Starting phenix.real_space_refine on Fri Mar 6 14:13:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wka_32564/03_2026/7wka_32564.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wka_32564/03_2026/7wka_32564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wka_32564/03_2026/7wka_32564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wka_32564/03_2026/7wka_32564.map" model { file = "/net/cci-nas-00/data/ceres_data/7wka_32564/03_2026/7wka_32564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wka_32564/03_2026/7wka_32564.cif" } resolution = 3.64 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= 0.033 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 139 5.16 5 C 20002 2.51 5 N 5231 2.21 5 O 5981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31353 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 996} Chain breaks: 7 Chain: "C" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "c" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "d" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "a" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 7.55, per 1000 atoms: 0.24 Number of scatterers: 31353 At special positions: 0 Unit cell: (218.6, 137.718, 178.159, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 139 16.00 O 5981 8.00 N 5231 7.00 C 20002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 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 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 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS c 147 " - pdb=" SG CYS c 202 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.04 Simple disulfide: pdb=" SG CYS d 138 " - pdb=" SG CYS d 198 " 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 a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 147 " - pdb=" SG CYS a 202 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " 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: 2.52 Conformation dependent library (CDL) restraints added in 1.3 seconds 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7540 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 68 sheets defined 18.4% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.516A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.779A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.640A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.819A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.667A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.831A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.691A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.539A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.643A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.704A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 931 removed outlier: 3.594A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 939 removed outlier: 3.525A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.866A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.752A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.981A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.872A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.538A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.815A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.731A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 4.079A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.686A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.659A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 752' Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.646A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.953A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.076A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.636A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.648A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.711A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.815A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.888A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.642A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.012A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.798A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 87 removed outlier: 4.124A pdb=" N ALA d 87 " --> pdb=" O GLU d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 132 removed outlier: 3.668A pdb=" N LEU d 129 " --> pdb=" O SER d 125 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER d 131 " --> pdb=" O GLU d 127 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.590A pdb=" N ARG d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.668A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.323A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.861A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.737A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.691A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.883A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.709A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.869A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 removed outlier: 3.882A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.603A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.628A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.689A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.749A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.802A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.607A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.892A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.914A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 32 removed outlier: 3.574A pdb=" N ARG a 31 " --> pdb=" O SER a 28 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE a 32 " --> pdb=" O PHE a 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 28 through 32' Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.896A pdb=" N SER a 91 " --> pdb=" O SER a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 198 removed outlier: 4.010A pdb=" N SER a 197 " --> pdb=" O SER a 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 87 removed outlier: 4.223A pdb=" N ALA b 87 " --> pdb=" O GLU b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 132 removed outlier: 3.612A pdb=" N LEU b 129 " --> pdb=" O SER b 125 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER b 131 " --> pdb=" O GLU b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 192 removed outlier: 3.894A pdb=" N ARG b 192 " --> pdb=" O ASP b 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.920A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.968A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.664A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.937A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.422A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.602A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 357 removed outlier: 4.380A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.670A pdb=" N TYR A 453 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.503A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.294A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.720A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.044A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.553A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.522A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.743A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC3, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.030A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.563A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 566 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.888A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.835A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.591A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.817A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.567A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.347A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.975A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'c' and resid 9 through 12 removed outlier: 6.565A pdb=" N GLU c 10 " --> pdb=" O THR c 117 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR c 95 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL c 37 " --> pdb=" O TYR c 95 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN c 35 " --> pdb=" O ALA c 97 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET c 34 " --> pdb=" O MET c 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N MET c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP c 36 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG c 40 " --> pdb=" O GLY c 44 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU c 57 " --> pdb=" O HIS c 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 9 through 12 removed outlier: 6.565A pdb=" N GLU c 10 " --> pdb=" O THR c 117 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS c 96 " --> pdb=" O TRP c 110 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TRP c 110 " --> pdb=" O CYS c 96 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG c 98 " --> pdb=" O ALA c 108 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 17 through 23 removed outlier: 3.620A pdb=" N LEU c 20 " --> pdb=" O MET c 81 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET c 81 " --> pdb=" O LEU c 20 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR c 71 " --> pdb=" O TYR c 80 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'c' and resid 127 through 131 removed outlier: 3.576A pdb=" N GLY c 146 " --> pdb=" O LEU c 131 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER c 187 " --> pdb=" O HIS c 171 