Starting phenix.real_space_refine on Sat Jun 21 16:13:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk2_32556/06_2025/7wk2_32556.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk2_32556/06_2025/7wk2_32556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wk2_32556/06_2025/7wk2_32556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk2_32556/06_2025/7wk2_32556.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk2_32556/06_2025/7wk2_32556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk2_32556/06_2025/7wk2_32556.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 114 5.16 5 C 15921 2.51 5 N 4146 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24879 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1001} Chain breaks: 7 Chain: "B" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1001} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1001} Chain breaks: 7 Time building chain proxies: 14.05, per 1000 atoms: 0.56 Number of scatterers: 24879 At special positions: 0 Unit cell: (148.648, 144.276, 178.159, 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 114 16.00 O 4698 8.00 N 4146 7.00 C 15921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.96 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.70 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.76 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=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.90 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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=2.04 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=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.35 Conformation dependent library (CDL) restraints added in 3.1 seconds 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5952 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 46 sheets defined 21.6% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.816A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.837A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.867A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.693A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.567A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.842A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.735A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.509A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 4.026A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.539A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.668A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.828A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.963A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 3.890A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.502A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 3.806A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.868A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.650A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.382A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.844A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.936A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.526A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 638' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.842A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 763 through 783 removed outlier: 3.669A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.738A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.609A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.821A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.644A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.514A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.827A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.524A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1031 removed outlier: 3.644A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B1012 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.878A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.602A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.509A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.302A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.961A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.535A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.581A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 824 removed outlier: 3.824A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.896A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 909 removed outlier: 3.789A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.631A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 919' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.753A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.917A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.671A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.665A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.883A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.287A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.516A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.872A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.880A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.580A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 359 removed outlier: 3.793A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.143A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.583A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.713A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.545A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.682A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 removed outlier: 4.185A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.370A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.558A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.673A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.690A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.747A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.519A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.501A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.960A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.879A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.501A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.534A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.201A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.843A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.590A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.506A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.580A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.580A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.474A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.037A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.531A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.953A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.788A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.750A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.978A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 716 hydrogen bonds defined for protein. 1941 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: 9.80 Time building geometry restraints manager: 6.