0.150 Angle : 0.632 9.370 33607 Z= 0.320 Chirality : 0.046 0.354 3928 Planarity : 0.005 0.058 4270 Dihedral : 7.599 111.123 4065 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.78 % Favored : 89.15 % Rotamer: Outliers : 2.29 % Allowed : 14.87 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.15), residues: 2949 helix: 0.79 (0.22), residues: 614 sheet: -1.26 (0.20), residues: 629 loop : -2.69 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.023 0.001 TYR C 423 PHE 0.018 0.001 PHE A1121 TRP 0.030 0.002 TRP A 64 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00349 (24553) covalent geometry : angle 0.61357 (33408) SS BOND : bond 0.00365 ( 38) SS BOND : angle 1.71080 ( 76) hydrogen bonds : bond 0.04434 ( 689) hydrogen bonds : angle 5.16611 ( 1911) Misc. bond : bond 0.00052 ( 1) link_BETA1-4 : bond 0.00427 ( 9) link_BETA1-4 : angle 1.88056 ( 27) link_NAG-ASN : bond 0.00508 ( 32) link_NAG-ASN : angle 2.37885 ( 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 191 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 131 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8284 (t) cc_final: 0.7984 (t) REVERT: A 580 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: A 697 MET cc_start: 0.8856 (ptm) cc_final: 0.8654 (ptm) REVERT: A 797 PHE cc_start: 0.7729 (m-80) cc_final: 0.7499 (m-10) REVERT: A 900 MET cc_start: 0.8304 (mtm) cc_final: 0.8010 (mtp) REVERT: A 959 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8705 (tt) REVERT: A 994 ASP cc_start: 0.7601 (t70) cc_final: 0.7253 (t0) REVERT: B 104 TRP cc_start: 0.8385 (m-90) cc_final: 0.7935 (m-90) REVERT: B 392 PHE cc_start: 0.6998 (m-80) cc_final: 0.6443 (m-80) REVERT: B 394 ASN cc_start: 0.6278 (t0) cc_final: 0.5997 (t0) REVERT: B 433 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 607 GLN cc_start: 0.7698 (mp10) cc_final: 0.7414 (mp10) REVERT: B 740 MET cc_start: 0.8674 (tpp) cc_final: 0.8369 (tpt) REVERT: B 1050 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7816 (mtm) REVERT: C 346 ARG cc_start: 0.8548 (ptm-80) cc_final: 0.8236 (ptm-80) REVERT: C 347 PHE cc_start: 0.6564 (m-10) cc_final: 0.5847 (m-10) REVERT: C 424 LYS cc_start: 0.8369 (tppp) cc_final: 0.7883 (ttmm) REVERT: C 515 PHE cc_start: 0.8530 (m-10) cc_final: 0.8214 (m-10) REVERT: C 740 MET cc_start: 0.8655 (mmm) cc_final: 0.8364 (tpp) REVERT: C 902 MET cc_start: 0.8836 (tpp) cc_final: 0.8498 (tpt) REVERT: C 1050 MET cc_start: 0.7630 (mtp) cc_final: 0.7275 (mtp) outliers start: 60 outliers final: 41 residues processed: 181 average time/residue: 0.1445 time to fit residues: 42.9220 Evaluate side-chains 167 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 42 VAL Chi-restraints excluded: chain B residue 51 THR 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 770 ILE Chi-restraints excluded: chain B residue 858 LEU 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 1050 MET 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 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 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 218 optimal weight: 4.9990 chunk 192 optimal weight: 0.0370 chunk 202 optimal weight: 0.0670 chunk 270 optimal weight: 0.8980 chunk 278 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.122462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.087643 restraints weight = 51652.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.090420 restraints weight = 27342.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.092204 restraints weight = 18337.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093320 restraints weight = 14215.