Starting phenix.real_space_refine on Mon Aug 25 19:16:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a95_11685/08_2025/7a95_11685.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a95_11685/08_2025/7a95_11685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a95_11685/08_2025/7a95_11685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a95_11685/08_2025/7a95_11685.map" model { file = "/net/cci-nas-00/data/ceres_data/7a95_11685/08_2025/7a95_11685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a95_11685/08_2025/7a95_11685.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 145 5.16 5 C 19081 2.51 5 N 4984 2.21 5 O 5677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 185 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29887 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8364 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "B" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 53, 'TRANS': 1013} Chain breaks: 5 Chain: "C" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 5 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Time building chain proxies: 7.69, per 1000 atoms: 0.26 Number of scatterers: 29887 At special positions: 0 Unit cell: (145.53, 161.7, 246.862, 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 145 16.00 O 5677 8.00 N 4984 7.00 C 19081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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 15 " - pdb=" SG CYS B 136 " 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 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 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 57 sheets defined 26.8% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.541A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.659A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.872A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.699A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.935A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 753 " --> pdb=" O CYS A 749 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 747 through 754' Processing helix chain 'A' and resid 756 through 779 removed outlier: 3.697A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.786A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.600A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.838A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.821A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.506A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.649A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.514A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.916A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.783A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.818A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.046A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 removed outlier: 4.012A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.933A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.007A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.862A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.537A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 885 removed outlier: 3.762A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 4.090A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 906 " --> pdb=" O MET B 902 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.799A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.616A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 931 " --> pdb=" O PHE B 927 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.902A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.755A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1032 removed outlier: 4.142A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.818A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.672A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.619A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.677A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 755 removed outlier: 3.512A pdb=" N GLN C 755 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.925A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.720A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.628A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 4.013A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.569A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.532A pdb=" N ILE C 931 " --> pdb=" O PHE C 927 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.631A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.831A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.757A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.767A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.607A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 80 removed outlier: 3.572A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 removed outlier: 3.613A pdb=" N GLN D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.822A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 112 through 129 removed outlier: 3.572A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.840A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 3.858A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU D 162 " --> pdb=" O TYR D 158 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TRP D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.556A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL D 184 " --> pdb=" O TYR D 180 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.674A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 