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 4060 1.30 - 1.43: 6814 1.43 - 1.56: 14441 1.56 - 1.70: 2 1.70 - 1.83: 144 Bond restraints: 25461 Sorted by residual: bond pdb=" CA ASN A 317 " pdb=" C ASN A 317 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.21e-02 6.83e+03 5.12e+01 bond pdb=" C THR B 573 " pdb=" O THR B 573 " ideal model delta sigma weight residual 1.234 1.166 0.068 1.35e-02 5.49e+03 2.51e+01 bond pdb=" C LYS A 856 " pdb=" O LYS A 856 " ideal model delta sigma weight residual 1.234 1.162 0.072 1.44e-02 4.82e+03 2.49e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.34e-02 1.83e+03 2.40e+01 bond pdb=" C GLY A 857 " pdb=" O GLY A 857 " ideal model delta sigma weight residual 1.238 1.167 0.071 1.45e-02 4.76e+03 2.38e+01 ... (remaining 25456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 33901 2.46 - 4.92: 612 4.92 - 7.39: 86 7.39 - 9.85: 13 9.85 - 12.31: 8 Bond angle restraints: 34620 Sorted by residual: angle pdb=" N GLY A 857 " pdb=" CA GLY A 857 " pdb=" C GLY A 857 " ideal model delta sigma weight residual 115.21 102.90 12.31 1.30e+00 5.92e-01 8.97e+01 angle pdb=" N THR B 573 " pdb=" CA THR B 573 " pdb=" C THR B 573 " ideal model delta sigma weight residual 110.53 121.50 -10.97 1.29e+00 6.01e-01 7.23e+01 angle pdb=" C ASP B 568 " pdb=" N ILE B 569 " pdb=" CA ILE B 569 " ideal model delta sigma weight residual 120.42 129.38 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 angle pdb=" C ASN C 122 " pdb=" N ALA C 123 " pdb=" CA ALA C 123 " ideal model delta sigma weight residual 121.54 132.46 -10.92 1.91e+00 2.74e-01 3.27e+01 ... (remaining 34615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.07: 14918 22.07 - 44.15: 248 44.15 - 66.22: 29 66.22 - 88.30: 0 88.30 - 110.37: 3 Dihedral angle restraints: 15198 sinusoidal: 5958 harmonic: 9240 Sorted by residual: dihedral pdb=" CA PHE A 157 " pdb=" C PHE A 157 " pdb=" N ARG A 158 " pdb=" CA ARG A 158 " ideal model delta harmonic sigma weight residual 180.00 69.63 110.37 0 5.00e+00 4.00e-02 4.87e+02 dihedral pdb=" CA PHE B 157 " pdb=" C PHE B 157 " pdb=" N ARG B 158 " pdb=" CA ARG B 158 " ideal model delta harmonic sigma weight residual 180.00 71.18 108.82 0 5.00e+00 4.00e-02 4.74e+02 dihedral pdb=" CA PHE C 157 " pdb=" C PHE C 157 " pdb=" N ARG C 158 " pdb=" CA ARG C 158 " ideal model delta harmonic sigma weight residual 180.00 71.66 108.34 0 5.00e+00 4.00e-02 4.70e+02 ... (remaining 15195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3569 0.099 - 0.197: 323 0.197 - 0.296: 22 0.296 - 0.395: 0 0.395 - 0.493: 1 Chirality restraints: 3915 Sorted by residual: chirality pdb=" CA THR B 573 " pdb=" N THR B 573 " pdb=" C THR B 573 " pdb=" CB THR B 573 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE B 312 " pdb=" CA ILE B 312 " pdb=" CG1 ILE B 312 " pdb=" CG2 ILE B 312 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 3912 not shown) Planarity restraints: 4473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 854 " -0.025 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C LYS A 854 " 0.082 2.00e-02 2.50e+03 pdb=" O LYS A 854 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE A 855 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 317 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C ASN A 317 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN A 317 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE A 318 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 25 " 0.064 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO C 26 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.052 5.00e-02 4.00e+02 ... (remaining 4470 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 7 2.31 - 2.96: 10641 2.96 - 3.61: 30789 3.61 - 4.25: 54415 4.25 - 4.90: 87777 Nonbonded interactions: 183629 Sorted by model distance: nonbonded pdb=" CZ PHE B 759 " pdb=" CD1 PHE C 970 " model vdw 1.667 3.640 nonbonded pdb=" CZ PHE B 759 " pdb=" CE1 PHE C 970 " model vdw 1.862 3.640 nonbonded pdb=" O THR B 761 " pdb=" CG GLN B 762 " model vdw 1.864 3.440 nonbonded pdb=" CE1 PHE B 759 " pdb=" CE1 PHE C 970 " model vdw 2.040 3.640 nonbonded pdb=" N ASN A 317 " pdb=" OD1 ASN A 317 " model vdw 2.180 3.120 ... (remaining 183624 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 54.390 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 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 : 0.012 0.925 25501 Z= 0.591 Angle : 0.924 48.119 34698 Z= 0.524 Chirality : 0.055 0.493 3915 Planarity : 0.007 0.099 4473 Dihedral : 8.836 110.369 9129 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.93 % Rotamer: Outliers : 0.22 % Allowed : 0.65 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.12), residues: 3123 helix: -4.95 (0.06), residues: 540 sheet: -0.04 (0.18), residues: 531 loop : -1.76 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 633 HIS 0.016 0.002 HIS B 954 PHE 0.038 0.003 PHE A 855 TYR 0.020 0.002 TYR C 904 ARG 0.009 0.001 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.34110 ( 704) hydrogen bonds : angle 10.87116 ( 1941) SS BOND : bond 0.25708 ( 39) SS BOND : angle 8.32646 ( 78) covalent geometry : bond 0.00611 (25461) covalent geometry : angle 0.83659 (34620) Misc. bond : bond 0.10105 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 790 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6817 (mtt90) cc_final: 0.6493 (mpt180) REVERT: A 191 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 308 VAL cc_start: 0.7832 (t) cc_final: 0.7569 (p) REVERT: A 356 LYS cc_start: 0.7665 (tptt) cc_final: 0.7425 (ttmt) REVERT: A 399 SER cc_start: 0.7897 (t) cc_final: 0.6911 (m) REVERT: A 537 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7707 (mtpp) REVERT: A 595 VAL cc_start: 0.8145 (t) cc_final: 0.7870 (m) REVERT: A 736 VAL cc_start: 0.9048 (t) cc_final: 0.8821 (p) REVERT: A 776 LYS cc_start: 0.7785 (mttt) cc_final: 0.7451 (mttt) REVERT: A 875 SER cc_start: 0.8619 (p) cc_final: 0.8317 (m) REVERT: A 905 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6278 (mtt90) REVERT: A 969 LYS cc_start: 0.8462 (mttt) cc_final: 0.8135 (mttm) REVERT: A 986 PRO cc_start: 0.7590 (Cg_exo) cc_final: 0.7371 (Cg_endo) REVERT: A 988 GLU cc_start: 0.7922 (tp30) cc_final: 0.7132 (tp30) REVERT: A 1028 LYS cc_start: 0.8017 (mttt) cc_final: 0.7265 (mttm) REVERT: A 1040 VAL cc_start: 0.7300 (t) cc_final: 0.7024 (t) REVERT: A 1041 ASP cc_start: 0.7266 (m-30) cc_final: 0.7060 (m-30) REVERT: A 1075 PHE cc_start: 0.6539 (m-10) cc_final: 0.6263 (m-80) REVERT: B 30 ASN cc_start: 0.8058 (m-40) cc_final: 0.7827 (p0) REVERT: B 54 LEU cc_start: 0.8118 (mt) cc_final: 0.7858 (mt) REVERT: B 125 ASN cc_start: 0.7469 (m-40) cc_final: 0.7049 (t0) REVERT: B 129 LYS cc_start: 0.7531 (mttt) cc_final: 0.7299 (mtmt) REVERT: B 177 MET cc_start: 0.1028 (mtt) cc_final: 0.0741 (mtt) REVERT: B 351 TYR cc_start: 0.7184 (p90) cc_final: 0.6510 (p90) REVERT: B 584 ILE cc_start: 0.8116 (mt) cc_final: 0.7905 (tt) REVERT: B 734 THR cc_start: 0.8121 (p) cc_final: 0.7005 (m) REVERT: B 748 GLU cc_start: 0.7332 (tp30) cc_final: 0.7120 (tt0) REVERT: B 768 THR cc_start: 0.8334 (m) cc_final: 0.8044 (p) REVERT: B 797 PHE cc_start: 0.6301 (m-10) cc_final: 0.6076 (m-10) REVERT: B 952 VAL cc_start: 0.8222 (t) cc_final: 0.8005 (m) REVERT: B 979 ASP cc_start: 0.7615 (m-30) cc_final: 0.7331 (m-30) REVERT: B 981 PHE cc_start: 0.6672 (t80) cc_final: 0.6424 (t80) REVERT: B 1073 LYS cc_start: 0.8047 (tttt) cc_final: 0.7773 (mtpp) REVERT: B 1084 ASP cc_start: 0.6391 (p0) cc_final: 0.5250 (p0) REVERT: B 1122 VAL cc_start: 0.8343 (t) cc_final: 0.8100 (p) REVERT: C 195 LYS cc_start: 0.8581 (pttt) cc_final: 0.7926 (pttp) REVERT: C 300 LYS cc_start: 0.7596 (mttt) cc_final: 0.7257 (mttp) REVERT: C 309 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6745 (mt-10) REVERT: C 323 THR cc_start: 0.8240 (m) cc_final: 0.6801 (p) REVERT: C 358 ILE cc_start: 0.7548 (mt) cc_final: 0.7345 (mt) REVERT: C 386 LYS cc_start: 0.7888 (mttt) cc_final: 0.7334 (mttt) REVERT: C 390 LEU cc_start: 0.8290 (mt) cc_final: 0.7883 (mt) REVERT: C 559 PHE cc_start: 0.6161 (m-10) cc_final: 0.5777 (m-10) REVERT: C 595 VAL cc_start: 0.8305 (t) cc_final: 0.7981 (p) REVERT: C 739 THR cc_start: 0.7770 (m) cc_final: 0.7254 (m) REVERT: C 752 LEU cc_start: 0.8992 (mp) cc_final: 0.8790 (mt) REVERT: C 827 THR cc_start: 0.7626 (p) cc_final: 0.7246 (p) REVERT: C 867 ASP cc_start: 0.7376 (m-30) cc_final: 0.7142 (m-30) REVERT: C 868 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6523 (mm-30) REVERT: C 873 TYR cc_start: 0.8062 (m-80) cc_final: 0.7759 (m-10) REVERT: C 875 SER cc_start: 0.8787 (p) cc_final: 0.8497 (m) REVERT: C 884 SER cc_start: 0.7752 (m) cc_final: 0.7510 (t) REVERT: C 969 LYS cc_start: 0.8758 (mttt) cc_final: 0.8519 (mttt) REVERT: C 984 LEU cc_start: 0.7707 (mt) cc_final: 0.7438 (mp) REVERT: C 988 GLU cc_start: 0.7939 (tp30) cc_final: 0.7352 (tp30) REVERT: C 1028 LYS cc_start: 0.8030 (mttt) cc_final: 0.7329 (mttm) REVERT: C 1073 LYS cc_start: 0.7474 (tttt) cc_final: 0.7100 (tttt) REVERT: C 1075 PHE cc_start: 0.7375 (m-10) cc_final: 0.6978 (m-10) REVERT: C 1084 ASP cc_start: 0.6580 (p0) cc_final: 0.6345 (t70) REVERT: C 1116 THR cc_start: 0.7745 (p) cc_final: 0.7362 (m) outliers start: 6 outliers final: 2 residues processed: 796 average time/residue: 0.3849 time to fit residues: 470.0271 Evaluate side-chains 593 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 591 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.7980 chunk 238 