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 127 through 131 removed outlier: 3.576A pdb=" N GLY c 146 " --> pdb=" O LEU c 131 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR c 152 " --> pdb=" O TYR c 182 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 158 through 161 removed outlier: 3.789A pdb=" N THR c 158 " --> pdb=" O ALA c 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.893A pdb=" N SER d 7 " --> pdb=" O SER d 22 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER d 22 " --> pdb=" O SER d 7 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS d 23 " --> pdb=" O PHE d 75 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE d 75 " --> pdb=" O CYS d 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP d 74 " --> pdb=" O SER d 71 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 10 through 14 removed outlier: 6.594A pdb=" N LEU d 11 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS d 111 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL d 13 " --> pdb=" O LYS d 111 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP d 39 " --> pdb=" O LEU d 51 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AE6, first strand: chain 'd' and resid 118 through 122 removed outlier: 3.672A pdb=" N VAL d 137 " --> pdb=" O PHE d 122 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR d 177 " --> pdb=" O ASN d 142 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 157 through 158 removed outlier: 3.941A pdb=" N TYR d 196 " --> pdb=" O PHE d 213 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE d 213 " --> pdb=" O TYR d 196 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.102A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.644A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.816A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.403A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.524A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.771A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.857A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.752A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.519A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.689A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AG2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.876A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG4, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.657A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS a 99 " --> pdb=" O TRP a 33 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP a 33 " --> pdb=" O LYS a 99 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET a 34 " --> pdb=" O MET a 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG a 40 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.657A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG a 98 " --> pdb=" O TYR a 109 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR a 109 " --> pdb=" O ARG a 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 17 through 23 removed outlier: 3.752A pdb=" N THR a 71 " --> pdb=" O TYR a 80 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 127 through 131 removed outlier: 3.548A pdb=" N SER a 186 " --> pdb=" O CYS a 147 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER a 187 " --> pdb=" O HIS a 171 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 127 through 131 removed outlier: 3.548A pdb=" N SER a 186 " --> pdb=" O CYS a 147 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR a 183 " --> pdb=" O VAL a 176 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'a' and resid 158 through 161 removed outlier: 3.508A pdb=" N THR a 211 " --> pdb=" O HIS a 206 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 5 through 7 removed outlier: 3.795A pdb=" N SER b 7 " --> pdb=" O SER b 22 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 21 " --> pdb=" O LEU b 77 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS b 23 " --> pdb=" O PHE b 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE b 75 " --> pdb=" O CYS b 23 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP b 74 " --> pdb=" O SER b 71 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 10 through 14 removed outlier: 6.296A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS b 111 " --> pdb=" O LEU b 11 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL b 13 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP b 39 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN b 41 " --> pdb=" O LYS b 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 10 through 14 removed outlier: 6.296A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS b 111 " --> pdb=" O LEU b 11 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL b 13 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS b 94 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA b 101 " --> pdb=" O HIS b 94 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 118 through 122 removed outlier: 3.551A pdb=" N VAL b 137 " --> pdb=" O PHE b 122 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR b 177 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 157 through 158 removed outlier: 3.758A pdb=" N TYR b 196 " --> pdb=" O PHE b 213 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE b 213 " --> pdb=" O TYR b 196 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA b 200 " --> pdb=" O ILE b 209 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE b 209 " --> pdb=" O ALA b 200 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2469 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: 7.79 Time building geometry restraints manager: 3.33 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: 6953 1.33 - 1.45: 7717 1.45 - 1.58: 17260 1.58 - 1.70: 0 1.70 - 1.83: 178 Bond restraints: 32108 Sorted by residual: bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.436 -0.102 2.34e-02 1.83e+03 1.91e+01 bond pdb=" N GLN C 271 " pdb=" CA GLN C 271 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.65e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.416 -0.082 2.34e-02 1.83e+03 1.23e+01 bond pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N VAL d 33 " pdb=" CA VAL d 33 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.89e+00 ... (remaining 32103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 42699 2.31 - 4.62: 875 4.62 - 6.93: 91 6.93 - 9.23: 22 9.23 - 11.54: 9 Bond angle restraints: 43696 Sorted by residual: angle pdb=" C VAL C 524 " pdb=" N CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 132.68 -11.14 1.91e+00 2.74e-01 3.40e+01 angle pdb=" C GLY B 639 " pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 121.54 131.99 -10.45 1.91e+00 2.74e-01 3.00e+01 angle pdb=" N SER B 161 " pdb=" CA SER B 161 " pdb=" C SER B 161 " ideal model delta sigma weight residual 111.04 102.66 8.38 1.55e+00 4.16e-01 2.92e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 ... (remaining 43691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.49: 18535 14.49 - 28.98: 489 28.98 - 43.47: 119 43.47 - 57.97: 18 57.97 - 72.46: 15 Dihedral angle restraints: 19176 sinusoidal: 7466 harmonic: 11710 Sorted by residual: dihedral pdb=" CA LYS C 795 " pdb=" C LYS C 795 " pdb=" N TYR C 796 " pdb=" CA TYR C 796 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA CYS C 525 " pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ARG C 634 " pdb=" C ARG C 634 " pdb=" N VAL C 635 " pdb=" CA VAL C 635 " ideal model delta harmonic sigma weight residual 180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 19173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4292 0.082 - 0.163: 593 0.163 - 0.245: 44 0.245 - 0.327: 5 0.327 - 0.408: 1 Chirality restraints: 4935 Sorted by residual: chirality pdb=" CA VAL B 159 " pdb=" N VAL B 159 " pdb=" C VAL B 159 " pdb=" CB VAL B 159 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB ILE A 312 " pdb=" CA ILE A 312 " pdb=" CG1 ILE A 312 " pdb=" CG2 ILE A 312 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4932 not shown) Planarity restraints: 5629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 266 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR A 266 " 0.061 2.00e-02 2.50e+03 pdb=" O TYR A 266 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 267 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 22 " -0.016 2.00e-02 2.50e+03 3.11e-02 9.68e+00 pdb=" C THR B 22 " 0.054 2.00e-02 2.50e+03 pdb=" O THR B 22 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN B 23 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 23 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C GLN C 23 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN C 23 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 24 " 0.017 2.00e-02 2.50e+03 ... (remaining 5626 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9878 2.86 - 3.37: 23783 3.37 - 3.88: 50617 3.88 - 4.39: 52037 4.39 - 4.90: 94601 Nonbonded interactions: 230916 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.353 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.354 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.356 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.356 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.360 3.040 ... (remaining 230911 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'b' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.390 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 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 : 0.005 0.102 32154 Z= 0.252 Angle : 0.794 11.544 43788 Z= 0.464 Chirality : 0.054 0.408 4935 Planarity : 0.006 0.072 5629 Dihedral : 8.145 66.816 11498 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.14 % Rotamer: Outliers : 0.23 % Allowed : 0.71 % Favored : 99.