225 through 233 removed outlier: 4.098A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.502A pdb=" N TYR D 243 " --> pdb=" O HIS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.653A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.658A pdb=" N MET D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.659A pdb=" N LYS D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.585A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 385 removed outlier: 3.780A pdb=" N LEU D 370 " --> pdb=" O MET D 366 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP D 382 " --> pdb=" O HIS D 378 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.643A pdb=" N VAL D 404 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.655A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.729A pdb=" N LYS D 458 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 463 " --> pdb=" O TRP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.697A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.659A pdb=" N ASN D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.700A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 553 removed outlier: 3.600A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 561 removed outlier: 3.843A pdb=" N LEU D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.647A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.621A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 597 removed outlier: 3.642A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.617A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.888A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.961A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.604A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 160 removed outlier: 3.864A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.883A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 355 removed outlier: 4.276A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.897A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.124A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.627A pdb=" N THR A 719 " --> pdb=" O VAL A1068 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.696A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.528A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.596A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.688A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.688A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 53 through 55 removed outlier: 4.121A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.554A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 152 through 160 removed outlier: 5.480A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.744A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.850A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 597 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.422A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 540 through 543 Processing sheet with id=AD6, first strand: chain 'B' and resid 551 through 553 removed outlier: 3.787A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.788A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD9, first strand: chain 'B' and resid 713 through 714 removed outlier: 3.673A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 717 through 722 removed outlier: 3.638A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 719 " --> pdb=" O VAL B1068 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.657A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.742A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.690A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE6, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.543A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.884A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.707A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.591A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.591A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 310 through 314 removed outlier: 3.628A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 354 through 355 removed outlier: 4.731A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 448 through 453 removed outlier: 7.701A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.972A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 713 through 715 Processing sheet with id=AF7, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.869A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.986A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.314A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG3, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.180A pdb=" N ALA D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 359 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP D 350 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ARG D 357 " --> pdb=" O ASP D 350 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 352 " --> pdb=" O ASP D 355 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2235 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.12 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8618 1.33 - 1.45: 5533 1.45 - 1.58: 16256 1.58 - 1.70: 0 1.70 - 1.82: 196 Bond restraints: 30603 Sorted by residual: bond pdb=" N GLN B 493 " pdb=" CA GLN B 493 " ideal model delta sigma weight residual 1.452 1.503 -0.051 1.25e-02 6.40e+03 1.64e+01 bond pdb=" N GLN B 498 " pdb=" CA GLN B 498 " ideal model delta sigma weight residual 1.453 