optimal weight: 0.1980 chunk 132 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 246 optimal weight: 0.0070 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 0.3980 chunk 183 optimal weight: 0.9990 chunk 286 optimal weight: 0.8980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 239 GLN A 343 ASN A 422 ASN A 563 GLN A 717 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1054 GLN B 188 ASN B 331 ASN B 505 HIS B 717 ASN B 954 HIS B 965 GLN B1002 GLN B1054 GLN B1083 HIS B1119 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 409 GLN C 422 ASN C 519 HIS C 563 GLN C 717 ASN C 787 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.174146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.147748 restraints weight = 47297.940| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.27 r_work: 0.3915 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25501 Z= 0.144 Angle : 0.626 9.751 34698 Z= 0.331 Chirality : 0.046 0.265 3915 Planarity : 0.005 0.048 4473 Dihedral : 5.407 68.045 3405 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.57 % Favored : 98.40 % Rotamer: Outliers : 2.20 % Allowed : 8.35 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.12), residues: 3123 helix: -2.48 (0.16), residues: 552 sheet: 0.17 (0.18), residues: 618 loop : -1.42 (0.12), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1102 HIS 0.004 0.001 HIS B1064 PHE 0.027 0.002 PHE C 855 TYR 0.018 0.001 TYR B 265 ARG 0.009 0.001 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.05350 ( 704) hydrogen bonds : angle 6.04102 ( 1941) SS BOND : bond 0.00467 ( 39) SS BOND : angle 1.48627 ( 78) covalent geometry : bond 0.00318 (25461) covalent geometry : angle 0.62317 (34620) Misc. bond : bond 0.00707 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 629 time to evaluate : 2.799 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 190 ARG cc_start: 0.7662 (mtt90) cc_final: 0.7113 (mtt90) REVERT: A 269 TYR cc_start: 0.7887 (m-80) cc_final: 0.7313 (m-80) REVERT: A 298 GLU cc_start: 0.8368 (tp30) cc_final: 0.8060 (tp30) REVERT: A 308 VAL cc_start: 0.7980 (t) cc_final: 0.7729 (p) REVERT: A 356 LYS cc_start: 0.7692 (tptt) cc_final: 0.7448 (tptm) REVERT: A 537 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7914 (mtpp) REVERT: A 780 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 950 ASP cc_start: 0.8062 (m-30) cc_final: 0.7729 (m-30) REVERT: A 969 LYS cc_start: 0.8963 (mttt) cc_final: 0.8641 (mttm) REVERT: A 987 PRO cc_start: 0.8952 (Cg_exo) cc_final: 0.8743 (Cg_endo) REVERT: A 988 GLU cc_start: 0.7967 (tp30) cc_final: 0.7151 (tp30) REVERT: A 1002 GLN cc_start: 0.8228 (tp40) cc_final: 0.7727 (tp40) REVERT: A 1019 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7477 (tpt170) REVERT: B 52 GLN cc_start: 0.8278 (tt0) cc_final: 0.7875 (tt0) REVERT: B 177 MET cc_start: 0.0912 (mtt) cc_final: 0.0527 (mtt) REVERT: B 338 PHE cc_start: 0.6540 (m-80) cc_final: 0.6320 (m-80) REVERT: B 351 TYR cc_start: 0.7337 (p90) cc_final: 0.6809 (p90) REVERT: B 576 VAL cc_start: 0.8218 (m) cc_final: 0.7857 (t) REVERT: B 586 ASP cc_start: 0.7556 (m-30) cc_final: 0.7353 (m-30) REVERT: B 773 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7375 (tt0) REVERT: B 817 PHE cc_start: 0.8335 (t80) cc_final: 0.7889 (t80) REVERT: B 868 GLU cc_start: 0.6858 (tp30) cc_final: 0.6600 (tp30) REVERT: B 952 VAL cc_start: 0.8399 (t) cc_final: 0.8193 (m) REVERT: B 1002 GLN cc_start: 0.8146 (mm110) cc_final: 0.7503 (mm-40) REVERT: C 97 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7085 (mmtm) REVERT: C 190 ARG cc_start: 0.7583 (mtm180) cc_final: 0.7359 (mtt180) REVERT: C 354 ASN cc_start: 0.7204 (p0) cc_final: 0.6989 (t0) REVERT: C 390 LEU cc_start: 0.8767 (mt) cc_final: 0.8425 (mt) REVERT: C 421 TYR cc_start: 0.7568 (m-80) cc_final: 0.7110 (m-80) REVERT: C 494 SER cc_start: 0.8561 (p) cc_final: 0.8286 (t) REVERT: C 559 PHE cc_start: 0.7292 (m-10) cc_final: 0.7037 (m-80) REVERT: C 581 THR cc_start: 0.7957 (p) cc_final: 0.5951 (m) REVERT: C 595 VAL cc_start: 0.8708 (t) cc_final: 0.8380 (p) REVERT: C 658 ASN cc_start: 0.8335 (p0) cc_final: 0.8065 (p0) REVERT: C 690 GLN cc_start: 0.7796 (mp10) cc_final: 0.7503 (mp10) REVERT: C 780 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7492 (mt-10) REVERT: C 814 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8036 (mmmt) REVERT: C 819 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7118 (mt-10) REVERT: C 868 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7097 (mm-30) REVERT: C 882 ILE cc_start: 0.8481 (mt) cc_final: 0.8158 (mt) REVERT: C 969 LYS cc_start: 0.8838 (mttt) cc_final: 0.8531 (mtmm) REVERT: C 988 GLU cc_start: 0.8231 (tp30) cc_final: 0.7437 (tp30) REVERT: C 1031 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8019 (mt-10) REVERT: C 1073 LYS cc_start: 0.8311 (tttt) cc_final: 0.7834 (mtpp) REVERT: C 1084 ASP cc_start: 0.6636 (p0) cc_final: 0.6379 (t70) outliers start: 61 outliers final: 26 residues processed: 653 average time/residue: 0.3593 time to fit residues: 367.9360 Evaluate side-chains 573 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 546 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 272 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 259 optimal weight: 0.0470 chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 109 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 949 GLN A 955 ASN A1119 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN B1119 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.160249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.132422 restraints weight = 45788.714| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.16 r_work: 0.3717 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 25501 Z= 0.200 Angle : 0.651 9.412 34698 Z= 0.341 Chirality : 0.048 0.267 3915 Planarity : 0.005 0.057 4473 Dihedral : 5.115 54.239 3403 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 2.30 % Allowed : 11.41 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 3123 helix: -0.82 (0.20), residues: 603 sheet: 0.46 (0.19), residues: 636 loop : -1.17 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 64 HIS 0.009 0.002 HIS A 207 PHE 0.030 0.002 PHE C 855 TYR 0.026 0.002 TYR B 365 ARG 0.011 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 704) hydrogen bonds : angle 5.34543 ( 1941) SS BOND : bond 0.00601 ( 39) SS BOND : angle 1.98609 ( 78) covalent geometry : bond 0.00461 (25461) covalent geometry : angle 0.64462 (34620) Misc. bond : bond 0.00481 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 601 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7862 (mtp-110) REVERT: A 269 TYR cc_start: 0.8058 (m-80) cc_final: 0.7252 (m-80) REVERT: A 308 VAL cc_start: 0.8336 (t) cc_final: 0.8046 (p) REVERT: A 356 LYS cc_start: 0.7591 (tptt) cc_final: 0.7320 (tptm) REVERT: A 410 ILE cc_start: 0.7013 (mm) cc_final: 0.6714 (tp) REVERT: A 532 ASN cc_start: 0.8319 (t0) cc_final: 0.8097 (t0) REVERT: A 537 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8280 (ttmm) REVERT: A 539 VAL cc_start: 0.8351 (m) cc_final: 0.7662 (p) REVERT: A 541 PHE cc_start: 0.5127 (m-80) cc_final: 0.4540 (m-10) REVERT: A 552 LEU cc_start: 0.7989 (mt) cc_final: 0.7680 (mm) REVERT: A 712 ILE cc_start: 0.8045 (tp) cc_final: 0.7833 (tp) REVERT: A 748 GLU cc_start: 0.7670 (pt0) cc_final: 0.7434 (pt0) REVERT: A 797 PHE cc_start: 0.8176 (m-10) cc_final: 0.7963 (m-80) REVERT: A 800 PHE cc_start: 0.5753 (m-10) cc_final: 0.5390 (m-10) REVERT: A 814 LYS cc_start: 0.8365 (mmmt) cc_final: 0.7931 (mmmt) REVERT: A 988 GLU cc_start: 0.7949 (tp30) cc_final: 0.7314 (tp30) REVERT: A 1002 GLN cc_start: 0.8259 (tp40) cc_final: 0.8037 (tp40) REVERT: A 1019 ARG cc_start: 0.7900 (tpt170) cc_final: 0.7506 (tpt170) REVERT: A 1144 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7978 (mm-30) REVERT: B 99 ASN cc_start: 0.8778 (p0) cc_final: 0.8565 (p0) REVERT: B 177 MET cc_start: 0.0861 (mtt) cc_final: 0.0598 (mtt) REVERT: B 281 GLU cc_start: 0.7512 (pp20) cc_final: 0.7082 (pp20) REVERT: B 338 PHE cc_start: 0.6262 (m-80) cc_final: 0.6010 (m-80) REVERT: B 346 ARG cc_start: 0.7106 (mmt-90) cc_final: 0.6885 (mmt-90) REVERT: B 351 TYR cc_start: 0.7528 (p90) cc_final: 0.6837 (p90) REVERT: B 489 TYR cc_start: 0.6911 (m-80) cc_final: 0.6309 (m-10) REVERT: B 586 ASP cc_start: 0.7678 (m-30) cc_final: 0.7387 (m-30) REVERT: B 595 VAL cc_start: 0.8290 (t) cc_final: 0.7973 (p) REVERT: B 751 ASN cc_start: 0.7978 (m-40) cc_final: 0.7717 (m-40) REVERT: B 773 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7715 (tt0) REVERT: B 796 TYR cc_start: 0.8272 (t80) cc_final: 0.8018 (t80) REVERT: B 797 PHE cc_start: 0.8061 (m-10) cc_final: 0.7603 (m-10) REVERT: B 894 LEU cc_start: 0.8280 (mt) cc_final: 0.8079 (mp) REVERT: B 988 GLU cc_start: 0.7871 (tp30) cc_final: 0.7481 (tp30) REVERT: B 990 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7380 (mm-30) REVERT: C 97 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7217 (mptt) REVERT: C 190 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7552 (mtt180) REVERT: C 191 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 231 ILE cc_start: 0.8525 (mm) cc_final: 0.8225 (mm) REVERT: C 356 LYS cc_start: 0.7874 (tppt) cc_final: 0.7517 (tppt) REVERT: C 390 LEU cc_start: 0.8863 (mt) cc_final: 0.8620 (mt) REVERT: C 508 TYR cc_start: 0.5055 (m-80) cc_final: 0.4803 (m-80) REVERT: C 539 VAL cc_start: 0.8578 (p) cc_final: 0.8324 (m) REVERT: C 658 ASN cc_start: 0.8328 (p0) cc_final: 0.8087 (p0) REVERT: C 691 SER cc_start: 0.8343 (p) cc_final: 0.8133 (m) REVERT: C 780 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7737 (mt-10) REVERT: C 814 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8123 (mmmt) REVERT: C 819 GLU cc_start: 0.7885 (mt-10) cc_final: 0.6919 (tt0) REVERT: C 859 THR cc_start: 0.8550 (t) cc_final: 0.8291 (p) REVERT: C 868 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7438 (mm-30) REVERT: C 872 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: C 933 LYS cc_start: 0.8237 (mttt) cc_final: 0.7933 (mttm) REVERT: C 969 LYS cc_start: 0.8997 (mttt) cc_final: 0.8613 (mtpp) REVERT: C 988 GLU cc_start: 0.8052 (tp30) cc_final: 0.7260 (tp30) REVERT: C 1002 GLN cc_start: 0.8131 (tp40) cc_final: 0.7859 (tp40) REVERT: C 1031 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7431 (mt-10) REVERT: C 1145 LEU cc_start: 0.6372 (mt) cc_final: 0.6110 (tt) outliers start: 64 outliers final: 32 residues processed: 624 average time/residue: 0.3711 time to fit residues: 357.7742 Evaluate side-chains 584 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 551 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 25 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 224 optimal weight: 5.9990 chunk 271 optimal weight: 0.7980 chunk 259 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 703 ASN A 949 GLN A 955 ASN A1054 GLN B 207 HIS B 422 ASN B 613 GLN B 872 GLN B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 563 GLN C 580 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.152753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.124317 restraints weight = 45739.009| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.18 r_work: 0.3600 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25501 Z= 0.208 Angle : 0.635 11.666 34698 Z= 0.332 Chirality : 0.047 0.267 3915 Planarity : 0.004 0.064 4473 Dihedral : 5.010 38.925 3402 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.99 % Allowed : 12.92 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3123 helix: -0.16 (0.21), residues: 615 sheet: 0.54 (0.19), residues: 633 loop : -1.13 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 64 HIS 0.047 0.002 HIS A 207 PHE 0.028 0.002 PHE C 855 TYR 0.022 0.002 TYR C 873 ARG 0.010 0.001 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 704) hydrogen bonds : angle 5.13163 ( 1941) SS BOND : bond 0.00385 ( 39) SS BOND : angle 1.94176 ( 78) covalent geometry : bond 0.00481 (25461) covalent geometry : angle 0.62945 (34620) Misc. bond : bond 0.00221 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 592 time to evaluate : 2.926 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 51 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8530 (p) REVERT: A 269 TYR cc_start: 0.8023 (m-80) cc_final: 0.7151 (m-80) REVERT: A 303 LEU cc_start: 0.8963 (mt) cc_final: 0.8752 (mp) REVERT: A 537 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8372 (ttmm) REVERT: A 541 PHE cc_start: 0.5289 (m-80) cc_final: 0.4721 (m-10) REVERT: A 574 ASP cc_start: 0.7546 (m-30) cc_final: 0.7304 (m-30) REVERT: A 588 THR cc_start: 0.7654 (m) cc_final: 0.7349 (t) REVERT: A 604 THR cc_start: 0.8610 (m) cc_final: 0.8365 (t) REVERT: A 814 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8167 (mmmt) REVERT: A 988 GLU cc_start: 0.7865 (tp30) cc_final: 0.7211 (tp30) REVERT: A 1019 ARG cc_start: 0.7901 (tpt170) cc_final: 0.7545 (tpp-160) REVERT: B 129 LYS cc_start: 0.7937 (mttt) cc_final: 0.7734 (mttt) REVERT: B 177 MET cc_start: 0.1034 (mtt) cc_final: 0.0675 (mtt) REVERT: B 238 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7984 (p90) REVERT: B 239 GLN cc_start: 0.7386 (tp40) cc_final: 0.6962 (tp40) REVERT: B 338 PHE cc_start: 0.6570 (m-80) cc_final: 0.6212 (m-80) REVERT: B 351 TYR cc_start: 0.7755 (p90) cc_final: 0.7078 (p90) REVERT: B 586 ASP cc_start: 0.7633 (m-30) cc_final: 0.7314 (m-30) REVERT: B 613 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8491 (tp40) REVERT: B 642 VAL cc_start: 0.9338 (OUTLIER) cc_final: 0.8991 (t) REVERT: B 751 ASN cc_start: 0.8192 (m-40) cc_final: 0.7934 (m-40) REVERT: B 756 TYR cc_start: 0.6085 (t80) cc_final: 0.5848 (t80) REVERT: B 773 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7760 (tt0) REVERT: B 929 SER cc_start: 0.8668 (m) cc_final: 0.8429 (m) REVERT: B 981 PHE cc_start: 0.7490 (t80) cc_final: 0.7282 (t80) REVERT: B 988 GLU cc_start: 0.8052 (tp30) cc_final: 0.7581 (tp30) REVERT: B 1107 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7412 (mmm160) REVERT: C 231 ILE cc_start: 0.8685 (mm) cc_final: 0.8418 (mm) REVERT: C 298 GLU cc_start: 0.8749 (tp30) cc_final: 0.7936 (tm-30) REVERT: C 340 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7866 (mp0) REVERT: C 349 SER cc_start: 0.7774 (m) cc_final: 0.7361 (p) REVERT: C 572 THR cc_start: 0.8168 (p) cc_final: 0.7731 (p) REVERT: C 655 TYR cc_start: 0.8539 (t80) cc_final: 0.8165 (t80) REVERT: C 691 SER cc_start: 0.8471 (p) cc_final: 0.8207 (m) REVERT: C 698 SER cc_start: 0.8744 (t) cc_final: 0.8470 (p) REVERT: C 773 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7213 (mm-30) REVERT: C 776 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7434 (ttpp) REVERT: C 780 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7681 (mt-10) REVERT: C 811 LYS cc_start: 0.6804 (tptp) cc_final: 0.6284 (tptt) REVERT: C 814 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8095 (mmmt) REVERT: C 859 THR cc_start: 0.8547 (t) cc_final: 0.8339 (p) REVERT: C 933 LYS cc_start: 0.8263 (mttt) cc_final: 0.7939 (mttm) REVERT: C 950 ASP cc_start: 0.8183 (m-30) cc_final: 0.7754 (m-30) REVERT: C 964 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8490 (mtpp) REVERT: C 969 LYS cc_start: 0.9201 (mttt) cc_final: 0.8807 (mtpp) REVERT: C 988 GLU cc_start: 0.8013 (tp30) cc_final: 0.7420 (tp30) REVERT: C 1005 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8118 (tp40) REVERT: C 1019 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7200 (tpp80) REVERT: C 1031 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7875 (mt-10) outliers start: 83 outliers final: 55 residues processed: 625 average time/residue: 0.4056 time to fit residues: 388.4108 Evaluate side-chains 587 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 528 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 161 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 64 optimal weight: 0.0670 chunk 200 optimal weight: 0.0070 chunk 249 optimal weight: 0.3980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.153104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.125102 restraints weight = 45878.130| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.13 r_work: 0.3608 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25501 Z= 0.140 Angle : 0.581 10.182 34698 Z= 0.302 Chirality : 0.045 0.225 3915 Planarity : 0.004 0.055 4473 Dihedral : 4.799 33.448 3402 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.88 % Allowed : 13.86 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3123 helix: 0.37 (0.21), residues: 615 sheet: 0.75 (0.19), residues: 618 loop : -1.08 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.004 0.001 HIS A1064 PHE 0.033 0.002 PHE C 201 TYR 0.019 0.001 TYR C 904 ARG 0.009 0.001 ARG C 983 