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.11), residues: 3961 helix: -4.92 (0.06), residues: 522 sheet: -0.32 (0.14), residues: 963 loop : -1.59 (0.10), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1039 TYR 0.019 0.002 TYR a 103 PHE 0.027 0.003 PHE B 490 TRP 0.020 0.002 TRP a 33 HIS 0.015 0.002 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00466 (32108) covalent geometry : angle 0.79397 (43696) SS BOND : bond 0.00196 ( 46) SS BOND : angle 0.81570 ( 92) hydrogen bonds : bond 0.32888 ( 901) hydrogen bonds : angle 11.26990 ( 2469) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 950 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8321 (t80) cc_final: 0.8092 (t80) REVERT: A 206 LYS cc_start: 0.7858 (tptt) cc_final: 0.7628 (tppt) REVERT: A 277 LEU cc_start: 0.8671 (mt) cc_final: 0.8410 (mp) REVERT: A 339 ASP cc_start: 0.8599 (m-30) cc_final: 0.8115 (t70) REVERT: A 385 THR cc_start: 0.8976 (p) cc_final: 0.8740 (p) REVERT: A 386 LYS cc_start: 0.7920 (mttt) cc_final: 0.7636 (mttt) REVERT: A 546 LEU cc_start: 0.8168 (tt) cc_final: 0.7888 (tt) REVERT: A 654 GLU cc_start: 0.7923 (tt0) cc_final: 0.7555 (tt0) REVERT: A 663 ASP cc_start: 0.7020 (m-30) cc_final: 0.6810 (m-30) REVERT: A 743 CYS cc_start: 0.6662 (m) cc_final: 0.6110 (m) REVERT: A 780 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 814 LYS cc_start: 0.8694 (mttt) cc_final: 0.8426 (mmmt) REVERT: A 964 LYS cc_start: 0.8639 (mttt) cc_final: 0.8373 (tppt) REVERT: A 1033 VAL cc_start: 0.7823 (t) cc_final: 0.7599 (t) REVERT: C 49 HIS cc_start: 0.7202 (t70) cc_final: 0.6791 (t70) REVERT: C 106 PHE cc_start: 0.7284 (m-10) cc_final: 0.6745 (m-10) REVERT: C 115 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7080 (mt0) REVERT: C 206 LYS cc_start: 0.7726 (tptt) cc_final: 0.7017 (tppt) REVERT: C 226 LEU cc_start: 0.7433 (tp) cc_final: 0.7209 (mt) REVERT: C 270 LEU cc_start: 0.8053 (mt) cc_final: 0.7731 (mt) REVERT: C 305 SER cc_start: 0.8796 (p) cc_final: 0.8462 (t) REVERT: C 338 PHE cc_start: 0.6882 (m-10) cc_final: 0.6099 (m-10) REVERT: C 339 ASP cc_start: 0.7535 (m-30) cc_final: 0.7299 (m-30) REVERT: C 540 ASN cc_start: 0.6191 (m-40) cc_final: 0.5990 (t0) REVERT: C 552 LEU cc_start: 0.7639 (mt) cc_final: 0.7254 (mt) REVERT: C 585 LEU cc_start: 0.6596 (mt) cc_final: 0.6391 (mt) REVERT: C 654 GLU cc_start: 0.7724 (tt0) cc_final: 0.7459 (tt0) REVERT: C 719 THR cc_start: 0.8078 (t) cc_final: 0.7766 (p) REVERT: C 725 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6287 (mt-10) REVERT: C 747 THR cc_start: 0.8021 (p) cc_final: 0.7717 (p) REVERT: C 751 ASN cc_start: 0.8597 (m-40) cc_final: 0.8343 (m-40) REVERT: C 775 ASP cc_start: 0.8079 (m-30) cc_final: 0.7800 (m-30) REVERT: C 780 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7276 (mt-10) REVERT: C 867 ASP cc_start: 0.8135 (m-30) cc_final: 0.7889 (m-30) REVERT: C 884 SER cc_start: 0.8491 (m) cc_final: 0.8228 (p) REVERT: C 894 LEU cc_start: 0.7091 (mp) cc_final: 0.6639 (mp) REVERT: C 953 ASN cc_start: 0.8447 (m-40) cc_final: 0.8036 (m-40) REVERT: C 969 LYS cc_start: 0.8471 (mttt) cc_final: 0.8152 (mmtm) REVERT: C 990 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7370 (mt-10) REVERT: C 1017 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 1051 SER cc_start: 0.8598 (m) cc_final: 0.8218 (p) REVERT: C 1061 VAL cc_start: 0.8763 (t) cc_final: 0.8505 (p) REVERT: C 1073 LYS cc_start: 0.8215 (tttt) cc_final: 0.8005 (tttp) REVERT: C 1084 ASP cc_start: 0.7502 (p0) cc_final: 0.6937 (p0) REVERT: C 1125 ASN cc_start: 0.8152 (p0) cc_final: 0.7943 (p0) REVERT: c 102 ASP cc_start: 0.3369 (OUTLIER) cc_final: 0.3058 (t0) REVERT: B 33 THR cc_start: 0.8330 (p) cc_final: 0.8077 (t) REVERT: B 36 VAL cc_start: 0.8765 (t) cc_final: 0.8456 (p) REVERT: B 55 PHE cc_start: 0.7334 (m-10) cc_final: 0.6592 (m-10) REVERT: B 106 PHE cc_start: 0.6238 (m-10) cc_final: 0.5981 (m-80) REVERT: B 119 ILE cc_start: 0.8889 (mt) cc_final: 0.8329 (mm) REVERT: B 127 VAL cc_start: 0.8617 (t) cc_final: 0.8310 (m) REVERT: B 189 LEU cc_start: 0.8591 (tp) cc_final: 0.8297 (tp) REVERT: B 221 SER cc_start: 0.8752 (t) cc_final: 0.8378 (m) REVERT: B 296 LEU cc_start: 0.8734 (tp) cc_final: 0.8483 (tp) REVERT: B 309 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7258 (mt-10) REVERT: B 492 LEU cc_start: 0.8337 (tp) cc_final: 0.8029 (pt) REVERT: B 534 VAL cc_start: 0.7721 (t) cc_final: 0.7293 (m) REVERT: B 535 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7636 (tmtt) REVERT: B 654 GLU cc_start: 0.7420 (tt0) cc_final: 0.7166 (tt0) REVERT: B 658 ASN cc_start: 0.8919 (m-40) cc_final: 0.8026 (m-40) REVERT: B 664 ILE cc_start: 0.8433 (mp) cc_final: 0.8057 (tt) REVERT: B 721 SER cc_start: 0.7856 (t) cc_final: 0.7323 (p) REVERT: B 740 MET cc_start: 0.7478 (mtp) cc_final: 0.7255 (mtt) REVERT: B 969 LYS cc_start: 0.8549 (mttt) cc_final: 0.8074 (mttm) REVERT: B 979 ASP cc_start: 0.8231 (m-30) cc_final: 0.7371 (m-30) REVERT: B 990 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7924 (mt-10) REVERT: B 1000 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7344 (mtm-85) REVERT: B 1073 LYS cc_start: 0.8083 (tttt) cc_final: 0.7822 (mtpp) REVERT: B 1106 GLN cc_start: 0.6251 (mm-40) cc_final: 0.6045 (mm-40) REVERT: B 1116 THR cc_start: 0.7278 (p) cc_final: 0.7015 (p) REVERT: B 1119 ASN cc_start: 0.7925 (m-40) cc_final: 0.7546 (m110) REVERT: a 33 TRP cc_start: 0.4326 (m-10) cc_final: 0.3416 (m-10) REVERT: a 61 ASN cc_start: 0.8206 (t0) cc_final: 0.7436 (t0) REVERT: a 69 THR cc_start: 0.7032 (m) cc_final: 0.6610 (p) REVERT: a 81 MET cc_start: 0.4890 (ttp) cc_final: 0.3031 (ttp) REVERT: b 43 LYS cc_start: 0.8017 (mttt) cc_final: 0.7816 (mmtt) REVERT: b 53 TYR cc_start: 0.6516 (p90) cc_final: 0.6289 (p90) REVERT: b 140 LEU cc_start: 0.5156 (mp) cc_final: 0.4613 (mp) outliers start: 8 outliers final: 4 residues processed: 958 average time/residue: 0.2123 time to fit residues: 318.5423 Evaluate side-chains 681 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 676 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain d residue 34 TYR Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain B residue 161 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.0570 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0170 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 188 ASN A 505 HIS A 675 GLN A 710 ASN A 755 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1048 HIS A1054 GLN A1088 HIS C 317 ASN C 343 ASN C 394 ASN C 519 HIS C 717 ASN C1054 GLN C1088 HIS C1106 GLN c 52 HIS d 6 GLN ** d 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 170 GLN B 505 HIS B 544 ASN B 717 ASN B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1113 GLN a 171 HIS b 93 HIS ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.189855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.150536 restraints weight = 78611.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.154705 restraints weight = 38950.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.157346 restraints weight = 23433.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.159027 restraints weight = 16321.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.160107 restraints weight = 12773.882| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 32154 Z= 0.138 Angle : 0.633 10.715 43788 Z= 0.334 Chirality : 0.045 0.291 4935 Planarity : 0.006 0.220 5629 Dihedral : 4.808 48.088 4319 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.84 % Favored : 98.06 % Rotamer: Outliers : 2.02 % Allowed : 8.18 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.11), residues: 3961 helix: -2.54 (0.16), residues: 591 sheet: 0.28 (0.15), residues: 984 loop : -1.36 (0.11), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 237 TYR 0.025 0.001 TYR B1110 PHE 0.037 0.002 PHE C 400 TRP 0.031 0.002 TRP a 36 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00307 (32108) covalent geometry : angle 0.63228 (43696) SS BOND : bond 0.00377 ( 46) SS BOND : angle 0.86099 ( 92) hydrogen bonds : bond 0.05268 ( 901) hydrogen bonds : angle 7.11999 ( 2469) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 710 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6807 (t80) cc_final: 0.6415 (t80) REVERT: A 195 LYS cc_start: 0.2925 (mmmt) cc_final: 0.2569 (tptp) REVERT: A 204 TYR cc_start: 0.6943 (m-80) cc_final: 0.6682 (m-80) REVERT: A 275 PHE cc_start: 0.7919 (m-80) cc_final: 0.7674 (m-80) REVERT: A 339 ASP cc_start: 0.8491 (m-30) cc_final: 0.8119 (t0) REVERT: A 386 LYS cc_start: 0.8067 (mttt) cc_final: 0.7736 (ptpt) REVERT: A 546 LEU cc_start: 0.8168 (tt) cc_final: 0.7865 (tt) REVERT: A 654 GLU cc_start: 0.7518 (tt0) cc_final: 0.7238 (tt0) REVERT: A 721 SER cc_start: 0.8060 (t) cc_final: 0.7645 (p) REVERT: A 823 PHE cc_start: 0.7962 (t80) cc_final: 0.7702 (t80) REVERT: A 883 THR cc_start: 0.8197 (m) cc_final: 0.7240 (p) REVERT: A 935 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7731 (mm-40) REVERT: A 955 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8756 (t0) REVERT: A 964 LYS cc_start: 0.8382 (mttt) cc_final: 0.8172 (tppt) REVERT: A 969 LYS cc_start: 0.8413 (mttt) cc_final: 0.8006 (mmtm) REVERT: A 1010 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7979 (mp10) REVERT: A 1031 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7098 (mm-30) REVERT: A 1072 GLU cc_start: 0.8849 (pm20) cc_final: 0.8534 (pm20) REVERT: A 1081 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7786 (mm) REVERT: A 1119 ASN cc_start: 0.8236 (m-40) cc_final: 0.7870 (m-40) REVERT: C 98 SER cc_start: 0.8359 (p) cc_final: 0.7964 (m) REVERT: C 192 PHE cc_start: 0.7708 (m-10) cc_final: 0.7190 (m-10) REVERT: C 195 LYS cc_start: 0.5537 (mmmt) cc_final: 0.5011 (mmmt) REVERT: C 224 GLU cc_start: 0.8320 (mp0) cc_final: 0.8092 (mp0) REVERT: C 226 LEU cc_start: 0.7642 (tp) cc_final: 0.7333 (mm) REVERT: C 269 TYR cc_start: 0.5142 (m-80) cc_final: 0.4898 (m-80) REVERT: C 298 GLU cc_start: 0.8690 (tp30) cc_final: 0.8169 (tm-30) REVERT: C 305 SER cc_start: 0.8850 (p) cc_final: 0.8598 (t) REVERT: C 396 TYR cc_start: 0.7904 (m-10) cc_final: 0.7616 (m-10) REVERT: C 509 ARG cc_start: 0.5086 (tmt170) cc_final: 0.4723 (ptm-80) REVERT: C 528 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7752 (mmtt) REVERT: C 643 PHE cc_start: 0.8228 (t80) cc_final: 0.8009 (t80) REVERT: C 654 GLU cc_start: 0.7410 (tt0) cc_final: 0.7162 (tt0) REVERT: C 725 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6386 (mt-10) REVERT: C 747 THR cc_start: 0.7980 (p) cc_final: 0.7721 (p) REVERT: C 775 ASP cc_start: 0.7965 (m-30) cc_final: 0.7683 (m-30) REVERT: C 884 SER cc_start: 0.8597 (m) cc_final: 0.8259 (p) REVERT: C 900 MET cc_start: 0.8391 (tpp) cc_final: 0.8104 (mtp) REVERT: C 990 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7028 (mt-10) REVERT: C 1031 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7483 (mm-30) REVERT: C 1051 SER cc_start: 0.8630 (m) cc_final: 0.8410 (p) REVERT: c 106 TRP cc_start: 0.6051 (p90) cc_final: 0.5737 (p90) REVERT: d 125 SER cc_start: 0.4287 (p) cc_final: 0.4069 (t) REVERT: B 36 VAL cc_start: 0.8888 (t) cc_final: 0.8555 (p) REVERT: B 55 PHE cc_start: 0.7332 (m-10) cc_final: 0.6841 (m-10) REVERT: B 106 PHE cc_start: 0.6307 (m-10) cc_final: 0.5934 (m-80) REVERT: B 127 VAL cc_start: 0.8834 (t) cc_final: 0.8448 (p) REVERT: B 133 PHE cc_start: 0.6905 (m-10) cc_final: 0.6560 (m-10) REVERT: B 204 TYR cc_start: 0.6511 (m-80) cc_final: 0.6267 (m-80) REVERT: B 221 SER cc_start: 0.8716 (t) cc_final: 0.8435 (m) REVERT: B 223 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7346 (mm) REVERT: B 298 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8347 (tp30) REVERT: B 309 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6936 (mt-10) REVERT: B 342 PHE cc_start: 0.7083 (t80) cc_final: 0.6808 (t80) REVERT: B 365 TYR cc_start: 0.7376 (m-80) cc_final: 0.7045 (m-80) REVERT: B 386 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7837 (mtmt) REVERT: B 492 LEU cc_start: 0.8434 (tp) cc_final: 0.8019 (pt) REVERT: B 581 THR cc_start: 0.5580 (p) cc_final: 0.4108 (m) REVERT: B 721 SER cc_start: 0.8585 (t) cc_final: 0.8365 (t) REVERT: B 978 ASN cc_start: 0.7929 (p0) cc_final: 0.7694 (p0) REVERT: B 979 ASP cc_start: 0.8177 (m-30) cc_final: 0.7511 (m-30) REVERT: B 980 ILE cc_start: 0.8765 (mt) cc_final: 0.8551 (mm) REVERT: B 1017 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 1073 LYS cc_start: 0.8352 (tttt) cc_final: 0.8048 (mtpp) REVERT: B 1106 GLN cc_start: 0.6359 (mm-40) cc_final: 0.5946 (mm-40) REVERT: B 1116 THR cc_start: 0.7463 (p) cc_final: 0.7202 (p) REVERT: B 1119 ASN cc_start: 0.8273 (m-40) cc_final: 0.7962 (m110) REVERT: a 34 MET cc_start: 0.7251 (mpp) cc_final: 0.7035 (mmm) REVERT: a 96 CYS cc_start: 0.3092 (p) cc_final: 0.2482 (m) REVERT: a 161 TRP cc_start: 0.4836 (m-90) cc_final: 0.4537 (m-90) REVERT: a 181 LEU cc_start: 0.7758 (tp) cc_final: 0.7551 (tp) REVERT: b 53 TYR cc_start: 0.6588 (p90) cc_final: 0.6328 (p90) outliers start: 71 outliers final: 39 residues processed: 748 average time/residue: 0.1983 time to fit residues: 237.7623 Evaluate side-chains 645 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 603 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 84 optimal weight: 4.9990 chunk 165 optimal weight: 0.1980 chunk 238 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 327 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 302 optimal weight: 2.9990 chunk 389 optimal weight: 10.0000 chunk 365 optimal weight: 4.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 717 ASN A 787 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1058 HIS A1088 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN d 38 HIS B 61 ASN B 239 GLN B 334 ASN B 895 GLN B 907 ASN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.188095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.150759 restraints weight = 77811.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.155130 restraints weight = 38042.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.157931 restraints weight = 22567.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.159722 restraints weight = 15347.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.160976 restraints weight = 11711.075| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 32154 Z= 0.136 Angle : 0.588 10.549 43788 Z= 0.304 Chirality : 0.045 0.315 4935 Planarity : 0.004 0.120 5629 Dihedral : 4.465 44.341 4313 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 2.08 % Allowed : 10.86 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 3961 helix: -1.00 (0.19), residues: 615 sheet: 0.54 (0.15), residues: 998 loop : -1.09 (0.11), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 237 TYR 0.020 0.001 TYR B1138 PHE 0.021 0.002 PHE C 133 TRP 0.051 0.002 TRP a 36 HIS 0.017 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00302 (32108) covalent geometry : angle 0.58725 (43696) SS BOND : bond 0.00297 ( 46) SS BOND : angle 0.97490 ( 92) hydrogen bonds : bond 0.04385 ( 901) hydrogen bonds : angle 6.21259 ( 2469) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 668 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7089 (t80) cc_final: 0.6664 (t80) REVERT: A 195 LYS cc_start: 0.3073 (mmmt) cc_final: 0.1718 (mmmt) REVERT: A 204 TYR cc_start: 0.7622 (m-80) cc_final: 0.7408 (m-80) REVERT: A 226 LEU cc_start: 0.8106 (tp) cc_final: 0.7731 (mt) REVERT: A 258 TRP cc_start: 0.4678 (m100) cc_final: 0.3757 (m-10) REVERT: A 275 PHE cc_start: 0.8108 (m-10) cc_final: 0.7859 (m-80) REVERT: A 290 ASP cc_start: 0.8163 (t0) cc_final: 0.7772 (t0) REVERT: A 339 ASP cc_start: 0.8487 (m-30) cc_final: 0.8060 (t70) REVERT: A 543 PHE cc_start: 0.8147 (m-80) cc_final: 0.7867 (m-80) REVERT: A 546 LEU cc_start: 0.8295 (tt) cc_final: 0.7980 (tt) REVERT: A 654 GLU cc_start: 0.7574 (tt0) cc_final: 0.7342 (tt0) REVERT: A 696 THR cc_start: 0.8834 (m) cc_final: 0.8407 (p) REVERT: A 721 SER cc_start: 0.8295 (t) cc_final: 0.7842 (p) REVERT: A 764 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8212 (ttpp) REVERT: A 814 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8416 (mmmt) REVERT: A 823 PHE cc_start: 0.8089 (t80) cc_final: 0.7872 (t80) REVERT: A 884 SER cc_start: 0.8348 (m) cc_final: 0.8070 (t) REVERT: A 935 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7993 (mm-40) REVERT: A 965 GLN cc_start: 0.8260 (tp40) cc_final: 0.8030 (tp40) REVERT: A 969 LYS cc_start: 0.8514 (mttt) cc_final: 0.8064 (mmtm) REVERT: A 1031 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7163 (mm-30) REVERT: A 1045 LYS cc_start: 0.8776 (mmmm) cc_final: 0.8555 (mmmm) REVERT: A 1072 GLU cc_start: 0.8877 (pm20) cc_final: 0.8621 (pm20) REVERT: A 1111 GLU cc_start: 0.8255 (tt0) cc_final: 0.7977 (mt-10) REVERT: A 1119 ASN cc_start: 0.8127 (m-40) cc_final: 0.7803 (m-40) REVERT: C 106 PHE cc_start: 0.7203 (m-10) cc_final: 0.6844 (m-10) REVERT: C 194 PHE cc_start: 0.7880 (m-10) cc_final: 0.7525 (m-80) REVERT: C 226 LEU cc_start: 0.7731 (tp) cc_final: 0.7351 (mm) REVERT: C 298 GLU cc_start: 0.8735 (tp30) cc_final: 0.8215 (tm-30) REVERT: C 305 SER cc_start: 0.8913 (p) cc_final: 0.8686 (t) REVERT: C 509 ARG cc_start: 0.5066 (tmt170) cc_final: 0.4654 (ptm-80) REVERT: C 565 PHE cc_start: 0.7648 (p90) cc_final: 0.7418 (p90) REVERT: C 613 GLN cc_start: 0.7229 (pt0) cc_final: 0.6880 (pt0) REVERT: C 643 PHE cc_start: 0.8188 (t80) cc_final: 0.7985 (t80) REVERT: C 654 GLU cc_start: 0.7304 (tt0) cc_final: 0.7039 (tt0) REVERT: C 725 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6532 (mt-10) REVERT: C 884 SER cc_start: 0.8560 (m) cc_final: 0.8120 (t) REVERT: C 902 MET cc_start: 0.8953 (mmt) cc_final: 0.8573 (mmt) REVERT: C 990 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6978 (mt-10) REVERT: C 1019 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7287 (tpp-160) REVERT: C 1031 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7520 (mm-30) REVERT: B 36 VAL cc_start: 0.8942 (t) cc_final: 0.8623 (p) REVERT: B 54 LEU cc_start: 0.8779 (mm) cc_final: 0.8481 (mm) REVERT: B 55 PHE cc_start: 0.7495 (m-10) cc_final: 0.7023 (m-10) REVERT: B 106 PHE cc_start: 0.6463 (m-10) cc_final: 0.6151 (m-80) REVERT: B 119 ILE cc_start: 0.8829 (mm) cc_final: 0.8354 (mm) REVERT: B 133 PHE cc_start: 0.7704 (m-80) cc_final: 0.6949 (m-10) REVERT: B 159 VAL cc_start: 0.4492 (m) cc_final: 0.3333 (t) REVERT: B 221 SER cc_start: 0.8750 (t) cc_final: 0.8539 (m) REVERT: B 223 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7676 (mm) REVERT: B 270 LEU cc_start: 0.7848 (mm) cc_final: 0.7545 (mm) REVERT: B 298 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8308 (tp30) REVERT: B 309 GLU cc_start: 0.7223 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 386 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8100 (pttt) REVERT: B 537 LYS cc_start: 0.9111 (tptt) cc_final: 0.8689 (tptt) REVERT: B 654 GLU cc_start: 0.6791 (mp0) cc_final: 0.6528 (mp0) REVERT: B 765 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7846 (ttp-170) REVERT: B 773 GLU cc_start: 0.8193 (tt0) cc_final: 0.7482 (tm-30) REVERT: B 954 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.8290 (m170) REVERT: B 969 LYS cc_start: 0.8685 (mttt) cc_final: 0.8276 (mtpp) REVERT: B 978 ASN cc_start: 0.8088 (p0) cc_final: 0.7609 (p0) REVERT: B 979 ASP cc_start: 0.8154 (m-30) cc_final: 0.7578 (m-30) REVERT: B 990 GLU cc_start: 0.7810 (pt0) cc_final: 0.7576 (pp20) REVERT: B 1017 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7604 (tm-30) REVERT: B 1073 LYS cc_start: 0.8398 (tttt) cc_final: 0.8152 (mtpp) REVERT: B 1106 GLN cc_start: 0.6458 (mm-40) cc_final: 0.6126 (mm-40) REVERT: B 1119 ASN cc_start: 0.8619 (m-40) cc_final: 0.8261 (m110) REVERT: a 4 LEU cc_start: 0.6526 (mp) cc_final: 0.6154 (mm) REVERT: a 161 TRP cc_start: 0.5095 (m-90) cc_final: 0.4814 (m-90) REVERT: b 53 TYR cc_start: 0.6831 (p90) cc_final: 0.6409 (p90) REVERT: b 171 ASP cc_start: 0.6950 (t70) cc_final: 0.6644 (p0) outliers start: 73 outliers final: 48 residues processed: 713 average time/residue: 0.1987 time to fit residues: 225.5238 Evaluate side-chains 661 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 611 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 174 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 348 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 343 optimal weight: 0.5980 chunk 258 optimal weight: 0.6980 chunk 33 optimal weight: 0.0030 chunk 169 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 342 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 188 ASN A 690 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1048 HIS A1113 GLN C 115 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN B 61 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.183758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.142344 restraints weight = 76503.