1.491 -0.037 9.20e-03 1.18e+04 1.64e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.11e-02 8.12e+03 1.44e+01 bond pdb=" N VAL A1129 " pdb=" CA VAL A1129 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.14e-02 7.69e+03 1.22e+01 bond pdb=" N VAL B1096 " pdb=" CA VAL B1096 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.18e+01 ... (remaining 30598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 40924 1.66 - 3.32: 620 3.32 - 4.98: 67 4.98 - 6.64: 13 6.64 - 8.29: 4 Bond angle restraints: 41628 Sorted by residual: angle pdb=" N SER B 494 " pdb=" CA SER B 494 " pdb=" C SER B 494 " ideal model delta sigma weight residual 112.94 121.23 -8.29 1.41e+00 5.03e-01 3.46e+01 angle pdb=" N GLN D 305 " pdb=" CA GLN D 305 " pdb=" C GLN D 305 " ideal model delta sigma weight residual 112.92 106.54 6.38 1.23e+00 6.61e-01 2.69e+01 angle pdb=" CA ASP C 745 " pdb=" C ASP C 745 " pdb=" O ASP C 745 " ideal model delta sigma weight residual 121.20 116.38 4.82 1.04e+00 9.25e-01 2.15e+01 angle pdb=" CA CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " ideal model delta sigma weight residual 119.56 116.87 2.69 5.80e-01 2.97e+00 2.14e+01 angle pdb=" CA GLN B 493 " pdb=" C GLN B 493 " pdb=" O GLN B 493 " ideal model delta sigma weight residual 121.82 116.40 5.42 1.21e+00 6.83e-01 2.01e+01 ... (remaining 41623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 17833 15.90 - 31.79: 348 31.79 - 47.69: 37 47.69 - 63.58: 5 63.58 - 79.48: 5 Dihedral angle restraints: 18228 sinusoidal: 7169 harmonic: 11059 Sorted by residual: dihedral pdb=" C PHE C1109 " pdb=" N PHE C1109 " pdb=" CA PHE C1109 " pdb=" CB PHE C1109 " ideal model delta harmonic sigma weight residual -122.60 -133.47 10.87 0 2.50e+00 1.60e-01 1.89e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -121.69 35.69 1 1.00e+01 1.00e-02 1.80e+01 dihedral pdb=" C ASN B 481 " pdb=" N ASN B 481 " pdb=" CA ASN B 481 " pdb=" CB ASN B 481 " ideal model delta harmonic sigma weight residual -122.60 -132.40 9.80 0 2.50e+00 1.60e-01 1.54e+01 ... (remaining 18225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4287 0.086 - 0.172: 344 0.172 - 0.258: 14 0.258 - 0.343: 5 0.343 - 0.429: 1 Chirality restraints: 4651 Sorted by residual: chirality pdb=" CA SER B 494 " pdb=" N SER B 494 " pdb=" C SER B 494 " pdb=" CB SER B 494 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA PHE C1109 " pdb=" N PHE C1109 " pdb=" C PHE C1109 " pdb=" CB PHE C1109 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA ASN B 481 " pdb=" N ASN B 481 " pdb=" C ASN B 481 " pdb=" CB ASN B 481 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4648 not shown) Planarity restraints: 5401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 521 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 528 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C LYS C 528 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS C 528 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS C 529 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 318 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C VAL D 318 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL D 318 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY D 319 " -0.012 2.00e-02 2.50e+03 ... (remaining 5398 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4278 2.76 - 3.30: 26062 3.30 - 3.83: 46005 3.83 - 4.37: 53819 4.37 - 4.90: 94425 Nonbonded interactions: 224589 Sorted by model distance: nonbonded pdb=" O GLN D 305 " pdb=" NE2 GLN D 305 " model vdw 2.226 3.120 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.302 3.040 nonbonded pdb=" OG1 THR D 365 " pdb=" OD1 ASP D 368 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR B 741 " pdb=" O LEU B 962 " model vdw 2.319 3.040 nonbonded pdb=" O PHE D 327 " pdb=" OG SER D 331 " model vdw 2.355 3.040 ... (remaining 224584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 827 or resid 852 through 1146)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 827 or resid 852 through 1146)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.200 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.003 0.051 30648 Z= 0.185 Angle : 0.472 8.295 41718 Z= 0.300 Chirality : 0.043 0.429 4651 Planarity : 0.003 0.052 5401 Dihedral : 5.772 79.479 10977 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 0.90 % Allowed : 2.98 % Favored : 96.12 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.57 (0.10), residues: 3754 helix: -4.11 (0.07), residues: 823 sheet: -2.07 (0.19), residues: 613 loop : -3.02 (0.10), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.008 0.000 TYR C1110 PHE 0.009 0.000 PHE C 329 TRP 0.003 0.000 TRP B1102 HIS 0.001 0.000 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00255 (30603) covalent geometry : angle 0.47187 (41628) SS BOND : bond 0.00288 ( 45) SS BOND : angle 0.42102 ( 90) hydrogen bonds : bond 0.33940 ( 813) hydrogen bonds : angle 9.85974 ( 2235) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 350 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.1715 (OUTLIER) cc_final: 0.0465 (ptp90) REVERT: A 368 LEU cc_start: 0.9442 (mt) cc_final: 0.9236 (pp) REVERT: A 780 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8043 (mm-30) REVERT: A 1138 TYR cc_start: 0.8752 (t80) cc_final: 0.8403 (t80) REVERT: B 365 TYR cc_start: 0.5094 (p90) cc_final: 0.4680 (p90) REVERT: B 390 LEU cc_start: 0.7799 (mt) cc_final: 0.7549 (mt) REVERT: B 497 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.5956 (p90) REVERT: B 699 LEU cc_start: 0.8753 (mt) cc_final: 0.7677 (pt) REVERT: B 822 LEU cc_start: 0.9291 (mt) cc_final: 0.9082 (tt) REVERT: B 869 MET cc_start: 0.8797 (mtt) cc_final: 0.8557 (mtp) REVERT: C 242 LEU cc_start: 0.8664 (mt) cc_final: 0.8464 (mt) REVERT: C 773 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8404 (mm-30) REVERT: C 1029 MET cc_start: 0.9640 (tpp) cc_final: 0.9207 (tpt) REVERT: C 1108 ASN cc_start: 0.8843 (m110) cc_final: 0.8307 (t0) REVERT: D 270 MET cc_start: 0.6616 (tpp) cc_final: 0.5978 (tpt) REVERT: D 557 MET cc_start: 0.8913 (ptt) cc_final: 0.8487 (ptm) outliers start: 30 outliers final: 8 residues processed: 379 average time/residue: 0.1845 time to fit residues: 112.0794 Evaluate side-chains 152 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.0050 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 0.6980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 17 ASN A 49 HIS A 52 GLN A 66 HIS A 115 GLN A 125 ASN A 173 GLN A 211 ASN A 239 GLN A 271 GLN A 414 GLN A 506 GLN A 580 GLN A 607 GLN A 613 GLN A 675 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 954 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1010 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN A1106 GLN B 14 GLN B 30 ASN B 52 GLN B 61 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 115 GLN B 173 GLN B 207 HIS B 239 GLN B 314 GLN B 493 GLN B 506 GLN B 564 GLN B 607 GLN B 675 GLN B 762 GLN B 784 GLN B 787 GLN B 872 GLN B 926 GLN B 949 GLN B 957 GLN B 965 GLN B 992 GLN B1005 GLN B1010 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1113 GLN B1134 ASN C 14 GLN C 61 ASN C 69 HIS C 87 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 234 ASN C 282 ASN C 409 GLN C 414 GLN C 439 ASN C 481 ASN C 564 GLN C 580 GLN C 607 GLN C 703 ASN C 762 GLN C 764 ASN C 853 GLN C 901 GLN C 913 GLN C 954 GLN C 965 GLN C1010 GLN C1011 GLN C1036 GLN C1054 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN D 24 GLN D 42 GLN D 86 GLN D 149 ASN D 175 GLN D 300 GLN D 345 HIS D 388 GLN D 397 ASN D 472 GLN D 522 GLN D 526 GLN D 552 GLN Total number of N/Q/H flips: 93 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.066693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.044344 restraints weight = 221886.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.045635 restraints weight = 113186.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.046503 restraints weight = 71547.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.047017 restraints weight = 52010.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.047400 restraints weight = 42451.189| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30648 Z= 0.130 Angle : 0.540 10.008 41718 Z= 0.279 Chirality : 0.042 0.177 4651 Planarity : 0.004 0.051 5401 Dihedral : 2.759 24.062 4069 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (0.12), residues: 3754 helix: -1.23 (0.16), residues: 850 sheet: -1.43 (0.20), residues: 612 loop : -2.59 (0.11), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 214 TYR 0.013 0.001 TYR B1110 PHE 0.023 0.001 PHE A 643 TRP 0.017 0.001 TRP D 328 HIS 0.010 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00262 (30603) covalent geometry : angle 0.53902 (41628) SS BOND : bond 0.00485 ( 45) SS BOND : angle 0.82099 ( 90) hydrogen bonds : bond 0.06602 ( 813) hydrogen bonds : angle 6.14090 ( 2235) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.094 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 805 ILE cc_start: 0.8644 (pt) cc_final: 0.8354 (mt) REVERT: A 1138 TYR cc_start: 0.8475 (t80) cc_final: 0.8213 (t80) REVERT: B 297 SER cc_start: 0.8995 (m) cc_final: 0.8581 (t) REVERT: B 390 LEU cc_start: 0.8068 (mt) cc_final: 0.7739 (mt) REVERT: B 489 TYR cc_start: 0.8854 (m-80) cc_final: 0.8586 (m-80) REVERT: B 731 MET cc_start: 0.8813 (ptm) cc_final: 0.7167 (ppp) REVERT: B 869 MET cc_start: 0.8983 (mtt) cc_final: 0.8566 (mtp) REVERT: B 979 ASP cc_start: 0.9326 (m-30) cc_final: 0.9025 (p0) REVERT: C 753 LEU cc_start: 0.9091 (mm) cc_final: 0.8869 (pp) REVERT: C 780 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8446 (tp30) REVERT: C 900 MET cc_start: 0.8323 (mmp) cc_final: 0.7651 (mmp) REVERT: C 902 MET cc_start: 0.9187 (mmm) cc_final: 0.8906 (tpp) REVERT: C 970 PHE cc_start: 0.8520 (m-80) cc_final: 0.8201 (m-10) REVERT: C 1029 MET cc_start: 0.9645 (tpp) cc_final: 0.9288 (tpp) REVERT: D 190 MET cc_start: 0.7579 (mmt) cc_final: 0.7293 (mmt) REVERT: D 270 MET cc_start: 0.6953 (tpp) cc_final: 0.6182 (tpp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1712 time to fit residues: 49.2491 Evaluate side-chains 119 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 73 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 339 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 259 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 69 HIS A 439 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 343 ASN B 519 HIS B 544 ASN B 607 GLN B 613 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS C 99 ASN C 607 GLN C 901 GLN C 913 GLN ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS D 58 ASN D 522 GLN D 535 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.063728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.041192 restraints weight = 225568.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.042501 restraints weight = 124556.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.042910 restraints weight = 70000.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.043024 restraints weight = 58583.