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 704) hydrogen bonds : angle 5.02542 ( 1941) SS BOND : bond 0.00311 ( 39) SS BOND : angle 2.14433 ( 78) covalent geometry : bond 0.00324 (25461) covalent geometry : angle 0.57244 (34620) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 552 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7592 (t) cc_final: 0.7343 (t) REVERT: A 269 TYR cc_start: 0.7962 (m-80) cc_final: 0.7205 (m-80) REVERT: A 281 GLU cc_start: 0.7670 (pp20) cc_final: 0.7352 (pp20) REVERT: A 355 ARG cc_start: 0.6608 (ttm110) cc_final: 0.6015 (ttm-80) REVERT: A 511 VAL cc_start: 0.7573 (p) cc_final: 0.7083 (m) REVERT: A 574 ASP cc_start: 0.7598 (m-30) cc_final: 0.7367 (m-30) REVERT: A 604 THR cc_start: 0.8577 (m) cc_final: 0.8348 (t) REVERT: A 814 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8113 (mmmt) REVERT: A 988 GLU cc_start: 0.7770 (tp30) cc_final: 0.7153 (tp30) REVERT: A 1019 ARG cc_start: 0.7928 (tpt170) cc_final: 0.7597 (tpp-160) REVERT: B 131 CYS cc_start: 0.5161 (t) cc_final: 0.4755 (t) REVERT: B 177 MET cc_start: 0.1012 (mtt) cc_final: 0.0662 (mtt) REVERT: B 239 GLN cc_start: 0.7350 (tp40) cc_final: 0.6981 (tp40) REVERT: B 281 GLU cc_start: 0.7052 (pp20) cc_final: 0.6837 (pp20) REVERT: B 298 GLU cc_start: 0.8510 (tp30) cc_final: 0.8205 (tp30) REVERT: B 303 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8694 (tt) REVERT: B 338 PHE cc_start: 0.6599 (m-80) cc_final: 0.6273 (m-80) REVERT: B 351 TYR cc_start: 0.7723 (p90) cc_final: 0.6954 (p90) REVERT: B 586 ASP cc_start: 0.7654 (m-30) cc_final: 0.7333 (m-30) REVERT: B 641 ASN cc_start: 0.7090 (m-40) cc_final: 0.6657 (p0) REVERT: B 751 ASN cc_start: 0.8247 (m-40) cc_final: 0.8032 (m-40) REVERT: B 752 LEU cc_start: 0.8445 (tt) cc_final: 0.8245 (tt) REVERT: B 773 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7704 (tt0) REVERT: B 902 MET cc_start: 0.8506 (mmt) cc_final: 0.7981 (mmm) REVERT: B 929 SER cc_start: 0.8693 (m) cc_final: 0.8456 (m) REVERT: B 981 PHE cc_start: 0.7384 (t80) cc_final: 0.7182 (t80) REVERT: B 988 GLU cc_start: 0.7981 (tp30) cc_final: 0.7538 (tp30) REVERT: C 191 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7724 (mt-10) REVERT: C 231 ILE cc_start: 0.8608 (mm) cc_final: 0.8354 (mm) REVERT: C 281 GLU cc_start: 0.6595 (pp20) cc_final: 0.6319 (pp20) REVERT: C 298 GLU cc_start: 0.8660 (tp30) cc_final: 0.8458 (tp30) REVERT: C 340 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8045 (mm-30) REVERT: C 349 SER cc_start: 0.7821 (m) cc_final: 0.7409 (p) REVERT: C 568 ASP cc_start: 0.7986 (p0) cc_final: 0.7709 (p0) REVERT: C 572 THR cc_start: 0.7942 (p) cc_final: 0.7527 (p) REVERT: C 691 SER cc_start: 0.8518 (p) cc_final: 0.8264 (m) REVERT: C 698 SER cc_start: 0.8649 (t) cc_final: 0.8399 (p) REVERT: C 776 LYS cc_start: 0.8347 (ttpp) cc_final: 0.7446 (ttpp) REVERT: C 780 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7634 (mt-10) REVERT: C 811 LYS cc_start: 0.6782 (tptp) cc_final: 0.6177 (tptt) REVERT: C 814 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8114 (mmmt) REVERT: C 819 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 859 THR cc_start: 0.8574 (t) cc_final: 0.8368 (p) REVERT: C 900 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7981 (mtm) REVERT: C 933 LYS cc_start: 0.8310 (mttt) cc_final: 0.7988 (mttm) REVERT: C 950 ASP cc_start: 0.8162 (m-30) cc_final: 0.7714 (m-30) REVERT: C 969 LYS cc_start: 0.9228 (mttt) cc_final: 0.8955 (mtpp) REVERT: C 988 GLU cc_start: 0.7887 (tp30) cc_final: 0.7327 (tp30) REVERT: C 993 ILE cc_start: 0.8168 (tt) cc_final: 0.7967 (mt) REVERT: C 1005 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8135 (tp40) outliers start: 80 outliers final: 57 residues processed: 586 average time/residue: 0.3914 time to fit residues: 352.3604 Evaluate side-chains 591 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 532 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 46 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 211 optimal weight: 0.0470 chunk 245 optimal weight: 0.7980 chunk 237 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 703 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 762 GLN B 949 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 580 GLN C 901 GLN C1135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.151649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123671 restraints weight = 45675.190| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.12 r_work: 0.3586 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25501 Z= 0.143 Angle : 0.574 12.933 34698 Z= 0.298 Chirality : 0.045 0.233 3915 Planarity : 0.004 0.051 4473 Dihedral : 4.680 28.546 3402 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.06 % Allowed : 14.11 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3123 helix: 0.79 (0.22), residues: 615 sheet: 0.66 (0.19), residues: 639 loop : -1.03 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.005 0.001 HIS A1064 PHE 0.036 0.002 PHE C 855 TYR 0.021 0.001 TYR B 707 ARG 0.008 0.001 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 704) hydrogen bonds : angle 4.90314 ( 1941) SS BOND : bond 0.00581 ( 39) SS BOND : angle 1.72124 ( 78) covalent geometry : bond 0.00329 (25461) covalent geometry : angle 0.56908 (34620) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 562 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7660 (OUTLIER) cc_final: 0.7400 (t) REVERT: A 190 ARG cc_start: 0.8121 (mtt90) cc_final: 0.7458 (mpt180) REVERT: A 269 TYR cc_start: 0.7985 (m-80) cc_final: 0.7295 (m-80) REVERT: A 355 ARG cc_start: 0.6740 (ttm110) cc_final: 0.6078 (ttm170) REVERT: A 537 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8234 (mtpp) REVERT: A 574 ASP cc_start: 0.7620 (m-30) cc_final: 0.7349 (m-30) REVERT: A 604 THR cc_start: 0.8512 (m) cc_final: 0.8297 (t) REVERT: A 697 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8327 (ptm) REVERT: A 814 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8113 (mmmt) REVERT: A 933 LYS cc_start: 0.8261 (mttt) cc_final: 0.7955 (mttm) REVERT: A 950 ASP cc_start: 0.8059 (m-30) cc_final: 0.7783 (m-30) REVERT: A 988 GLU cc_start: 0.7696 (tp30) cc_final: 0.7068 (tp30) REVERT: A 1019 ARG cc_start: 0.7987 (tpt170) cc_final: 0.7711 (tpp-160) REVERT: B 81 ASN cc_start: 0.7148 (m110) cc_final: 0.6853 (m-40) REVERT: B 177 MET cc_start: 0.0955 (mtt) cc_final: 0.0621 (mtt) REVERT: B 239 GLN cc_start: 0.7343 (tp40) cc_final: 0.6990 (tp40) REVERT: B 298 GLU cc_start: 0.8400 (tp30) cc_final: 0.8075 (tp30) REVERT: B 338 PHE cc_start: 0.6627 (m-80) cc_final: 0.6326 (m-80) REVERT: B 351 TYR cc_start: 0.7635 (p90) cc_final: 0.6764 (p90) REVERT: B 559 PHE cc_start: 0.6495 (m-10) cc_final: 0.6175 (m-10) REVERT: B 586 ASP cc_start: 0.7572 (m-30) cc_final: 0.7253 (m-30) REVERT: B 595 VAL cc_start: 0.8510 (t) cc_final: 0.8283 (p) REVERT: B 641 ASN cc_start: 0.7082 (m-40) cc_final: 0.6778 (p0) REVERT: B 642 VAL cc_start: 0.9333 (OUTLIER) cc_final: 0.9046 (t) REVERT: B 751 ASN cc_start: 0.8317 (m-40) cc_final: 0.8082 (m-40) REVERT: B 752 LEU cc_start: 0.8538 (tt) cc_final: 0.8332 (tt) REVERT: B 773 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7441 (tp30) REVERT: B 823 PHE cc_start: 0.8532 (t80) cc_final: 0.8146 (t80) REVERT: B 935 GLN cc_start: 0.7912 (tt0) cc_final: 0.7561 (tp40) REVERT: B 981 PHE cc_start: 0.7339 (t80) cc_final: 0.7113 (t80) REVERT: B 988 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: C 191 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7866 (mt-10) REVERT: C 231 ILE cc_start: 0.8632 (mm) cc_final: 0.8367 (mm) REVERT: C 281 GLU cc_start: 0.6533 (pp20) cc_final: 0.6310 (pp20) REVERT: C 298 GLU cc_start: 0.8572 (tp30) cc_final: 0.7456 (tp30) REVERT: C 340 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7993 (mm-30) REVERT: C 349 SER cc_start: 0.8019 (m) cc_final: 0.7615 (p) REVERT: C 451 TYR cc_start: 0.5791 (m-10) cc_final: 0.5566 (m-10) REVERT: C 568 ASP cc_start: 0.7975 (p0) cc_final: 0.7695 (p0) REVERT: C 572 THR cc_start: 0.7757 (p) cc_final: 0.7278 (p) REVERT: C 651 ILE cc_start: 0.8733 (pt) cc_final: 0.8505 (mt) REVERT: C 691 SER cc_start: 0.8576 (p) cc_final: 0.8305 (m) REVERT: C 698 SER cc_start: 0.8709 (t) cc_final: 0.8419 (p) REVERT: C 731 MET cc_start: 0.9010 (ptp) cc_final: 0.8777 (ptp) REVERT: C 748 GLU cc_start: 0.8044 (pt0) cc_final: 0.7462 (pt0) REVERT: C 750 SER cc_start: 0.9047 (m) cc_final: 