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.146611 restraints weight = 38104.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.149212 restraints weight = 23055.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.150906 restraints weight = 16294.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.151964 restraints weight = 12860.388| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32154 Z= 0.123 Angle : 0.578 10.434 43788 Z= 0.295 Chirality : 0.044 0.273 4935 Planarity : 0.004 0.099 5629 Dihedral : 4.286 27.906 4311 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.80 % Rotamer: Outliers : 2.31 % Allowed : 12.43 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.12), residues: 3961 helix: -0.12 (0.21), residues: 617 sheet: 0.62 (0.15), residues: 993 loop : -0.98 (0.11), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 983 TYR 0.021 0.001 TYR B 655 PHE 0.024 0.001 PHE C 306 TRP 0.046 0.002 TRP a 36 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00279 (32108) covalent geometry : angle 0.57684 (43696) SS BOND : bond 0.00480 ( 46) SS BOND : angle 0.89462 ( 92) hydrogen bonds : bond 0.03848 ( 901) hydrogen bonds : angle 5.82730 ( 2469) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 639 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8356 (m) cc_final: 0.7900 (p) REVERT: A 135 PHE cc_start: 0.6887 (t80) cc_final: 0.6625 (t80) REVERT: A 195 LYS cc_start: 0.3718 (mmmt) cc_final: 0.3203 (pptt) REVERT: A 226 LEU cc_start: 0.7981 (tp) cc_final: 0.7617 (mt) REVERT: A 258 TRP cc_start: 0.4770 (m100) cc_final: 0.3782 (m-10) REVERT: A 275 PHE cc_start: 0.8079 (m-10) cc_final: 0.7827 (m-80) REVERT: A 339 ASP cc_start: 0.8400 (m-30) cc_final: 0.8026 (t70) REVERT: A 546 LEU cc_start: 0.8278 (tt) cc_final: 0.7961 (tt) REVERT: A 654 GLU cc_start: 0.7512 (tt0) cc_final: 0.7251 (tt0) REVERT: A 696 THR cc_start: 0.8792 (m) cc_final: 0.8473 (p) REVERT: A 764 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8207 (ttpp) REVERT: A 814 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8356 (mmmt) REVERT: A 819 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 823 PHE cc_start: 0.8160 (t80) cc_final: 0.7874 (t80) REVERT: A 868 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 878 LEU cc_start: 0.8444 (tp) cc_final: 0.8214 (tt) REVERT: A 884 SER cc_start: 0.8429 (m) cc_final: 0.8185 (t) REVERT: A 1031 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 1111 GLU cc_start: 0.8301 (tt0) cc_final: 0.7935 (mt-10) REVERT: A 1119 ASN cc_start: 0.8066 (m-40) cc_final: 0.7799 (m110) REVERT: C 64 TRP cc_start: 0.4874 (t60) cc_final: 0.4644 (t60) REVERT: C 190 ARG cc_start: 0.2797 (tpt170) cc_final: 0.1686 (tpp80) REVERT: C 277 LEU cc_start: 0.8826 (mm) cc_final: 0.8590 (mp) REVERT: C 338 PHE cc_start: 0.7495 (t80) cc_final: 0.7293 (t80) REVERT: C 396 TYR cc_start: 0.7896 (m-10) cc_final: 0.7381 (m-10) REVERT: C 509 ARG cc_start: 0.5143 (tmt170) cc_final: 0.4844 (tmt170) REVERT: C 533 LEU cc_start: 0.8772 (mt) cc_final: 0.8530 (mt) REVERT: C 613 GLN cc_start: 0.7305 (pt0) cc_final: 0.7032 (pt0) REVERT: C 643 PHE cc_start: 0.8170 (t80) cc_final: 0.7890 (t80) REVERT: C 654 GLU cc_start: 0.7347 (tt0) cc_final: 0.7087 (tt0) REVERT: C 725 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6739 (mt-10) REVERT: C 884 SER cc_start: 0.8539 (m) cc_final: 0.8143 (t) REVERT: C 935 GLN cc_start: 0.8029 (tp40) cc_final: 0.7427 (tm-30) REVERT: C 990 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6892 (mt-10) REVERT: C 1031 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7520 (mm-30) REVERT: c 81 MET cc_start: 0.5497 (ttp) cc_final: 0.5239 (mtp) REVERT: B 36 VAL cc_start: 0.8948 (t) cc_final: 0.8570 (m) REVERT: B 55 PHE cc_start: 0.7313 (m-10) cc_final: 0.6989 (m-10) REVERT: B 67 VAL cc_start: 0.6838 (OUTLIER) cc_final: 0.6523 (p) REVERT: B 133 PHE cc_start: 0.7381 (m-80) cc_final: 0.6845 (m-10) REVERT: B 190 ARG cc_start: 0.5854 (ttm170) cc_final: 0.5465 (ttm170) REVERT: B 194 PHE cc_start: 0.6449 (m-80) cc_final: 0.6157 (m-80) REVERT: B 223 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7726 (mm) REVERT: B 298 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8007 (tp30) REVERT: B 386 LYS cc_start: 0.8303 (mtmt) cc_final: 0.8062 (pttt) REVERT: B 515 PHE cc_start: 0.6873 (m-10) cc_final: 0.6646 (m-10) REVERT: B 537 LYS cc_start: 0.9125 (tptt) cc_final: 0.8887 (tmtt) REVERT: B 654 GLU cc_start: 0.6562 (mp0) cc_final: 0.6318 (mp0) REVERT: B 748 GLU cc_start: 0.8275 (pm20) cc_final: 0.7959 (pt0) REVERT: B 765 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7843 (ttp-170) REVERT: B 773 GLU cc_start: 0.8139 (tt0) cc_final: 0.7456 (tm-30) REVERT: B 776 LYS cc_start: 0.8703 (tttt) cc_final: 0.8363 (tmtt) REVERT: B 969 LYS cc_start: 0.8726 (mttt) cc_final: 0.8311 (mtpp) REVERT: B 978 ASN cc_start: 0.8200 (p0) cc_final: 0.7852 (p0) REVERT: B 979 ASP cc_start: 0.8261 (m-30) cc_final: 0.7578 (m-30) REVERT: B 1017 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 1106 GLN cc_start: 0.6639 (mm-40) cc_final: 0.6329 (mm-40) REVERT: B 1119 ASN cc_start: 0.8639 (m-40) cc_final: 0.8367 (m110) REVERT: a 34 MET cc_start: 0.7627 (mmm) cc_final: 0.7373 (mmt) REVERT: a 50 MET cc_start: 0.7746 (ttp) cc_final: 0.7510 (ttp) REVERT: a 161 TRP cc_start: 0.5134 (m-90) cc_final: 0.4815 (m-90) REVERT: b 49 LYS cc_start: 0.7333 (mttt) cc_final: 0.7090 (mttt) outliers start: 81 outliers final: 49 residues processed: 692 average time/residue: 0.2149 time to fit residues: 236.8098 Evaluate side-chains 648 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 597 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 333 optimal weight: 2.9990 chunk 352 optimal weight: 0.9980 chunk 229 optimal weight: 0.0870 chunk 147 optimal weight: 2.9990 chunk 324 optimal weight: 0.7980 chunk 262 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.182290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.140381 restraints weight = 77009.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.144606 restraints weight = 38242.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.147207 restraints weight = 23152.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.148903 restraints weight = 16360.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.149953 restraints weight = 12907.834| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32154 Z= 0.116 Angle : 0.565 11.011 43788 Z= 0.288 Chirality : 0.044 0.256 4935 Planarity : 0.004 0.079 5629 Dihedral : 4.203 26.825 4311 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.97 % Favored : 97.93 % Rotamer: Outliers : 2.00 % Allowed : 13.48 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 3961 helix: 0.33 (0.21), residues: 635 sheet: 0.79 (0.16), residues: 944 loop : -0.95 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 765 TYR 0.021 0.001 TYR B1138 PHE 0.030 0.001 PHE A 515 TRP 0.045 0.002 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00263 (32108) covalent geometry : angle 0.56369 (43696) SS BOND : bond 0.00493 ( 46) SS BOND : angle 1.02315 ( 92) hydrogen bonds : bond 0.03582 ( 901) hydrogen bonds : angle 5.58490 ( 2469) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 636 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8384 (m) cc_final: 0.7931 (p) REVERT: A 226 LEU cc_start: 0.8006 (tp) cc_final: 0.7723 (mm) REVERT: A 258 TRP cc_start: 0.4826 (m100) cc_final: 0.3875 (m-10) REVERT: A 275 PHE cc_start: 0.8078 (m-10) cc_final: 0.7873 (m-80) REVERT: A 338 PHE cc_start: 0.5224 (m-80) cc_final: 0.4895 (m-80) REVERT: A 339 ASP cc_start: 0.8406 (m-30) cc_final: 0.8074 (t70) REVERT: A 546 LEU cc_start: 0.8306 (tt) cc_final: 0.7999 (tt) REVERT: A 654 GLU cc_start: 0.7531 (tt0) cc_final: 0.7266 (tt0) REVERT: A 748 GLU cc_start: 0.8236 (pt0) cc_final: 0.7966 (pt0) REVERT: A 764 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8210 (ttpp) REVERT: A 814 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8487 (mmmt) REVERT: A 819 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7398 (mt-10) REVERT: A 823 PHE cc_start: 0.8207 (t80) cc_final: 0.7913 (t80) REVERT: A 868 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6864 (tm-30) REVERT: A 884 SER cc_start: 0.8420 (m) cc_final: 0.8146 (t) REVERT: A 918 GLU cc_start: 0.7772 (mp0) cc_final: 0.7563 (mp0) REVERT: A 935 