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043193 restraints weight = 54355.131| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30648 Z= 0.172 Angle : 0.536 10.944 41718 Z= 0.271 Chirality : 0.041 0.161 4651 Planarity : 0.004 0.048 5401 Dihedral : 2.898 17.565 4069 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.13), residues: 3754 helix: 0.08 (0.18), residues: 864 sheet: -1.13 (0.20), residues: 650 loop : -2.26 (0.11), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 102 TYR 0.012 0.001 TYR C 873 PHE 0.018 0.001 PHE C 135 TRP 0.010 0.001 TRP A 886 HIS 0.015 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00360 (30603) covalent geometry : angle 0.53526 (41628) SS BOND : bond 0.00440 ( 45) SS BOND : angle 0.69803 ( 90) hydrogen bonds : bond 0.05062 ( 813) hydrogen bonds : angle 5.36292 ( 2235) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.181 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 365 TYR cc_start: 0.8561 (m-80) cc_final: 0.8340 (m-80) REVERT: A 869 MET cc_start: 0.9128 (ptp) cc_final: 0.8799 (mpp) REVERT: A 1138 TYR cc_start: 0.8762 (t80) cc_final: 0.8412 (t80) REVERT: B 92 PHE cc_start: 0.8651 (t80) cc_final: 0.8371 (t80) REVERT: B 489 TYR cc_start: 0.9033 (m-80) cc_final: 0.8704 (m-80) REVERT: B 740 MET cc_start: 0.8210 (ttt) cc_final: 0.7134 (tmm) REVERT: B 869 MET cc_start: 0.9218 (mtt) cc_final: 0.8738 (mtp) REVERT: B 979 ASP cc_start: 0.9593 (m-30) cc_final: 0.8522 (t70) REVERT: C 784 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8676 (mm-40) REVERT: C 1029 MET cc_start: 0.9690 (tpp) cc_final: 0.9156 (tpp) REVERT: D 190 MET cc_start: 0.7423 (mmt) cc_final: 0.7143 (mmt) REVERT: D 270 MET cc_start: 0.7072 (tpp) cc_final: 0.6183 (tpp) REVERT: D 297 MET cc_start: 0.7938 (mtm) cc_final: 0.7595 (ttt) REVERT: D 323 MET cc_start: 0.4884 (ptm) cc_final: 0.3632 (ppp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1787 time to fit residues: 39.1855 Evaluate side-chains 95 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 211 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 281 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 149 ASN B 474 GLN B 607 GLN B 762 GLN B 954 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 66 HIS C 607 GLN C 784 GLN C 913 GLN C 953 ASN C1134 ASN D 345 HIS D 373 HIS D 442 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.062004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.039134 restraints weight = 223678.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.039996 restraints weight = 146906.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.040546 restraints weight = 82901.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040650 restraints weight = 66577.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.040684 restraints weight = 64229.872| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30648 Z= 0.169 Angle : 0.538 10.634 41718 Z= 0.270 Chirality : 0.041 0.355 4651 Planarity : 0.004 0.053 5401 Dihedral : 3.178 17.519 4069 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.13), residues: 3754 helix: 0.62 (0.18), residues: 886 sheet: -1.09 (0.19), residues: 695 loop : -1.99 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 245 TYR 0.029 0.001 TYR D 385 PHE 0.021 0.001 PHE D 315 TRP 0.015 0.001 TRP A 886 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00361 (30603) covalent geometry : angle 0.53753 (41628) SS BOND : bond 0.00664 ( 45) SS BOND : angle 0.66561 ( 90) hydrogen bonds : bond 0.04346 ( 813) hydrogen bonds : angle 4.88633 ( 2235) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8410 (m-30) cc_final: 0.7637 (t0) REVERT: A 365 TYR cc_start: 0.9150 (m-80) cc_final: 0.8740 (m-80) REVERT: A 1138 TYR cc_start: 0.8843 (t80) cc_final: 0.8517 (t80) REVERT: B 177 MET cc_start: 0.8508 (tpt) cc_final: 0.8253 (tpp) REVERT: B 489 TYR cc_start: 0.9130 (m-80) cc_final: 0.8798 (m-80) REVERT: B 869 MET cc_start: 0.9319 (mtt) cc_final: 0.8791 (mtp) REVERT: B 979 ASP cc_start: 0.9627 (m-30) cc_final: 0.9030 (t70) REVERT: C 900 MET cc_start: 0.9099 (mmp) cc_final: 0.8835 (mmp) REVERT: C 1029 MET cc_start: 0.9660 (tpp) cc_final: 0.9112 (tpp) REVERT: D 190 MET cc_start: 0.7231 (mmt) cc_final: 0.6926 (mmt) REVERT: D 270 MET cc_start: 0.7048 (tpp) cc_final: 0.6188 (tpp) REVERT: D 297 MET cc_start: 0.8059 (mtm) cc_final: 0.7709 (ttt) REVERT: D 516 TYR cc_start: 0.9244 (t80) cc_final: 0.8556 (t80) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1701 time to fit residues: 32.8865 Evaluate side-chains 83 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 346 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 351 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 374 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 360 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1064 HIS ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 784 GLN C 913 GLN C 965 GLN C1054 GLN C1113 GLN D 194 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.059788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.037656 restraints weight = 229327.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.037713 restraints weight = 125528.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.038051 restraints weight = 92390.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.037986 restraints weight = 81675.