0.8769 (m) REVERT: C 776 LYS cc_start: 0.8329 (ttpp) cc_final: 0.7425 (ttpp) REVERT: C 780 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 814 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8108 (mmmt) REVERT: C 819 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7739 (mt-10) REVERT: C 900 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8037 (mtm) REVERT: C 933 LYS cc_start: 0.8344 (mttt) cc_final: 0.8033 (mttm) REVERT: C 950 ASP cc_start: 0.8183 (m-30) cc_final: 0.7740 (m-30) REVERT: C 969 LYS cc_start: 0.9284 (mttt) cc_final: 0.9066 (mttp) REVERT: C 988 GLU cc_start: 0.7840 (tp30) cc_final: 0.7267 (tp30) REVERT: C 1005 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8050 (tp40) outliers start: 85 outliers final: 63 residues processed: 602 average time/residue: 0.3989 time to fit residues: 366.7459 Evaluate side-chains 600 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 532 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 244 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 245 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 6 optimal weight: 0.0170 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 133 optimal weight: 0.0370 chunk 64 optimal weight: 0.9980 chunk 217 optimal weight: 0.4980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 703 ASN A1002 GLN B 207 HIS B 613 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C1135 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.152131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.124240 restraints weight = 45690.532| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.11 r_work: 0.3595 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25501 Z= 0.114 Angle : 0.566 11.249 34698 Z= 0.291 Chirality : 0.044 0.220 3915 Planarity : 0.004 0.093 4473 Dihedral : 4.534 24.636 3402 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.56 % Allowed : 15.44 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3123 helix: 1.06 (0.22), residues: 615 sheet: 0.78 (0.19), residues: 648 loop : -1.02 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 436 HIS 0.024 0.001 HIS B 207 PHE 0.036 0.002 PHE C 855 TYR 0.024 0.001 TYR C 660 ARG 0.010 0.001 ARG C1019 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 704) hydrogen bonds : angle 4.83914 ( 1941) SS BOND : bond 0.00303 ( 39) SS BOND : angle 1.56001 ( 78) covalent geometry : bond 0.00261 (25461) covalent geometry : angle 0.56162 (34620) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 536 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7661 (OUTLIER) cc_final: 0.6921 (t) REVERT: A 190 ARG cc_start: 0.8110 (mtt90) cc_final: 0.7719 (mpt180) REVERT: A 237 ARG cc_start: 0.8084 (mtm180) cc_final: 0.7726 (mtp-110) REVERT: A 269 TYR cc_start: 0.7979 (m-80) cc_final: 0.7309 (m-80) REVERT: A 281 GLU cc_start: 0.7687 (pp20) cc_final: 0.7285 (pp20) REVERT: A 319 ARG cc_start: 0.7608 (mmt-90) cc_final: 0.7377 (tpp-160) REVERT: A 355 ARG cc_start: 0.6758 (ttm110) cc_final: 0.6005 (ttm-80) REVERT: A 421 TYR cc_start: 0.7515 (m-10) cc_final: 0.7132 (m-80) REVERT: A 537 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8223 (mtpp) REVERT: A 574 ASP cc_start: 0.7680 (m-30) cc_final: 0.7416 (m-30) REVERT: A 697 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8371 (ptm) REVERT: A 814 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8138 (mmmt) REVERT: A 933 LYS cc_start: 0.8242 (mttt) cc_final: 0.7940 (mtmm) REVERT: A 988 GLU cc_start: 0.7625 (tp30) cc_final: 0.7018 (tp30) REVERT: B 81 ASN cc_start: 0.7029 (m110) cc_final: 0.6796 (m-40) REVERT: B 177 MET cc_start: 0.0941 (mtt) cc_final: 0.0609 (mtt) REVERT: B 191 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7529 (mt-10) REVERT: B 206 LYS cc_start: 0.8517 (tttt) cc_final: 0.8217 (tttt) REVERT: B 239 GLN cc_start: 0.7293 (tp40) cc_final: 0.6930 (tp40) REVERT: B 298 GLU cc_start: 0.8350 (tp30) cc_final: 0.8115 (tp30) REVERT: B 338 PHE cc_start: 0.6681 (m-80) cc_final: 0.6392 (m-80) REVERT: B 351 TYR cc_start: 0.7634 (p90) cc_final: 0.6765 (p90) REVERT: B 586 ASP cc_start: 0.7567 (m-30) cc_final: 0.7228 (m-30) REVERT: B 595 VAL cc_start: 0.8478 (t) cc_final: 0.8238 (p) REVERT: B 613 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8649 (tp40) REVERT: B 641 ASN cc_start: 0.7043 (m-40) cc_final: 0.6784 (p0) REVERT: B 751 ASN cc_start: 0.8230 (m-40) cc_final: 0.7952 (m-40) REVERT: B 752 LEU cc_start: 0.8535 (tt) cc_final: 0.8103 (mp) REVERT: B 773 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7356 (tp30) REVERT: B 804 GLN cc_start: 0.8161 (mt0) cc_final: 0.7882 (mt0) REVERT: B 823 PHE cc_start: 0.8482 (t80) cc_final: 0.8086 (t80) REVERT: B 935 GLN cc_start: 0.7828 (tt0) cc_final: 0.7352 (tp40) REVERT: B 950 ASP cc_start: 0.7417 (t70) cc_final: 0.7206 (t70) REVERT: B 981 PHE cc_start: 0.7235 (t80) cc_final: 0.6981 (t80) REVERT: C 191 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7842 (mt-10) REVERT: C 231 ILE cc_start: 0.8561 (mm) cc_final: 0.8316 (mm) REVERT: C 281 GLU cc_start: 0.6548 (pp20) cc_final: 0.6332 (pp20) REVERT: C 298 GLU cc_start: 0.8518 (tp30) cc_final: 0.7413 (tp30) REVERT: C 349 SER cc_start: 0.7968 (m) cc_final: 0.7542 (p) REVERT: C 568 ASP cc_start: 0.7946 (p0) cc_final: 0.7400 (p0) REVERT: C 651 ILE cc_start: 0.8713 (pt) cc_final: 0.8498 (mt) REVERT: C 691 SER cc_start: 0.8554 (p) cc_final: 0.8294 (m) REVERT: C 698 SER cc_start: 0.8697 (t) cc_final: 0.8407 (p) REVERT: C 731 MET cc_start: 0.8984 (ptp) cc_final: 0.8757 (ptp) REVERT: C 776 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7412 (ttpp) REVERT: C 780 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 814 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8081 (mmmt) REVERT: C 819 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7600 (mt-10) REVERT: C 896 ILE cc_start: 0.8014 (tp) cc_final: 0.7763 (tt) REVERT: C 900 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8103 (mtm) REVERT: C 918 GLU cc_start: 0.8099 (mp0) cc_final: 0.7607 (mp0) REVERT: C 933 LYS cc_start: 0.8324 (mttt) cc_final: 0.8017 (mttm) REVERT: C 950 ASP cc_start: 0.8117 (m-30) cc_final: 0.7729 (m-30) REVERT: C 969 LYS cc_start: 0.9274 (mttt) cc_final: 0.9056 (mttp) REVERT: C 988 GLU cc_start: 0.7712 (tp30) cc_final: 0.7156 (tp30) REVERT: C 1005 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8050 (tp40) outliers start: 71 outliers final: 56 residues processed: 563 average time/residue: 0.3919 time to fit residues: 334.0186 Evaluate side-chains 574 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 514 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 272 optimal weight: 0.0970 chunk 314 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 703 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 207 HIS B 505 HIS B 519 HIS B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 751 ASN C 913 GLN C1135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.145125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117334 restraints weight = 45267.258| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.09 r_work: 0.3492 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.7729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25501 Z= 0.253 Angle : 0.683 11.475 34698 Z= 0.357 Chirality : 0.049 0.284 3915 Planarity : 0.004 0.075 4473 Dihedral : 4.931 23.955 3402 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.31 % Allowed : 14.97 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3123 helix: 0.87 (0.22), residues: 612 sheet: 0.58 (0.19), residues: 669 loop : -1.08 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 436 HIS 0.008 0.002 HIS A1064 PHE 0.054 0.003 PHE B 559 TYR 0.025 0.002 TYR B 904 ARG 0.011 0.001 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 704) hydrogen bonds : angle 5.09498 ( 1941) SS BOND : bond 0.00476 ( 39) SS BOND : angle 2.27041 ( 78) covalent geometry : bond 0.00594 (25461) covalent geometry : angle 0.67571 (34620) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 544 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7768 (mpt180) REVERT: A 239 GLN cc_start: 0.7796 (mt0) cc_final: 0.7530 (mt0) REVERT: A 269 TYR cc_start: 0.7790 (m-80) cc_final: 0.7334 (m-80) REVERT: A 309 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7812 (mm-30) REVERT: A 340 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7797 (tm-30) REVERT: A 355 ARG