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7721 (mm-40) REVERT: A 969 LYS cc_start: 0.8600 (mttt) cc_final: 0.8056 (mmtp) REVERT: A 1031 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 1072 GLU cc_start: 0.8801 (pm20) cc_final: 0.8568 (pm20) REVERT: A 1097 SER cc_start: 0.8876 (t) cc_final: 0.8598 (p) REVERT: A 1111 GLU cc_start: 0.8336 (tt0) cc_final: 0.7978 (mt-10) REVERT: C 64 TRP cc_start: 0.5027 (t60) cc_final: 0.4826 (t60) REVERT: C 277 LEU cc_start: 0.8846 (mm) cc_final: 0.8594 (mp) REVERT: C 294 ASP cc_start: 0.8163 (m-30) cc_final: 0.7677 (p0) REVERT: C 298 GLU cc_start: 0.8832 (tp30) cc_final: 0.8205 (tm-30) REVERT: C 613 GLN cc_start: 0.7380 (pt0) cc_final: 0.7146 (pt0) REVERT: C 643 PHE cc_start: 0.8171 (t80) cc_final: 0.7894 (t80) REVERT: C 654 GLU cc_start: 0.7318 (tt0) cc_final: 0.7087 (tt0) REVERT: C 675 GLN cc_start: 0.8515 (pp30) cc_final: 0.8309 (pp30) REVERT: C 725 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6773 (mt-10) REVERT: C 884 SER cc_start: 0.8536 (m) cc_final: 0.8158 (t) REVERT: C 933 LYS cc_start: 0.8332 (mttt) cc_final: 0.8097 (mmmm) REVERT: C 935 GLN cc_start: 0.8130 (tp40) cc_final: 0.7585 (tm-30) REVERT: C 969 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8193 (mmmm) REVERT: C 983 ARG cc_start: 0.7098 (mmm-85) cc_final: 0.6804 (mmm160) REVERT: C 990 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6960 (mt-10) REVERT: C 1031 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7532 (mm-30) REVERT: c 50 MET cc_start: 0.5753 (ttp) cc_final: 0.5338 (mmt) REVERT: c 81 MET cc_start: 0.5555 (ttp) cc_final: 0.5293 (mtp) REVERT: B 36 VAL cc_start: 0.8968 (t) cc_final: 0.8616 (m) REVERT: B 49 HIS cc_start: 0.7430 (t-170) cc_final: 0.7218 (t-170) REVERT: B 67 VAL cc_start: 0.6815 (OUTLIER) cc_final: 0.6495 (p) REVERT: B 133 PHE cc_start: 0.7375 (m-80) cc_final: 0.6652 (m-10) REVERT: B 204 TYR cc_start: 0.6806 (m-80) cc_final: 0.6549 (m-80) REVERT: B 298 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8239 (tp30) REVERT: B 315 THR cc_start: 0.7910 (m) cc_final: 0.7637 (m) REVERT: B 386 LYS cc_start: 0.8314 (mtmt) cc_final: 0.8091 (pttt) REVERT: B 515 PHE cc_start: 0.6991 (m-10) cc_final: 0.6707 (m-10) REVERT: B 537 LYS cc_start: 0.9211 (tptt) cc_final: 0.8988 (tmtt) REVERT: B 773 GLU cc_start: 0.8114 (tt0) cc_final: 0.7464 (tm-30) REVERT: B 776 LYS cc_start: 0.8732 (tttt) cc_final: 0.8416 (tmtt) REVERT: B 969 LYS cc_start: 0.8718 (mttt) cc_final: 0.8368 (mtpp) REVERT: B 978 ASN cc_start: 0.8190 (p0) cc_final: 0.7935 (p0) REVERT: B 979 ASP cc_start: 0.8297 (m-30) cc_final: 0.7588 (m-30) REVERT: B 984 LEU cc_start: 0.7580 (mt) cc_final: 0.7252 (tp) REVERT: B 988 GLU cc_start: 0.7569 (mp0) cc_final: 0.7345 (mp0) REVERT: B 1017 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 1119 ASN cc_start: 0.8653 (m-40) cc_final: 0.8412 (m110) REVERT: b 49 LYS cc_start: 0.7350 (mttt) cc_final: 0.7102 (mttt) REVERT: b 89 THR cc_start: 0.6626 (m) cc_final: 0.6239 (m) outliers start: 70 outliers final: 51 residues processed: 679 average time/residue: 0.1998 time to fit residues: 216.2543 Evaluate side-chains 653 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 601 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 224 optimal weight: 30.0000 chunk 332 optimal weight: 0.6980 chunk 259 optimal weight: 6.9990 chunk 174 optimal weight: 0.2980 chunk 307 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 226 optimal weight: 50.0000 chunk 287 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.178510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.138048 restraints weight = 76799.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.142216 restraints weight = 37574.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.144852 restraints weight = 22446.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.146555 restraints weight = 15538.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.147563 restraints weight = 12089.525| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32154 Z= 0.138 Angle : 0.575 10.298 43788 Z= 0.294 Chirality : 0.044 0.266 4935 Planarity : 0.004 0.081 5629 Dihedral : 4.219 26.281 4311 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 2.45 % Allowed : 14.17 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.13), residues: 3961 helix: 0.65 (0.22), residues: 632 sheet: 0.83 (0.16), residues: 961 loop : -0.88 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 577 TYR 0.021 0.001 TYR C1138 PHE 0.048 0.002 PHE A 497 TRP 0.050 0.002 TRP a 36 HIS 0.011 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00314 (32108) covalent geometry : angle 0.57360 (43696) SS BOND : bond 0.00338 ( 46) SS BOND : angle 1.08252 ( 92) hydrogen bonds : bond 0.03536 ( 901) hydrogen bonds : angle 5.39893 ( 2469) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 635 time to evaluate : 1.154 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 50 SER cc_start: 0.8369 (m) cc_final: 0.7942 (p) REVERT: A 200 TYR cc_start: 0.7272 (t80) cc_final: 0.6849 (t80) REVERT: A 226 LEU cc_start: 0.8028 (tp) cc_final: 0.7701 (pp) REVERT: A 338 PHE cc_start: 0.5486 (m-80) cc_final: 0.5128 (m-80) REVERT: A 339 ASP cc_start: 0.8419 (m-30) cc_final: 0.8084 (t70) REVERT: A 356 LYS cc_start: 0.6919 (mptt) cc_final: 0.6709 (mmtm) REVERT: A 546 LEU cc_start: 0.8434 (tt) cc_final: 0.8111 (tt) REVERT: A 654 GLU cc_start: 0.7523 (tt0) cc_final: 0.7293 (tt0) REVERT: A 675 GLN cc_start: 0.8413 (pp30) cc_final: 0.8189 (pp30) REVERT: A 739 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8604 (p) REVERT: A 764 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8225 (ttpp) REVERT: A 780 GLU cc_start: 0.7656 (tt0) cc_final: 0.7450 (tt0) REVERT: A 814 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8496 (mmmt) REVERT: A 819 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 821 LEU cc_start: 0.8342 (mt) cc_final: 0.7846 (mp) REVERT: A 823 PHE cc_start: 0.8247 (t80) cc_final: 0.7914 (t80) REVERT: A 868 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6885 (tm-30) REVERT: A 884 SER cc_start: 0.8453 (m) cc_final: 0.8130 (t) REVERT: A 900 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8181 (mtt) REVERT: A 935 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7691 (mm-40) REVERT: A 969 LYS cc_start: 0.8727 (mttt) cc_final: 0.8261 (mmtm) REVERT: A 1031 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7141 (mm-30) REVERT: A 1073 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8548 (mtpp) REVERT: A 1097 SER cc_start: 0.8905 (t) cc_final: 0.8618 (p) REVERT: C 49 HIS cc_start: 0.7380 (t70) cc_final: 0.7179 (t70) REVERT: C 190 ARG cc_start: 0.3224 (tpt170) cc_final: 0.2838 (mmt180) REVERT: C 203 ILE cc_start: 0.8552 (pt) cc_final: 0.8270 (mp) REVERT: C 277 LEU cc_start: 0.8917 (mm) cc_final: 0.8673 (mp) REVERT: C 298 GLU cc_start: 0.8865 (tp30) cc_final: 0.8335 (tm-30) REVERT: C 304 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8480 (tppt) REVERT: C 613 GLN cc_start: 0.7511 (pt0) cc_final: 0.7298 (pt0) REVERT: C 643 PHE cc_start: 0.8154 (t80) cc_final: 0.7876 (t80) REVERT: C 654 GLU cc_start: 0.7304 (tt0) cc_final: 0.7065 (tt0) REVERT: C 725 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6789 (mt-10) REVERT: C 816 SER cc_start: 0.8106 (p) cc_final: 0.7784 (p) REVERT: C 819 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7725 (mt-10) REVERT: C 884 SER cc_start: 0.8518 (m) cc_final: 0.8096 (t) REVERT: C 900 MET cc_start: 0.8727 (mtp) cc_final: 0.8480 (mtp) REVERT: C 902 MET cc_start: 0.8786 (mmt) cc_final: 0.8566 (mmt) REVERT: C 933 LYS cc_start: 0.8379 (mttt) cc_final: 0.8156 (mmmm) REVERT: C 935 GLN cc_start: 0.8105 (tp40) cc_final: 0.7588 (tm-30) REVERT: C 969 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8320 (mmmm) REVERT: C 990 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6944 (mt-10) REVERT: C 1107 ARG cc_start: 0.8348 (tpp80) cc_final: 0.8141 (tpp80) REVERT: C 1129 VAL cc_start: 0.8740 (t) cc_final: 0.8380 (m) REVERT: c 50 MET cc_start: 0.5966 (ttp) cc_final: 0.5645 (mmt) REVERT: c 81 MET cc_start: 0.5343 (ttp) cc_final: 0.5041 (mtp) REVERT: B 49 HIS cc_start: 0.7476 (t-170) cc_final: 0.7244 (t-170) REVERT: B 55 PHE cc_start: 0.7160 (m-10) cc_final: 0.6786 (m-10) REVERT: B 67 VAL cc_start: 0.6842 (OUTLIER) cc_final: 0.6521 (p) REVERT: B 119 ILE cc_start: 0.8928 (mm) cc_final: 0.8722 (mm) REVERT: B 129 LYS cc_start: 0.8551 (mttt) cc_final: 0.8273 (mmtm) REVERT: B 133 PHE cc_start: 0.7633 (m-80) cc_final: 0.6723 (m-80) REVERT: B 159 VAL cc_start: 0.4870 (OUTLIER) cc_final: 0.3464 (t) REVERT: B 204 TYR cc_start: 0.6957 (m-80) cc_final: 0.6648 (m-80) REVERT: B 223 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7853 (mm) REVERT: B 229 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 271 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8337 (mm-40) REVERT: B 315 THR cc_start: 0.8213 (m) cc_final: 0.7946 (m) REVERT: B 515 PHE cc_start: 0.7174 (m-10) cc_final: 0.6912 (m-10) REVERT: B 537 LYS cc_start: 0.9211 (tptt) cc_final: 0.8968 (tmtt) REVERT: B 558 LYS cc_start: 0.8254 (tmtt) cc_final: 0.7911 (tmtt) REVERT: B 603 ASN cc_start: 0.8149 (p0) cc_final: 0.7633 (p0) REVERT: B 690 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7640 (mm-40) REVERT: B 751 ASN cc_start: 0.8252 (m-40) cc_final: 0.7875 (m-40) REVERT: B 755 GLN cc_start: 0.8513 (mp10) cc_final: 0.8312 (mp10) REVERT: B 773 GLU cc_start: 0.8051 (tt0) cc_final: 0.7483 (tm-30) REVERT: B 776 LYS cc_start: 0.8807 (tttt) cc_final: 0.8482 (tmtt) REVERT: B 808 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.6872 (p0) REVERT: B 921 LYS cc_start: 0.8566 (mttt) cc_final: 0.8267 (mmtp) REVERT: B 969 LYS cc_start: 0.8728 (mttt) cc_final: 0.8393 (mtpp) REVERT: B 974 SER cc_start: 0.8261 (p) cc_final: 0.7740 (t) REVERT: B 978 ASN cc_start: 0.8208 (p0) cc_final: 0.7750 (p0) REVERT: B 979 ASP cc_start: 0.8272 (m-30) cc_final: 0.7624 (m-30) REVERT: B 984 LEU cc_start: 0.7773 (mt) cc_final: 0.7414 (tp) REVERT: B 1017 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 1119 ASN cc_start: 0.8665 (m-40) cc_final: 0.8390 (m110) REVERT: b 49 LYS cc_start: 0.7386 (mttt) cc_final: 0.7116 (mttt) outliers start: 86 outliers final: 62 residues processed: 681 average time/residue: 0.2034 time to fit residues: 219.2002 Evaluate side-chains 674 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 605 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 134 optimal weight: 3.9990 chunk 320 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 150 optimal weight: 0.0370 chunk 377 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 224 optimal weight: 30.0000 chunk 350 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 658 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1048 HIS A1088 HIS A1113 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 957 GLN C1010 GLN C1048 HIS C1083 HIS B 207 HIS B 343 ASN B1088 HIS B1113 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.168833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.126122 restraints weight = 74053.