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.038081 restraints weight = 70893.426| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 30648 Z= 0.269 Angle : 0.659 13.490 41718 Z= 0.332 Chirality : 0.043 0.191 4651 Planarity : 0.004 0.056 5401 Dihedral : 3.827 19.416 4069 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 0.03 % Allowed : 1.26 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.13), residues: 3754 helix: 0.41 (0.17), residues: 916 sheet: -1.07 (0.19), residues: 724 loop : -1.88 (0.12), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 319 TYR 0.021 0.002 TYR B 873 PHE 0.026 0.002 PHE B1042 TRP 0.034 0.002 TRP A 886 HIS 0.013 0.002 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00578 (30603) covalent geometry : angle 0.65887 (41628) SS BOND : bond 0.00313 ( 45) SS BOND : angle 0.84691 ( 90) hydrogen bonds : bond 0.04834 ( 813) hydrogen bonds : angle 5.26786 ( 2235) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8715 (m-30) cc_final: 0.8055 (t0) REVERT: A 365 TYR cc_start: 0.9327 (m-80) cc_final: 0.8790 (m-80) REVERT: A 1138 TYR cc_start: 0.8879 (t80) cc_final: 0.8553 (t80) REVERT: B 117 LEU cc_start: 0.9582 (tp) cc_final: 0.9367 (tt) REVERT: B 118 LEU cc_start: 0.9722 (tt) cc_final: 0.9142 (mp) REVERT: B 177 MET cc_start: 0.8639 (tpt) cc_final: 0.8324 (tpp) REVERT: B 489 TYR cc_start: 0.9208 (m-80) cc_final: 0.8903 (m-80) REVERT: B 869 MET cc_start: 0.9427 (mtt) cc_final: 0.8984 (mtt) REVERT: C 1029 MET cc_start: 0.9642 (tpp) cc_final: 0.9147 (tpp) REVERT: D 190 MET cc_start: 0.7461 (mmt) cc_final: 0.7002 (mmt) REVERT: D 516 TYR cc_start: 0.9359 (t80) cc_final: 0.8786 (t80) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1829 time to fit residues: 32.3849 Evaluate side-chains 76 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 231 optimal weight: 0.1980 chunk 284 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 297 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 203 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 374 optimal weight: 8.9990 chunk 330 optimal weight: 20.0000 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 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 607 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 913 GLN C1054 GLN D 34 HIS D 373 HIS D 526 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.064831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.043800 restraints weight = 251719.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.044831 restraints weight = 123371.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.045492 restraints weight = 76488.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.045929 restraints weight = 56387.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046142 restraints weight = 46921.029| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30648 Z= 0.090 Angle : 0.461 9.773 41718 Z= 0.230 Chirality : 0.041 0.138 4651 Planarity : 0.003 0.050 5401 Dihedral : 3.293 17.481 4069 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.13), residues: 3754 helix: 1.01 (0.18), residues: 914 sheet: -0.99 (0.19), residues: 706 loop : -1.71 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1019 TYR 0.010 0.001 TYR C 873 PHE 0.017 0.001 PHE B1062 TRP 0.018 0.001 TRP A 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00190 (30603) covalent geometry : angle 0.46115 (41628) SS BOND : bond 0.00166 ( 45) SS BOND : angle 0.58849 ( 90) hydrogen bonds : bond 0.03960 ( 813) hydrogen bonds : angle 4.66324 ( 2235) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8454 (m-30) cc_final: 0.7784 (t0) REVERT: A 365 TYR cc_start: 0.9148 (m-80) cc_final: 0.8776 (m-80) REVERT: A 977 LEU cc_start: 0.9057 (pt) cc_final: 0.8832 (pp) REVERT: B 489 TYR cc_start: 0.9225 (m-80) cc_final: 0.8872 (m-80) REVERT: B 869 MET cc_start: 0.9328 (mtt) cc_final: 0.8895 (mtp) REVERT: C 1029 MET cc_start: 0.9612 (tpp) cc_final: 0.9118 (tpp) REVERT: D 190 MET cc_start: 0.7451 (mmt) cc_final: 0.7159 (mmt) REVERT: D 270 MET cc_start: 0.6962 (tpt) cc_final: 0.6154 (tpt) REVERT: D 323 MET cc_start: 0.7162 (ptm) cc_final: 0.6122 (ppp) REVERT: D 366 MET cc_start: 0.9664 (tpt) cc_final: 0.9461 (tpt) REVERT: D 516 TYR cc_start: 0.9332 (t80) cc_final: 0.8654 (t80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1833 time to fit residues: 33.1815 Evaluate side-chains 78 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 315 optimal weight: 0.7980 chunk 211 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 280 optimal weight: 0.6980 chunk 317 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 146 optimal weight: 0.0770 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 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.064736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.043719 restraints weight = 252431.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.044768 restraints weight = 123563.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.045456 restraints weight = 76645.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.045897 restraints weight = 56255.