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094053 restraints weight = 12089.986| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2816 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= 0.113 Angle : 0.605 9.253 33607 Z= 0.306 Chirality : 0.045 0.340 3928 Planarity : 0.004 0.058 4270 Dihedral : 7.260 110.035 4065 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.60 % Favored : 90.34 % Rotamer: Outliers : 2.14 % Allowed : 15.29 % Favored : 82.57 % 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: -2.14 (0.15), residues: 2949 helix: 1.06 (0.22), residues: 607 sheet: -1.16 (0.20), residues: 633 loop : -2.61 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.015 0.001 TYR B 904 PHE 0.013 0.001 PHE A 238 TRP 0.023 0.002 TRP A 64 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00256 (24553) covalent geometry : angle 0.58762 (33408) SS BOND : bond 0.00306 ( 38) SS BOND : angle 1.45574 ( 76) hydrogen bonds : bond 0.04035 ( 689) hydrogen bonds : angle 5.00669 ( 1911) Misc. bond : bond 0.00023 ( 1) link_BETA1-4 : bond 0.00463 ( 9) link_BETA1-4 : angle 1.81008 ( 27) link_NAG-ASN : bond 0.00522 ( 32) link_NAG-ASN : angle 2.29142 ( 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 199 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7960 (t) REVERT: A 580 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: A 797 PHE cc_start: 0.7640 (m-80) cc_final: 0.7427 (m-10) REVERT: A 900 MET cc_start: 0.8205 (mtm) cc_final: 0.7881 (mtp) REVERT: A 959 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8689 (tt) REVERT: A 1005 GLN cc_start: 0.8737 (tp40) cc_final: 0.8316 (mm-40) REVERT: B 104 TRP cc_start: 0.8330 (m-90) cc_final: 0.7829 (m-90) REVERT: B 349 SER cc_start: 0.3492 (OUTLIER) cc_final: 0.3231 (m) REVERT: B 392 PHE cc_start: 0.6960 (m-80) cc_final: 0.6424 (m-80) REVERT: B 394 ASN cc_start: 0.6119 (t0) cc_final: 0.5822 (t0) REVERT: B 433 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8103 (p) REVERT: B 740 MET cc_start: 0.8608 (tpp) cc_final: 0.8302 (tpt) REVERT: B 927 PHE cc_start: 0.8938 (t80) cc_final: 0.8620 (t80) REVERT: B 1050 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7707 (mtm) REVERT: C 346 ARG cc_start: 0.8539 (ptm-80) cc_final: 0.8234 (ptm-80) REVERT: C 347 PHE cc_start: 0.6516 (m-10) cc_final: 0.5852 (m-10) REVERT: C 424 LYS cc_start: 0.8422 (tppp) cc_final: 0.7964 (ttmm) REVERT: C 515 PHE cc_start: 0.8366 (m-10) cc_final: 0.8061 (m-10) REVERT: C 740 MET cc_start: 0.8476 (mmm) cc_final: 0.8262 (mmm) REVERT: C 902 MET cc_start: 0.8722 (tpp) cc_final: 0.8495 (tpt) REVERT: C 1050 MET cc_start: 0.7546 (mtp) cc_final: 0.7211 (mtp) REVERT: C 1127 ASP cc_start: 0.8125 (m-30) cc_final: 0.7792 (t0) outliers start: 56 outliers final: 41 residues processed: 190 average time/residue: 0.1405 time to fit residues: 44.4240 Evaluate side-chains 174 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 823 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 VAL 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 349 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 483 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 973 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET 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 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 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: 1.9990 chunk 73 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 286 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN B 856 ASN C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.121268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.086558 restraints weight = 51825.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.089254 restraints weight = 27543.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091014 restraints weight = 18629.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.092084 restraints weight = 14462.