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.129830 restraints weight = 37127.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.132343 restraints weight = 22900.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.133988 restraints weight = 16400.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.134632 restraints weight = 13196.423| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.6929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 32154 Z= 0.290 Angle : 0.754 10.823 43788 Z= 0.391 Chirality : 0.049 0.303 4935 Planarity : 0.005 0.085 5629 Dihedral : 4.983 26.455 4311 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 3.34 % Allowed : 14.22 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 3961 helix: 0.22 (0.21), residues: 657 sheet: 0.44 (0.15), residues: 1045 loop : -1.07 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 319 TYR 0.039 0.002 TYR C 660 PHE 0.031 0.003 PHE B 906 TRP 0.062 0.003 TRP A 104 HIS 0.011 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00647 (32108) covalent geometry : angle 0.75041 (43696) SS BOND : bond 0.00899 ( 46) SS BOND : angle 1.68100 ( 92) hydrogen bonds : bond 0.04601 ( 901) hydrogen bonds : angle 5.91067 ( 2469) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 694 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8413 (m) cc_final: 0.8172 (p) REVERT: A 338 PHE cc_start: 0.6353 (m-80) cc_final: 0.5899 (m-80) REVERT: A 339 ASP cc_start: 0.8507 (m-30) cc_final: 0.8291 (t70) REVERT: A 532 ASN cc_start: 0.7758 (t0) cc_final: 0.7439 (t0) REVERT: A 537 LYS cc_start: 0.8847 (tptp) cc_final: 0.8582 (tmtt) REVERT: A 546 LEU cc_start: 0.8573 (tt) cc_final: 0.8265 (tt) REVERT: A 654 GLU cc_start: 0.7691 (tt0) cc_final: 0.7440 (tt0) REVERT: A 764 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8472 (ttmm) REVERT: A 780 GLU cc_start: 0.7679 (tt0) cc_final: 0.7445 (tt0) REVERT: A 814 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8011 (mmmt) REVERT: A 819 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 821 LEU cc_start: 0.8431 (mt) cc_final: 0.7964 (mp) REVERT: A 823 PHE cc_start: 0.8445 (t80) cc_final: 0.7997 (t80) REVERT: A 884 SER cc_start: 0.8599 (m) cc_final: 0.8241 (t) REVERT: A 900 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8138 (mtt) REVERT: A 922 LEU cc_start: 0.8385 (tp) cc_final: 0.8048 (tp) REVERT: A 926 GLN cc_start: 0.8076 (mt0) cc_final: 0.7804 (mt0) REVERT: A 935 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7829 (mm-40) REVERT: A 950 ASP cc_start: 0.8167 (t0) cc_final: 0.7939 (t0) REVERT: A 969 LYS cc_start: 0.9032 (mttt) cc_final: 0.8590 (mtpp) REVERT: A 1029 MET cc_start: 0.8733 (tpt) cc_final: 0.8477 (tpt) REVERT: A 1073 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8479 (mtpp) REVERT: A 1097 SER cc_start: 0.9004 (t) cc_final: 0.8768 (p) REVERT: C 49 HIS cc_start: 0.7616 (t70) cc_final: 0.7302 (t70) REVERT: C 190 ARG cc_start: 0.3764 (tpt170) cc_final: 0.2941 (tpt-90) REVERT: C 277 LEU cc_start: 0.9095 (mm) cc_final: 0.8870 (mp) REVERT: C 298 GLU cc_start: 0.9023 (tp30) cc_final: 0.8430 (tm-30) REVERT: C 365 TYR cc_start: 0.7126 (m-10) cc_final: 0.6827 (m-10) REVERT: C 392 PHE cc_start: 0.8425 (m-80) cc_final: 0.8165 (m-80) REVERT: C 613 GLN cc_start: 0.8064 (pt0) cc_final: 0.7731 (pt0) REVERT: C 643 PHE cc_start: 0.8151 (t80) cc_final: 0.7931 (t80) REVERT: C 654 GLU cc_start: 0.7459 (tt0) cc_final: 0.7216 (tt0) REVERT: C 819 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 861 LEU cc_start: 0.8802 (mm) cc_final: 0.8489 (mt) REVERT: C 884 SER cc_start: 0.8597 (m) cc_final: 0.8136 (t) REVERT: C 886 TRP cc_start: 0.8591 (OUTLIER) cc_final: 0.8177 (p90) REVERT: C 933 LYS cc_start: 0.8432 (mttt) cc_final: 0.8231 (mmmm) REVERT: C 935 GLN cc_start: 0.8240 (tp40) cc_final: 0.7647 (tm-30) REVERT: C 969 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8608 (mmmm) REVERT: C 973 ILE cc_start: 0.9140 (pt) cc_final: 0.8563 (pt) REVERT: C 980 ILE cc_start: 0.8375 (mt) cc_final: 0.8054 (mm) REVERT: C 990 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7061 (mt-10) REVERT: C 1010 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8670 (mm-40) REVERT: C 1031 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7184 (mm-30) REVERT: C 1040 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8905 (m) REVERT: C 1129 VAL cc_start: 0.9201 (t) cc_final: 0.8985 (m) REVERT: C 1139 ASP cc_start: 0.8474 (t0) cc_final: 0.8066 (t0) REVERT: B 36 VAL cc_start: 0.9010 (t) cc_final: 0.8756 (m) REVERT: B 49 HIS cc_start: 0.7752 (t-170) cc_final: 0.7514 (t-170) REVERT: B 55 PHE cc_start: 0.7252 (m-10) cc_final: 0.6776 (m-10) REVERT: B 106 PHE cc_start: 0.6648 (m-10) cc_final: 0.6391 (m-10) REVERT: B 119 ILE cc_start: 0.9044 (mm) cc_final: 0.8738 (mm) REVERT: B 129 LYS cc_start: 0.8733 (mttt) cc_final: 0.8467 (mmmm) REVERT: B 223 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8011 (mm) REVERT: B 229 LEU cc_start: 0.8197 (mm) cc_final: 0.7809 (mm) REVERT: B 328 ARG cc_start: 0.7575 (mmm160) cc_final: 0.7322 (mmt180) REVERT: B 386 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8124 (pttt) REVERT: B 450 ASN cc_start: 0.7130 (m-40) cc_final: 0.6788 (t0) REVERT: B 515 PHE cc_start: 0.7585 (m-10) cc_final: 0.7188 (m-10) REVERT: B 537 LYS cc_start: 0.9258 (tptt) cc_final: 0.8986 (tmtt) REVERT: B 558 LYS cc_start: 0.8208 (tmtt) cc_final: 0.7889 (tmtt) REVERT: B 559 PHE cc_start: 0.7934 (m-10) cc_final: 0.7732 (m-10) REVERT: B 603 ASN cc_start: 0.8359 (p0) cc_final: 0.7832 (p0) REVERT: B 673 SER cc_start: 0.8958 (t) cc_final: 0.8369 (p) REVERT: B 707 TYR cc_start: 0.3356 (m-80) cc_final: 0.2633 (m-80) REVERT: B 739 THR cc_start: 0.7775 (m) cc_final: 0.7558 (p) REVERT: B 751 ASN cc_start: 0.8457 (m-40) cc_final: 0.8166 (m-40) REVERT: B 765 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7769 (ttp-170) REVERT: B 773 GLU cc_start: 0.8264 (tt0) cc_final: 0.7896 (tm-30) REVERT: B 808 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7075 (p0) REVERT: B 921 LYS cc_start: 0.8637 (mttt) cc_final: 0.8386 (mmmm) REVERT: B 978 ASN cc_start: 0.8242 (p0) cc_final: 0.7795 (p0) REVERT: B 979 ASP cc_start: 0.8317 (m-30) cc_final: 0.7667 (m-30) REVERT: B 984 LEU cc_start: 0.8009 (mt) cc_final: 0.7615 (tp) REVERT: B 990 GLU cc_start: 0.7697 (pp20) cc_final: 0.7432 (pp20) REVERT: B 1017 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 1125 ASN cc_start: 0.8225 (p0) cc_final: 0.7963 (p0) REVERT: a 152 TYR cc_start: 0.7940 (p90) cc_final: 0.7663 (p90) REVERT: b 49 LYS cc_start: 0.7679 (mttt) cc_final: 0.7428 (mttt) outliers start: 117 outliers final: 85 residues processed: 756 average time/residue: 0.2042 time to fit residues: 242.7380 Evaluate side-chains 729 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 637 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 182 TYR Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 295 optimal weight: 0.0010 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 152 optimal weight: 0.0070 chunk 191 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 474 GLN A 658 ASN A 710 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1083 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.173507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.132970 restraints weight = 75620.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.137070 restraints weight = 36684.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.139573 restraints weight = 21771.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.141083 restraints weight = 15043.