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046115 restraints weight = 46652.715| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30648 Z= 0.092 Angle : 0.452 10.052 41718 Z= 0.224 Chirality : 0.040 0.153 4651 Planarity : 0.003 0.051 5401 Dihedral : 3.121 16.729 4069 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.14), residues: 3754 helix: 1.20 (0.18), residues: 919 sheet: -0.86 (0.19), residues: 706 loop : -1.63 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.010 0.001 TYR C 873 PHE 0.009 0.001 PHE B1042 TRP 0.017 0.001 TRP A 886 HIS 0.011 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00197 (30603) covalent geometry : angle 0.45219 (41628) SS BOND : bond 0.00133 ( 45) SS BOND : angle 0.52749 ( 90) hydrogen bonds : bond 0.03645 ( 813) hydrogen bonds : angle 4.51235 ( 2235) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8467 (m-30) cc_final: 0.7795 (t0) REVERT: A 365 TYR cc_start: 0.9249 (m-80) cc_final: 0.8822 (m-80) REVERT: A 869 MET cc_start: 0.9051 (ptp) cc_final: 0.8730 (mpp) REVERT: B 489 TYR cc_start: 0.9215 (m-80) cc_final: 0.8860 (m-80) REVERT: B 869 MET cc_start: 0.9308 (mtt) cc_final: 0.8901 (mtp) REVERT: B 979 ASP cc_start: 0.9366 (m-30) cc_final: 0.8944 (t70) REVERT: C 1029 MET cc_start: 0.9594 (tpp) cc_final: 0.9098 (tpp) REVERT: D 190 MET cc_start: 0.7593 (mmt) cc_final: 0.7247 (mmt) REVERT: D 270 MET cc_start: 0.6895 (tpt) cc_final: 0.5999 (tpt) REVERT: D 323 MET cc_start: 0.7214 (ptm) cc_final: 0.6215 (ppp) REVERT: D 376 MET cc_start: 0.8881 (ptp) cc_final: 0.8671 (ptp) REVERT: D 516 TYR cc_start: 0.9316 (t80) cc_final: 0.8624 (t80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1859 time to fit residues: 31.7964 Evaluate side-chains 79 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 310 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 346 optimal weight: 0.4980 chunk 198 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 99 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN D 34 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.060107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.038017 restraints weight = 228888.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038528 restraints weight = 143918.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.038201 restraints weight = 103688.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.038456 restraints weight = 95080.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038649 restraints weight = 81690.055| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 30648 Z= 0.160 Angle : 0.517 11.122 41718 Z= 0.257 Chirality : 0.041 0.137 4651 Planarity : 0.003 0.051 5401 Dihedral : 3.401 17.708 4069 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.14), residues: 3754 helix: 1.14 (0.18), residues: 934 sheet: -0.84 (0.19), residues: 700 loop : -1.59 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.014 0.001 TYR C 904 PHE 0.016 0.001 PHE B1042 TRP 0.022 0.001 TRP A 886 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00348 (30603) covalent geometry : angle 0.51699 (41628) SS BOND : bond 0.00194 ( 45) SS BOND : angle 0.62234 ( 90) hydrogen bonds : bond 0.03879 ( 813) hydrogen bonds : angle 4.62069 ( 2235) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8759 (m-30) cc_final: 0.8125 (t0) REVERT: A 189 LEU cc_start: 0.9647 (tp) cc_final: 0.9418 (pp) REVERT: A 365 TYR cc_start: 0.9342 (m-80) cc_final: 0.8691 (m-80) REVERT: A 1138 TYR cc_start: 0.8946 (t80) cc_final: 0.8546 (t80) REVERT: B 489 TYR cc_start: 0.9180 (m-80) cc_final: 0.8864 (m-80) REVERT: B 869 MET cc_start: 0.9353 (mtt) cc_final: 0.9047 (mtp) REVERT: B 979 ASP cc_start: 0.9628 (m-30) cc_final: 0.9071 (t0) REVERT: C 177 MET cc_start: 0.3594 (tmm) cc_final: 0.3208 (tmm) REVERT: C 456 PHE cc_start: 0.9623 (m-80) cc_final: 0.9421 (m-80) REVERT: C 1029 MET cc_start: 0.9615 (tpp) cc_final: 0.9063 (tpp) REVERT: D 190 MET cc_start: 0.7497 (mmt) cc_final: 0.7027 (mmt) REVERT: D 297 MET cc_start: 0.8457 (ttt) cc_final: 0.7663 (ptp) REVERT: D 376 MET cc_start: 0.9128 (ptp) cc_final: 0.8907 (ptm) REVERT: D 516 TYR cc_start: 0.9295 (t80) cc_final: 0.8673 (t80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1993 time to fit residues: 32.9883 Evaluate side-chains 76 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 329 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 369 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 57 optimal weight: 0.2980 chunk 183 optimal weight: 0.7980 chunk 299 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 368 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 607 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN D 522 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.060937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.038580 restraints weight = 226725.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.039073 restraints weight = 151257.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.039346 restraints weight = 91798.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.039425 restraints weight = 85964.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039572 restraints weight = 75446.348| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30648 Z= 0.085 Angle : 0.460 13.601 41718 Z= 0.226 Chirality : 0.041 0.134 4651 Planarity : 0.003 0.051 5401 Dihedral : 3.190 16.165 4069 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.14), residues: 3754 helix: 1.35 (0.18), residues: 934 sheet: -0.70 (0.20), residues: 691 loop : -1.56 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.009 0.001 TYR C 873 PHE 0.012 0.001 PHE D 438 TRP 0.015 0.001 TRP A 886 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00178 (30603) covalent geometry : angle 0.45945 (41628) SS BOND : bond 0.00125 ( 45) SS BOND : angle 0.62714 ( 90) hydrogen bonds : bond 0.03517 ( 813) hydrogen bonds : angle 4.37983 ( 2235) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8645 (m-30) cc_final: 0.8029 (t0) REVERT: A 189 LEU cc_start: 0.9610 (tp) cc_final: 0.9379 (pp) REVERT: A 365 TYR cc_start: 0.9251 (m-80) cc_final: 0.8647 (m-80) REVERT: A 869 MET cc_start: 0.9019 (ptp) cc_final: 0.8810 (mpp) REVERT: A 1138 TYR cc_start: 0.8883 (t80) cc_final: 0.8525 (t80) REVERT: B 177 MET cc_start: 0.8895 (mtm) cc_final: 0.8521 (ptm) REVERT: B 489 TYR cc_start: 0.9077 (m-80) cc_final: 0.8778 (m-80) REVERT: B 869 MET cc_start: 0.9300 (mtt) cc_final: 0.9006 (mtp) REVERT: B 979 ASP cc_start: 0.9619 (m-30) cc_final: 0.9092 (t0) REVERT: C 456 PHE cc_start: 0.9588 (m-80) cc_final: 0.9381 (m-80) REVERT: C 909 ILE cc_start: 0.9317 (pt) cc_final: 0.8973 (mt) REVERT: C 1029 MET cc_start: 0.9586 (tpp) cc_final: 0.9093 (tpp) REVERT: D 190 MET cc_start: 0.7431 (mmt) cc_final: 0.6924 (mmt) REVERT: D 270 MET cc_start: 0.7615 (tpt) cc_final: 0.6461 (tpt) REVERT: D 297 MET cc_start: 0.8389 (ttt) cc_final: 0.7621 (ptp) REVERT: D 360 MET cc_start: 0.8247 (mmm) cc_final: 0.7959 (mmm) REVERT: D 376 MET cc_start: 0.9170 (ptp) cc_final: 0.8900 (ptp) REVERT: D 516 TYR cc_start: 0.9208 (t80) cc_final: 0.8568 (t80) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1909 time to fit residues: 33.9225 Evaluate side-chains 79 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 310 optimal weight: 0.9980 chunk 337 optimal weight: 9.9990 chunk 248 optimal weight: 0.5980 chunk 16 optimal weight: 20.0000 chunk 238 optimal weight: 0.5980 chunk 313 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 357 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 607 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN D 522 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.063475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.043231 restraints weight = 251292.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.044235 restraints weight = 135900.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.044331 restraints weight = 83095.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.044487 restraints weight = 69012.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.044735 restraints weight = 62814.463| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30648 Z= 0.135 Angle : 0.496 9.713 41718 Z= 0.245 Chirality : 0.041 0.133 4651 Planarity : 0.003 0.051 5401 Dihedral : 3.292 16.960 4069 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.14), residues: 3754 helix: 1.34 (0.18), residues: 925 sheet: -0.71 (0.20), residues: 693 loop : -1.51 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.012 0.001 TYR C 904 PHE 0.013 0.001 PHE B1042 TRP 0.021 0.001 TRP A 886 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00294 (30603) covalent geometry : angle 0.49576 (41628) SS BOND : bond 0.00144 ( 45) SS BOND : angle 0.57508 ( 90) hydrogen bonds : bond 0.03617 ( 813) hydrogen bonds : angle 4.49059 ( 2235) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8679 (m-30) cc_final: 0.8123 (t0) REVERT: A 189 LEU cc_start: 0.9685 (tp) cc_final: 0.9451 (pp) REVERT: A 365 TYR cc_start: 0.9364 (m-80) cc_final: 0.8762 (m-80) REVERT: A 869 MET cc_start: 0.9062 (ptp) cc_final: 0.8766 (mpp) REVERT: A 1138 TYR cc_start: 0.8823 (t80) cc_final: 0.8532 (t80) REVERT: B 177 MET cc_start: 0.8891 (mtm) cc_final: 0.8514 (ptm) REVERT: B 489 TYR cc_start: 0.9265 (m-80) cc_final: 0.8926 (m-80) REVERT: B 869 MET cc_start: 0.9285 (mtt) cc_final: 0.8959 (mtp) REVERT: B 979 ASP cc_start: 0.9558 (m-30) cc_final: 0.9033 (t0) REVERT: C 177 MET cc_start: 0.3458 (tmm) cc_final: 0.3111 (tmm) REVERT: C 805 ILE cc_start: 0.9347 (pt) cc_final: 0.9114 (mt) REVERT: C 900 MET cc_start: 0.8852 (mmp) cc_final: 0.8644 (mmp) REVERT: C 909 ILE cc_start: 0.9338 (pt) cc_final: 0.9077 (mt) REVERT: C 1029 MET cc_start: 0.9608 (tpp) cc_final: 0.9076 (tpp) REVERT: D 190 MET cc_start: 0.7473 (mmt) cc_final: 0.7020 (mmt) REVERT: D 270 MET cc_start: 0.6790 (tpt) cc_final: 0.6162 (tpt) REVERT: D 297 MET cc_start: 0.8438 (ttt) cc_final: 0.7665 (ptp) REVERT: D 376 MET cc_start: 0.9069 (ptp) cc_final: 0.8816 (ptp) REVERT: D 516 TYR cc_start: 0.9285 (t80) cc_final: 0.8651 (t80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1913 time to fit residues: 32.3342 Evaluate side-chains 78 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 279 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 258 optimal weight: 10.0000 chunk 353 optimal weight: 6.9990 chunk 199 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 chunk 13 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 607 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.064152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.044193 restraints weight = 252248.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.045026 restraints weight = 139222.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.045583 restraints weight = 79015.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.045639 restraints weight = 66204.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.045738 restraints weight = 57227.894| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30648 Z= 0.091 Angle : 0.457 10.120 41718 Z= 0.226 Chirality : 0.040 0.133 4651 Planarity : 0.003 0.051 5401 Dihedral : 3.175 15.882 4069 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.14), residues: 3754 helix: 1.42 (0.18), residues: 937 sheet: -0.65 (0.20), residues: 700 loop : -1.48 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.010 0.001 TYR C 904 PHE 0.012 0.001 PHE D 438 TRP 0.017 0.001 TRP A 886 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00197 (30603) covalent geometry : angle 0.45653 (41628) SS BOND : bond 0.00119 ( 45) SS BOND : angle 0.54054 ( 90) hydrogen bonds : bond 0.03437 ( 813) hydrogen bonds : angle 4.32552 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5466.90 seconds wall clock time: 95 minutes 13.79 seconds (5713.79 seconds total)