cc_start: 0.6851 (ttm110) cc_final: 0.6265 (ttm170) REVERT: A 398 ASP cc_start: 0.7464 (m-30) cc_final: 0.6675 (m-30) REVERT: A 421 TYR cc_start: 0.7643 (m-10) cc_final: 0.7211 (m-80) REVERT: A 573 THR cc_start: 0.8893 (m) cc_final: 0.8491 (p) REVERT: A 574 ASP cc_start: 0.7701 (m-30) cc_final: 0.7226 (t0) REVERT: A 576 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7878 (t) REVERT: A 776 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7885 (ttpp) REVERT: A 814 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8223 (mmmt) REVERT: A 884 SER cc_start: 0.8748 (t) cc_final: 0.8331 (p) REVERT: A 933 LYS cc_start: 0.8244 (mttt) cc_final: 0.8035 (mtmm) REVERT: A 950 ASP cc_start: 0.8093 (m-30) cc_final: 0.7803 (m-30) REVERT: A 988 GLU cc_start: 0.7742 (tp30) cc_final: 0.7105 (tp30) REVERT: A 1019 ARG cc_start: 0.7994 (tpt170) cc_final: 0.7667 (tpp-160) REVERT: A 1038 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8449 (mmtm) REVERT: A 1107 ARG cc_start: 0.8664 (ttm170) cc_final: 0.8404 (mtm-85) REVERT: A 1142 GLN cc_start: 0.8598 (pp30) cc_final: 0.8383 (pp30) REVERT: B 81 ASN cc_start: 0.7434 (m110) cc_final: 0.7226 (m-40) REVERT: B 113 LYS cc_start: 0.7884 (ptpt) cc_final: 0.7679 (pttt) REVERT: B 177 MET cc_start: 0.0988 (mtt) cc_final: 0.0644 (mtt) REVERT: B 206 LYS cc_start: 0.8553 (tttt) cc_final: 0.8136 (tttt) REVERT: B 238 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7932 (p90) REVERT: B 239 GLN cc_start: 0.7325 (tp40) cc_final: 0.7023 (tp40) REVERT: B 338 PHE cc_start: 0.6555 (m-80) cc_final: 0.6251 (m-80) REVERT: B 351 TYR cc_start: 0.7745 (p90) cc_final: 0.6813 (p90) REVERT: B 365 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6830 (t80) REVERT: B 495 TYR cc_start: 0.6348 (m-80) cc_final: 0.5537 (m-80) REVERT: B 586 ASP cc_start: 0.7643 (m-30) cc_final: 0.7290 (m-30) REVERT: B 613 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8716 (mm-40) REVERT: B 641 ASN cc_start: 0.7144 (m-40) cc_final: 0.6901 (p0) REVERT: B 642 VAL cc_start: 0.9398 (OUTLIER) cc_final: 0.9143 (t) REVERT: B 751 ASN cc_start: 0.8410 (m-40) cc_final: 0.8043 (m-40) REVERT: B 752 LEU cc_start: 0.8727 (tt) cc_final: 0.8332 (mp) REVERT: B 773 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7646 (tm-30) REVERT: B 804 GLN cc_start: 0.8287 (mt0) cc_final: 0.8083 (mt0) REVERT: B 935 GLN cc_start: 0.8042 (tt0) cc_final: 0.7638 (tp40) REVERT: B 969 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8805 (mtmt) REVERT: B 981 PHE cc_start: 0.7376 (t80) cc_final: 0.7133 (t80) REVERT: C 190 ARG cc_start: 0.8318 (mtm180) cc_final: 0.7782 (mtt-85) REVERT: C 191 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7966 (mt-10) REVERT: C 231 ILE cc_start: 0.8690 (mm) cc_final: 0.8466 (mm) REVERT: C 281 GLU cc_start: 0.6523 (pp20) cc_final: 0.6273 (pp20) REVERT: C 349 SER cc_start: 0.8339 (m) cc_final: 0.7947 (p) REVERT: C 436 TRP cc_start: 0.2952 (OUTLIER) cc_final: 0.2545 (t60) REVERT: C 454 ARG cc_start: 0.7675 (ptm160) cc_final: 0.7411 (ptm160) REVERT: C 691 SER cc_start: 0.8600 (p) cc_final: 0.8329 (m) REVERT: C 698 SER cc_start: 0.8871 (t) cc_final: 0.8582 (p) REVERT: C 750 SER cc_start: 0.9073 (m) cc_final: 0.8798 (m) REVERT: C 776 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7409 (ttpp) REVERT: C 780 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7734 (mt-10) REVERT: C 814 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8033 (mmmt) REVERT: C 900 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8110 (mtm) REVERT: C 933 LYS cc_start: 0.8430 (mttt) cc_final: 0.8129 (mttm) REVERT: C 950 ASP cc_start: 0.8214 (m-30) cc_final: 0.7796 (m-30) REVERT: C 969 LYS cc_start: 0.9272 (mttt) cc_final: 0.9002 (mtpp) REVERT: C 988 GLU cc_start: 0.7856 (tp30) cc_final: 0.7259 (tp30) REVERT: C 1005 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8152 (tp40) outliers start: 92 outliers final: 71 residues processed: 591 average time/residue: 0.4052 time to fit residues: 361.1190 Evaluate side-chains 594 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 516 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 161 optimal weight: 0.7980 chunk 218 optimal weight: 0.1980 chunk 214 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 304 optimal weight: 0.8980 chunk 310 optimal weight: 0.6980 chunk 296 optimal weight: 0.8980 chunk 213 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 chunk 110 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 207 HIS B 563 GLN B 613 GLN B 949 GLN B 955 ASN B1002 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C1135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.147175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.119124 restraints weight = 45288.534| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.11 r_work: 0.3525 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.7903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25501 Z= 0.135 Angle : 0.621 11.870 34698 Z= 0.320 Chirality : 0.046 0.259 3915 Planarity : 0.004 0.054 4473 Dihedral : 4.754 25.352 3402 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.48 % Allowed : 17.10 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3123 helix: 1.14 (0.22), residues: 612 sheet: 0.63 (0.19), residues: 669 loop : -1.07 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.010 0.001 HIS B 207 PHE 0.035 0.002 PHE C 855 TYR 0.016 0.001 TYR B 28 ARG 0.009 0.001 ARG C 493 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 704) hydrogen bonds : angle 4.99862 ( 1941) SS BOND : bond 0.00326 ( 39) SS BOND : angle 2.03100 ( 78) covalent geometry : bond 0.00310 (25461) covalent geometry : angle 0.61386 (34620) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 523 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7561 (p) cc_final: 0.7142 (p) REVERT: A 190 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7680 (mpt180) REVERT: A 235 ILE cc_start: 0.5628 (tt) cc_final: 0.5391 (tp) REVERT: A 269 TYR cc_start: 0.7899 (m-80) cc_final: 0.7310 (m-80) REVERT: A 281 GLU cc_start: 0.7804 (pp20) cc_final: 0.7362 (pp20) REVERT: A 309 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 346 ARG cc_start: 0.6612 (tpt170) cc_final: 0.6399 (tpm170) REVERT: A 355 ARG cc_start: 0.6747 (ttm110) cc_final: 0.6103 (ttm170) REVERT: A 398 ASP cc_start: 0.7394 (m-30) cc_final: 0.6487 (m-30) REVERT: A 421 TYR cc_start: 0.7596 (m-10) cc_final: 0.7215 (m-80) REVERT: A 552 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8407 (mt) REVERT: A 576 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7816 (t) REVERT: A 697 MET cc_start: 0.8744 (ttp) cc_final: 0.8343 (ptm) REVERT: A 804 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8287 (mm-40) REVERT: A 814 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8103 (mmmt) REVERT: A 884 SER cc_start: 0.8673 (t) cc_final: 0.8250 (p) REVERT: A 933 LYS cc_start: 0.8191 (mttt) cc_final: 0.7950 (mtmm) REVERT: A 988 GLU cc_start: 0.7651 (tp30) cc_final: 0.7014 (tp30) REVERT: A 1038 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8407 (mmtm) REVERT: A 1107 ARG cc_start: 0.8610 (ttm170) cc_final: 0.8335 (mtm-85) REVERT: A 1144 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7875 (mp0) REVERT: B 177 MET cc_start: 0.0984 (mtt) cc_final: 0.0649 (mtt) REVERT: B 206 LYS cc_start: 0.8592 (tttt) cc_final: 0.8371 (tttp) REVERT: B 239 GLN cc_start: 0.7284 (tp40) cc_final: 0.6821 (tp-100) REVERT: B 338 PHE cc_start: 0.6689 (m-80) cc_final: 0.6459 (m-80) REVERT: B 351 TYR cc_start: 0.7641 (p90) cc_final: 0.6732 (p90) REVERT: B 495 TYR cc_start: 0.6130 (m-80) cc_final: 0.5742 (m-10) REVERT: B 586 ASP cc_start: 0.7698 (m-30) cc_final: 0.7316 (m-30) REVERT: B 595 VAL cc_start: 0.8536 (t) cc_final: 0.8285 (p) REVERT: B 613 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8540 (mm-40) REVERT: B 751 ASN cc_start: 0.8371 (m-40) cc_final: 0.8043 (m-40) REVERT: B 752 LEU cc_start: 0.8734 (tt) cc_final: 0.8371 (mp) REVERT: B 773 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7420 (tp30) REVERT: B 776 LYS cc_start: 0.8273 (ttpp) cc_final: 0.7817 (tmmt) REVERT: B 804 GLN cc_start: 0.8246 (mt0) cc_final: 0.8022 (mt0) REVERT: B 823 PHE cc_start: 0.8490 (t80) cc_final: 0.8074 (t80) REVERT: B 935 GLN cc_start: 0.8030 (tt0) cc_final: 0.7646 (tp40) REVERT: B 981 PHE cc_start: 0.7334 (t80) cc_final: 0.7069 (t80) REVERT: B 988 GLU cc_start: 0.7660 (tp30) cc_final: 0.7441 (tp30) REVERT: C 231 ILE cc_start: 0.8621 (mm) cc_final: 0.8407 (mm) REVERT: C 340 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7537 (mp0) REVERT: C 454 ARG cc_start: 0.7599 (ptm160) cc_final: 0.7179 (ptm160) REVERT: C 691 SER cc_start: 0.8557 (p) cc_final: 0.8295 (m) REVERT: C 698 SER cc_start: 0.8762 (t) cc_final: 0.8474 (p) REVERT: C 725 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7817 (tt0) REVERT: C 750 SER cc_start: 0.8968 (m) cc_final: 0.8628 (m) REVERT: C 814 LYS cc_start: 0.8447 (mmtt) cc_final: 0.7995 (mmmt) REVERT: C 900 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7969 (mtm) REVERT: C 933 LYS cc_start: 0.8302 (mttt) cc_final: 0.7996 (mttm) REVERT: C 950 ASP cc_start: 0.8146 (m-30) cc_final: 0.7727 (m-30) REVERT: C 969 LYS cc_start: 0.9262 (mttt) cc_final: 0.8993 (mtpp) REVERT: C 1005 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8154 (tp40) outliers start: 69 outliers final: 54 residues processed: 551 average time/residue: 0.3904 time to fit residues: 324.5296 Evaluate side-chains 565 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 507 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 288 optimal weight: 0.0980 chunk 143 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 703 ASN A1002 GLN B 207 HIS B 563 GLN B 613 GLN B1002 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 394 ASN C 895 GLN C 901 GLN C1002 GLN C1135 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.147009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119053 restraints weight = 45085.098| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.09 r_work: 0.3522 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.8039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25501 Z= 0.141 Angle : 0.636 12.374 34698 Z= 0.326 Chirality : 0.046 0.361 3915 Planarity : 0.004 0.058 4473 Dihedral : 4.733 30.395 3402 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.45 % Allowed : 17.49 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3123 helix: 1.18 (0.22), residues: 612 sheet: 0.69 (0.20), residues: 657 loop : -1.06 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.005 0.001 HIS B 207 PHE 0.038 0.002 PHE C 855 TYR 0.014 0.001 TYR B 707 ARG 0.010 0.001 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 704) hydrogen bonds : angle 4.94195 ( 1941) SS BOND : bond 0.00323 ( 39) SS BOND : angle 1.98492 ( 78) covalent geometry : bond 0.00332 (25461) covalent geometry : angle 0.63013 (34620) Misc. bond : bond 0.00047 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 528 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8367 (mp) cc_final: 0.8163 (mp) REVERT: A 235 ILE cc_start: 0.5870 (tt) cc_final: 0.5520 (tp) REVERT: A 269 TYR cc_start: 0.7933 (m-80) cc_final: 0.7381 (m-80) REVERT: A 281 GLU cc_start: 0.7834 (pp20) cc_final: 0.7389 (pp20) REVERT: A 309 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 319 ARG cc_start: 0.7756 (mmt-90) cc_final: 0.7476 (tpp-160) REVERT: A 346 ARG cc_start: 0.6621 (tpt170) cc_final: 0.6411 (tpm170) REVERT: A 355 ARG cc_start: 0.6676 (ttm110) cc_final: 0.6270 (ttm-80) REVERT: A 398 ASP cc_start: 0.7392 (m-30) cc_final: 0.6614 (m-30) REVERT: A 421 TYR cc_start: 0.7618 (m-10) cc_final: 0.7249 (m-80) REVERT: A 537 LYS cc_start: 0.8212 (ttmm) cc_final: 0.8008 (mtpp) REVERT: A 552 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8362 (mt) REVERT: A 576 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7800 (t) REVERT: A 697 MET cc_start: 0.8766 (ttp) cc_final: 0.8418 (ptm) REVERT: A 804 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8331 (mm-40) REVERT: A 814 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8126 (mmmt) REVERT: A 884 SER cc_start: 0.8710 (t) cc_final: 0.8284 (p) REVERT: A 933 LYS cc_start: 0.8182 (mttt) cc_final: 0.7947 (mtmm) REVERT: A 988 GLU cc_start: 0.7634 (tp30) cc_final: 0.6991 (tp30) REVERT: A 1019 ARG cc_start: 0.7899 (tpt170) cc_final: 0.7516 (tpp-160) REVERT: A 1038 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8418 (mmmm) REVERT: A 1107 ARG cc_start: 0.8595 (ttm170) cc_final: 0.8332 (mtm-85) REVERT: A 1144 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7807 (mp0) REVERT: B 81 ASN cc_start: 0.7424 (m-40) cc_final: 0.7212 (m-40) REVERT: B 177 MET cc_start: 0.0972 (mtt) cc_final: 0.0643 (mtt) REVERT: B 206 LYS cc_start: 0.8604 (tttt) cc_final: 0.8342 (tttp) REVERT: B 239 GLN cc_start: 0.7280 (tp40) cc_final: 0.6833 (tp-100) REVERT: B 338 PHE cc_start: 0.6627 (m-80) cc_final: 0.6410 (m-80) REVERT: B 351 TYR cc_start: 0.7645 (p90) cc_final: 0.6727 (p90) REVERT: B 496 SER cc_start: 0.8627 (m) cc_final: 0.8343 (t) REVERT: B 574 ASP cc_start: 0.8097 (m-30) cc_final: 0.7634 (t0) REVERT: B 586 ASP cc_start: 0.7683 (m-30) cc_final: 0.7217 (m-30) REVERT: B 595 VAL cc_start: 0.8543 (t) cc_final: 0.8287 (p) REVERT: B 613 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8510 (tp40) REVERT: B 751 ASN cc_start: 0.8398 (m-40) cc_final: 0.8051 (m-40) REVERT: B 752 LEU cc_start: 0.8684 (tt) cc_final: 0.8343 (mp) REVERT: B 773 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7410 (tp30) REVERT: B 804 GLN cc_start: 0.8232 (mt0) cc_final: 0.8017 (mt0) REVERT: B 823 PHE cc_start: 0.8497 (t80) cc_final: 0.8094 (t80) REVERT: B 933 LYS cc_start: 0.8314 (mttt) cc_final: 0.8012 (mttp) REVERT: B 935 GLN cc_start: 0.8008 (tt0) cc_final: 0.7615 (tp40) REVERT: B 981 PHE cc_start: 0.7348 (t80) cc_final: 0.7069 (t80) REVERT: B 988 GLU cc_start: 0.7670 (tp30) cc_final: 0.7417 (tp30) REVERT: C 231 ILE cc_start: 0.8617 (mm) cc_final: 0.8408 (mm) REVERT: C 281 GLU cc_start: 0.6565 (pp20) cc_final: 0.6332 (pp20) REVERT: C 408 ARG cc_start: 0.8465 (ttp80) cc_final: 0.7907 (ppt170) REVERT: C 454 ARG cc_start: 0.7615 (ptm160) cc_final: 0.7254 (ptm160) REVERT: C 539 VAL cc_start: 0.8388 (m) cc_final: 0.8182 (p) REVERT: C 691 SER cc_start: 0.8560 (p) cc_final: 0.8311 (m) REVERT: C 725 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7819 (tt0) REVERT: C 752 LEU cc_start: 0.9142 (mm) cc_final: 0.8900 (mt) REVERT: C 773 GLU cc_start: 0.7848 (tt0) cc_final: 0.7561 (tt0) REVERT: C 814 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8008 (mmmt) REVERT: C 900 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7993 (mtm) REVERT: C 933 LYS cc_start: 0.8317 (mttt) cc_final: 0.8012 (mttm) REVERT: C 950 ASP cc_start: 0.8140 (m-30) cc_final: 0.7740 (m-30) REVERT: C 969 LYS cc_start: 0.9246 (mttt) cc_final: 0.8971 (mtpp) REVERT: C 1005 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8142 (tp40) outliers start: 68 outliers final: 57 residues processed: 559 average time/residue: 0.4048 time to fit residues: 340.8273 Evaluate side-chains 577 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 516 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 280 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 222 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 278 optimal weight: 0.7980 chunk 277 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 187 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A1002 GLN B 207 HIS B 563 GLN B 613 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 895 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.146596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.118614 restraints weight = 45132.614| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.09 r_work: 0.3512 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.8144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25501 Z= 0.146 Angle : 0.646 12.385 34698 Z= 0.330 Chirality : 0.047 0.400 3915 Planarity : 0.004 0.050 4473 Dihedral : 4.723 27.745 3402 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.45 % Allowed : 17.64 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3123 helix: 1.21 (0.22), residues: 612 sheet: 0.67 (0.20), residues: 657 loop : -1.06 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.004 0.001 HIS A1064 PHE 0.037 0.002 PHE C 855 TYR 0.027 0.001 TYR C 660 ARG 0.010 0.001 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 704) hydrogen bonds : angle 4.93751 ( 1941) SS BOND : bond 0.00275 ( 39) SS BOND : angle 1.95351 ( 78) covalent geometry : bond 0.00346 (25461) covalent geometry : angle 0.63970 (34620) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13389.02 seconds wall clock time: 229 minutes 24.51 seconds (13764.51 seconds total)