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092829 restraints weight = 12345.479| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2913 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= 0.140 Angle : 0.625 13.026 33607 Z= 0.315 Chirality : 0.046 0.330 3928 Planarity : 0.004 0.056 4270 Dihedral : 7.141 108.575 4065 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.38 % Favored : 89.56 % Rotamer: Outliers : 2.25 % Allowed : 16.13 % Favored : 81.62 % 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: -2.16 (0.15), residues: 2949 helix: 0.98 (0.22), residues: 615 sheet: -1.23 (0.20), residues: 648 loop : -2.58 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.018 0.001 TYR B 501 PHE 0.016 0.001 PHE A1121 TRP 0.021 0.002 TRP A 64 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00328 (24553) covalent geometry : angle 0.60666 (33408) SS BOND : bond 0.00463 ( 38) SS BOND : angle 1.70494 ( 76) hydrogen bonds : bond 0.04214 ( 689) hydrogen bonds : angle 5.02737 ( 1911) Misc. bond : bond 0.00044 ( 1) link_BETA1-4 : bond 0.00404 ( 9) link_BETA1-4 : angle 1.82403 ( 27) link_NAG-ASN : bond 0.00508 ( 32) link_NAG-ASN : angle 2.33590 ( 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 190 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 131 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.7990 (t) REVERT: A 568 ASP cc_start: 0.7609 (t0) cc_final: 0.7342 (t0) REVERT: A 580 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7056 (mp10) REVERT: A 797 PHE cc_start: 0.7715 (m-80) cc_final: 0.7510 (m-10) REVERT: A 900 MET cc_start: 0.8268 (mtm) cc_final: 0.8014 (mtp) REVERT: A 959 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 1005 GLN cc_start: 0.8765 (tp40) cc_final: 0.8337 (mm-40) REVERT: A 1029 MET cc_start: 0.9125 (tpp) cc_final: 0.8533 (ttm) REVERT: B 104 TRP cc_start: 0.8398 (m-90) cc_final: 0.7991 (m-90) REVERT: B 394 ASN cc_start: 0.6123 (t0) cc_final: 0.5840 (t0) REVERT: B 433 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8145 (p) REVERT: B 607 GLN cc_start: 0.7908 (mp10) cc_final: 0.7351 (mp10) REVERT: B 1050 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7786 (mtm) REVERT: C 346 ARG cc_start: 0.8534 (ptm-80) cc_final: 0.8223 (ptm-80) REVERT: C 347 PHE cc_start: 0.6523 (m-10) cc_final: 0.5885 (m-10) REVERT: C 424 LYS cc_start: 0.8475 (tppp) cc_final: 0.8068 (ttmm) REVERT: C 515 PHE cc_start: 0.8405 (m-10) cc_final: 0.8111 (m-10) REVERT: C 740 MET cc_start: 0.8345 (mmm) cc_final: 0.8065 (mmm) REVERT: C 1127 ASP cc_start: 0.8171 (m-30) cc_final: 0.7930 (t0) outliers start: 59 outliers final: 46 residues processed: 183 average time/residue: 0.1455 time to fit residues: 44.5232 Evaluate side-chains 176 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 752 LEU 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 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 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET 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 320 VAL 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 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: 0.7980 chunk 289 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 130 optimal weight: 0.6980 chunk 281 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 248 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 HIS ** 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 = 0.3827 r_free = 0.3827 target = 0.122307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087500 restraints weight = 51826.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.090269 restraints weight = 27466.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.092036 restraints weight = 18454.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093175 restraints weight = 14349.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093884 restraints weight = 12203.555| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3034 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= 0.118 Angle : 0.605 9.978 33607 Z= 0.305 Chirality : 0.045 0.322 3928 Planarity : 0.004 0.057 4270 Dihedral : 6.946 107.479 4065 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.77 % Favored : 90.17 % Rotamer: Outliers : 2.29 % Allowed : 16.21 % Favored : 81.50 % 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: 1.15 (0.22), residues: 609 sheet: -1.13 (0.20), residues: 660 loop : -2.58 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.017 0.001 TYR B 501 PHE 0.013 0.001 PHE A 238 TRP 0.020 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00272 (24553) covalent geometry : angle 0.58767 (33408) SS BOND : bond 0.00337 ( 38) SS BOND : angle 1.55739 ( 76) hydrogen bonds : bond 0.03986 ( 689) hydrogen bonds : angle 4.93280 ( 1911) Misc. bond : bond 0.00028 ( 1) link_BETA1-4 : bond 0.00450 ( 9) link_BETA1-4 : angle 1.79407 ( 27) link_NAG-ASN : bond 0.00508 ( 32) link_NAG-ASN : angle 2.28107 ( 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 195 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7885 (m-90) cc_final: 0.7065 (m-90) REVERT: A 227 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7967 (t) REVERT: A 568 ASP cc_start: 0.7681 (t0) cc_final: 0.7415 (t0) REVERT: A 580 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6943 (mp10) REVERT: A 797 PHE cc_start: 0.7674 (m-80) cc_final: 0.7464 (m-10) REVERT: A 900 MET cc_start: 0.8143 (mtm) cc_final: 0.7885 (mtp) REVERT: A 959 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8662 (tt) REVERT: A 1005 GLN cc_start: 0.8740 (tp40) cc_final: 0.8326 (mm-40) REVERT: A 1029 MET cc_start: 0.9053 (tpp) cc_final: 0.8519 (ttm) REVERT: B 104 TRP cc_start: 0.8376 (m-90) cc_final: 0.7933 (m-90) REVERT: B 392 PHE cc_start: 0.6789 (m-80) cc_final: 0.6385 (m-80) REVERT: B 394 ASN cc_start: 0.6103 (t0) cc_final: 0.5789 (t0) REVERT: B 433 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 927 PHE cc_start: 0.8954 (t80) cc_final: 0.8636 (t80) REVERT: B 1050 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7698 (mtm) REVERT: C 287 ASP cc_start: 0.8343 (t0) cc_final: 0.7754 (t0) REVERT: C 346 ARG cc_start: 0.8537 (ptm-80) cc_final: 0.8222 (ptm-80) REVERT: C 347 PHE cc_start: 0.6468 (m-10) cc_final: 0.5929 (m-10) REVERT: C 515 PHE cc_start: 0.8417 (m-10) cc_final: 0.8158 (m-10) REVERT: C 570 ASP cc_start: 0.8614 (m-30) cc_final: 0.7651 (p0) REVERT: C 740 MET cc_start: 0.8567 (mmm) cc_final: 0.8335 (mmm) outliers start: 60 outliers final: 50 residues processed: 185 average time/residue: 0.1446 time to fit residues: 43.9388 Evaluate side-chains 184 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 752 LEU 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 A residue 991 VAL 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 858 LEU 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 B residue 1050 MET 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 191 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 246 optimal weight: 0.6980 chunk 287 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 297 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 HIS ** 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 = 0.3808 r_free = 0.3808 target = 0.120973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.086307 restraints weight = 51939.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089027 restraints weight = 27597.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090758 restraints weight = 18550.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091898 restraints weight = 14428.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.092624 restraints weight = 12258.379| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24633 Z= 0.150 Angle : 0.629 10.217 33607 Z= 0.318 Chirality : 0.046 0.326 3928 Planarity : 0.004 0.060 4270 Dihedral : 6.927 106.260 4065 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.78 % Favored : 89.15 % 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: -2.09 (0.15), residues: 2949 helix: 1.05 (0.22), residues: 615 sheet: -1.16 (0.20), residues: 663 loop : -2.57 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.018 0.001 TYR B 501 PHE 0.019 0.001 PHE A1121 TRP 0.022 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00353 (24553) covalent geometry : angle 0.61180 (33408) SS BOND : bond 0.00344 ( 38) SS BOND : angle 1.60976 ( 76) hydrogen bonds : bond 0.04225 ( 689) hydrogen bonds : angle 5.00139 ( 1911) Misc. bond : bond 0.00044 ( 1) link_BETA1-4 : bond 0.00399 ( 9) link_BETA1-4 : angle 1.83822 ( 27) link_NAG-ASN : bond 0.00501 ( 32) link_NAG-ASN : angle 2.33720 ( 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 187 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7967 (m-90) cc_final: 0.7106 (m-90) REVERT: A 227 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.8001 (t) REVERT: A 568 ASP cc_start: 0.7733 (t0) cc_final: 0.7409 (t0) REVERT: A 580 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: A 873 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: A 900 MET cc_start: 0.8339 (mtm) cc_final: 0.8119 (mtp) REVERT: A 959 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8731 (tt) REVERT: A 1005 GLN cc_start: 0.8757 (tp40) cc_final: 0.8313 (mm-40) REVERT: A 1029 MET cc_start: 0.9099 (tpp) cc_final: 0.8588 (ttm) REVERT: B 104 TRP cc_start: 0.8406 (m-90) cc_final: 0.7969 (m-90) REVERT: B 392 PHE cc_start: 0.6817 (m-80) cc_final: 0.6399 (m-80) REVERT: B 394 ASN cc_start: 0.6251 (t0) cc_final: 0.6016 (t0) REVERT: B 433 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 1050 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7777 (mtm) REVERT: C 287 ASP cc_start: 0.8361 (t0) cc_final: 0.7798 (t0) REVERT: C 346 ARG cc_start: 0.8592 (ptm-80) cc_final: 0.8204 (ptm-80) REVERT: C 347 PHE cc_start: 0.6555 (m-10) cc_final: 0.5984 (m-10) REVERT: C 515 PHE cc_start: 0.8445 (m-10) cc_final: 0.8184 (m-10) REVERT: C 570 ASP cc_start: 0.8636 (m-30) cc_final: 0.7666 (p0) outliers start: 59 outliers final: 47 residues processed: 179 average time/residue: 0.1467 time to fit residues: 42.9307 Evaluate side-chains 180 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 752 LEU 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 959 LEU Chi-restraints excluded: chain A residue 991 VAL 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 B residue 1050 MET 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 320 VAL 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 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: 0.6980 chunk 297 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 268 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 228 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 HIS ** 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 = 0.3824 r_free = 0.3824 target = 0.121912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087344 restraints weight = 51668.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.090091 restraints weight = 27266.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091843 restraints weight = 18270.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.092990 restraints weight = 14149.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093626 restraints weight = 12018.258| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24633 Z= 0.118 Angle : 0.604 9.936 33607 Z= 0.304 Chirality : 0.045 0.320 3928 Planarity : 0.004 0.061 4270 Dihedral : 6.768 105.217 4065 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.26 % Favored : 90.67 % Rotamer: Outliers : 2.29 % Allowed : 16.67 % Favored : 81.05 % 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: -2.00 (0.15), residues: 2949 helix: 1.20 (0.22), residues: 609 sheet: -1.11 (0.20), residues: 652 loop : -2.52 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1019 TYR 0.017 0.001 TYR B 501 PHE 0.013 0.001 PHE A 238 TRP 0.020 0.002 TRP A 64 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00273 (24553) covalent geometry : angle 0.58638 (33408) SS BOND : bond 0.00369 ( 38) SS BOND : angle 1.54864 ( 76) hydrogen bonds : bond 0.03953 ( 689) hydrogen bonds : angle 4.92460 ( 1911) Misc. bond : bond 0.00023 ( 1) link_BETA1-4 : bond 0.00444 ( 9) link_BETA1-4 : angle 1.81808 ( 27) link_NAG-ASN : bond 0.00506 ( 32) link_NAG-ASN : angle 2.26950 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3700.96 seconds wall clock time: 64 minutes 41.96 seconds (3881.96 seconds total)