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.142153 restraints weight = 11810.371| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.6955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32154 Z= 0.120 Angle : 0.634 12.633 43788 Z= 0.321 Chirality : 0.045 0.266 4935 Planarity : 0.004 0.088 5629 Dihedral : 4.580 26.138 4311 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.47 % Favored : 97.45 % Rotamer: Outliers : 2.00 % Allowed : 17.62 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 3961 helix: 0.83 (0.22), residues: 631 sheet: 0.51 (0.16), residues: 1041 loop : -0.91 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1039 TYR 0.025 0.001 TYR C 660 PHE 0.032 0.002 PHE A 497 TRP 0.077 0.002 TRP A 104 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00277 (32108) covalent geometry : angle 0.63271 (43696) SS BOND : bond 0.00294 ( 46) SS BOND : angle 1.14155 ( 92) hydrogen bonds : bond 0.03603 ( 901) hydrogen bonds : angle 5.39792 ( 2469) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 657 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8416 (m) cc_final: 0.8144 (p) REVERT: A 291 CYS cc_start: 0.6629 (t) cc_final: 0.6256 (t) REVERT: A 296 LEU cc_start: 0.9123 (tp) cc_final: 0.8843 (tp) REVERT: A 304 LYS cc_start: 0.8274 (mttt) cc_final: 0.7994 (mptt) REVERT: A 338 PHE cc_start: 0.6072 (m-80) cc_final: 0.5763 (m-80) REVERT: A 339 ASP cc_start: 0.8518 (m-30) cc_final: 0.8263 (t70) REVERT: A 346 ARG cc_start: 0.8061 (mmp-170) cc_final: 0.7778 (mmp-170) REVERT: A 537 LYS cc_start: 0.8814 (tptp) cc_final: 0.8564 (tmtt) REVERT: A 546 LEU cc_start: 0.8511 (tt) cc_final: 0.8149 (tt) REVERT: A 654 GLU cc_start: 0.7587 (tt0) cc_final: 0.7320 (tt0) REVERT: A 764 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8332 (ttmm) REVERT: A 780 GLU cc_start: 0.7675 (tt0) cc_final: 0.7435 (tt0) REVERT: A 814 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8438 (mmmt) REVERT: A 823 PHE cc_start: 0.8385 (t80) cc_final: 0.7910 (t80) REVERT: A 884 SER cc_start: 0.8469 (m) cc_final: 0.8116 (t) REVERT: A 900 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7740 (mtt) REVERT: A 926 GLN cc_start: 0.7984 (mt0) cc_final: 0.7695 (mt0) REVERT: A 950 ASP cc_start: 0.8021 (t0) cc_final: 0.7816 (t0) REVERT: A 969 LYS cc_start: 0.8958 (mttt) cc_final: 0.8485 (mtpp) REVERT: A 1045 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8481 (mmmm) REVERT: A 1073 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8415 (mtpp) REVERT: A 1097 SER cc_start: 0.8922 (t) cc_final: 0.8698 (p) REVERT: C 49 HIS cc_start: 0.7642 (t70) cc_final: 0.7309 (t70) REVERT: C 170 TYR cc_start: 0.7642 (t80) cc_final: 0.7400 (t80) REVERT: C 190 ARG cc_start: 0.3626 (tpt170) cc_final: 0.2535 (mmt90) REVERT: C 200 TYR cc_start: 0.6950 (m-80) cc_final: 0.6672 (m-80) REVERT: C 277 LEU cc_start: 0.8922 (mm) cc_final: 0.8666 (mp) REVERT: C 365 TYR cc_start: 0.6859 (m-10) cc_final: 0.6568 (m-10) REVERT: C 421 TYR cc_start: 0.6285 (m-10) cc_final: 0.4351 (m-10) REVERT: C 509 ARG cc_start: 0.4909 (tmt170) cc_final: 0.4544 (ptm160) REVERT: C 613 GLN cc_start: 0.7832 (pt0) cc_final: 0.7567 (pt0) REVERT: C 654 GLU cc_start: 0.7260 (tt0) cc_final: 0.7025 (tt0) REVERT: C 819 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7616 (mt-10) REVERT: C 861 LEU cc_start: 0.8780 (mm) cc_final: 0.8490 (mt) REVERT: C 884 SER cc_start: 0.8523 (m) cc_final: 0.8066 (t) REVERT: C 935 GLN cc_start: 0.8097 (tp40) cc_final: 0.7685 (tm-30) REVERT: C 969 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8455 (mmmm) REVERT: C 973 ILE cc_start: 0.9117 (pt) cc_final: 0.8604 (pt) REVERT: C 990 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7017 (mt-10) REVERT: C 1040 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8119 (m) REVERT: C 1129 VAL cc_start: 0.9078 (t) cc_final: 0.8823 (m) REVERT: C 1139 ASP cc_start: 0.8286 (t0) cc_final: 0.7879 (t0) REVERT: B 36 VAL cc_start: 0.8988 (t) cc_final: 0.8700 (m) REVERT: B 49 HIS cc_start: 0.7633 (t-170) cc_final: 0.7355 (t-170) REVERT: B 55 PHE cc_start: 0.7083 (m-10) cc_final: 0.6653 (m-10) REVERT: B 67 VAL cc_start: 0.6830 (OUTLIER) cc_final: 0.6486 (p) REVERT: B 106 PHE cc_start: 0.6609 (m-10) cc_final: 0.6326 (m-10) REVERT: B 119 ILE cc_start: 0.9005 (mm) cc_final: 0.8674 (mm) REVERT: B 125 ASN cc_start: 0.6235 (p0) cc_final: 0.5006 (t0) REVERT: B 129 LYS cc_start: 0.8714 (mttt) cc_final: 0.8268 (mmmm) REVERT: B 195 LYS cc_start: 0.3936 (tptt) cc_final: 0.3209 (tppt) REVERT: B 204 TYR cc_start: 0.7024 (m-80) cc_final: 0.6749 (m-80) REVERT: B 229 LEU cc_start: 0.8138 (mm) cc_final: 0.7903 (mm) REVERT: B 271 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8257 (mm-40) REVERT: B 328 ARG cc_start: 0.7597 (mmm160) cc_final: 0.7258 (mmt180) REVERT: B 353 TRP cc_start: 0.6576 (p90) cc_final: 0.6369 (p90) REVERT: B 450 ASN cc_start: 0.7056 (m-40) cc_final: 0.6740 (t0) REVERT: B 515 PHE cc_start: 0.7518 (m-10) cc_final: 0.7118 (m-10) REVERT: B 603 ASN cc_start: 0.8245 (p0) cc_final: 0.7684 (p0) REVERT: B 615 VAL cc_start: 0.8920 (p) cc_final: 0.8663 (m) REVERT: B 751 ASN cc_start: 0.8394 (m-40) cc_final: 0.8120 (m110) REVERT: B 755 GLN cc_start: 0.8354 (mp10) cc_final: 0.8030 (mp10) REVERT: B 773 GLU cc_start: 0.8177 (tt0) cc_final: 0.7707 (tm-30) REVERT: B 776 LYS cc_start: 0.8768 (tttt) cc_final: 0.8565 (ttpp) REVERT: B 808 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7066 (p0) REVERT: B 884 SER cc_start: 0.8712 (m) cc_final: 0.8180 (t) REVERT: B 921 LYS cc_start: 0.8593 (mttt) cc_final: 0.8342 (mmmm) REVERT: B 978 ASN cc_start: 0.8165 (p0) cc_final: 0.7694 (p0) REVERT: B 979 ASP cc_start: 0.8189 (m-30) cc_final: 0.7484 (m-30) REVERT: B 984 LEU cc_start: 0.7979 (mt) cc_final: 0.7552 (tp) REVERT: B 990 GLU cc_start: 0.7573 (pp20) cc_final: 0.7263 (pp20) REVERT: B 1017 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7684 (tm-30) REVERT: B 1030 SER cc_start: 0.9103 (m) cc_final: 0.8414 (t) REVERT: b 49 LYS cc_start: 0.7433 (mttt) cc_final: 0.7217 (mttt) REVERT: b 59 GLU cc_start: 0.7208 (tp30) cc_final: 0.6905 (tm-30) outliers start: 70 outliers final: 47 residues processed: 689 average time/residue: 0.2135 time to fit residues: 231.4547 Evaluate side-chains 676 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 625 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 322 optimal weight: 1.9990 chunk 345 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 48 optimal weight: 0.0670 chunk 335 optimal weight: 1.9990 chunk 380 optimal weight: 0.4980 chunk 189 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN B 439 ASN B1083 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.170712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.129263 restraints weight = 74479.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.132461 restraints weight = 37507.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.134936 restraints weight = 22893.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.136614 restraints weight = 15974.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.137370 restraints weight = 12468.248| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32154 Z= 0.168 Angle : 0.670 13.007 43788 Z= 0.340 Chirality : 0.046 0.276 4935 Planarity : 0.005 0.092 5629 Dihedral : 4.626 29.772 4311 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 2.22 % Allowed : 18.10 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 3961 helix: 0.84 (0.22), residues: 642 sheet: 0.40 (0.15), residues: 1078 loop : -0.89 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 457 TYR 0.026 0.002 TYR C 660 PHE 0.072 0.002 PHE A 135 TRP 0.087 0.002 TRP A 104 HIS 0.008 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00384 (32108) covalent geometry : angle 0.66765 (43696) SS BOND : bond 0.00337 ( 46) SS BOND : angle 1.27509 ( 92) hydrogen bonds : bond 0.03751 ( 901) hydrogen bonds : angle 5.43494 ( 2469) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 648 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8460 (m) cc_final: 0.8217 (p) REVERT: A 291 CYS cc_start: 0.6776 (t) cc_final: 0.6425 (t) REVERT: A 304 LYS cc_start: 0.8338 (mttt) cc_final: 0.8052 (mptt) REVERT: A 338 PHE cc_start: 0.6122 (m-80) cc_final: 0.5493 (m-80) REVERT: A 346 ARG cc_start: 0.8130 (mmp-170) cc_final: 0.7895 (mmp-170) REVERT: A 386 LYS cc_start: 0.8267 (mttt) cc_final: 0.7821 (ptpt) REVERT: A 537 LYS cc_start: 0.8819 (tptp) cc_final: 0.8531 (tmtt) REVERT: A 546 LEU cc_start: 0.8579 (tt) cc_final: 0.8265 (tt) REVERT: A 654 GLU cc_start: 0.7613 (tt0) cc_final: 0.7365 (tt0) REVERT: A 750 SER cc_start: 0.9269 (m) cc_final: 0.8855 (p) REVERT: A 764 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8356 (ttmm) REVERT: A 780 GLU cc_start: 0.7679 (tt0) cc_final: 0.7434 (tt0) REVERT: A 814 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8591 (mmmt) REVERT: A 821 LEU cc_start: 0.8423 (mt) cc_final: 0.8151 (mp) REVERT: A 823 PHE cc_start: 0.8415 (t80) cc_final: 0.7908 (t80) REVERT: A 884 SER cc_start: 0.8500 (m) cc_final: 0.8177 (t) REVERT: A 900 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7972 (mtt) REVERT: A 926 GLN cc_start: 0.8065 (mt0) cc_final: 0.7739 (mt0) REVERT: A 950 ASP cc_start: 0.8103 (t0) cc_final: 0.7850 (t0) REVERT: A 965 GLN cc_start: 0.8681 (tp40) cc_final: 0.8407 (tp40) REVERT: A 969 LYS cc_start: 0.8990 (mttt) cc_final: 0.8520 (mtpp) REVERT: A 1005 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8024 (mm-40) REVERT: A 1073 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8459 (mtpp) REVERT: A 1097 SER cc_start: 0.8940 (t) cc_final: 0.8705 (p) REVERT: C 49 HIS cc_start: 0.7653 (t70) cc_final: 0.7273 (t70) REVERT: C 170 TYR cc_start: 0.7825 (t80) cc_final: 0.7582 (t80) REVERT: C 190 ARG cc_start: 0.3698 (tpt170) cc_final: 0.2659 (mmt90) REVERT: C 200 TYR cc_start: 0.6982 (m-80) cc_final: 0.6735 (m-80) REVERT: C 277 LEU cc_start: 0.9002 (mm) cc_final: 0.8758 (mp) REVERT: C 298 GLU cc_start: 0.8976 (tp30) cc_final: 0.8326 (tm-30) REVERT: C 365 TYR cc_start: 0.7226 (m-10) cc_final: 0.6878 (m-10) REVERT: C 392 PHE cc_start: 0.8310 (m-80) cc_final: 0.8040 (m-80) REVERT: C 421 TYR cc_start: 0.6549 (m-10) cc_final: 0.6339 (m-10) REVERT: C 509 ARG cc_start: 0.4961 (tmt170) cc_final: 0.4555 (ptm160) REVERT: C 528 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7684 (mmtm) REVERT: C 613 GLN cc_start: 0.7892 (pt0) cc_final: 0.7609 (pt0) REVERT: C 654 GLU cc_start: 0.7379 (tt0) cc_final: 0.7143 (tt0) REVERT: C 819 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7718 (mt-10) REVERT: C 861 LEU cc_start: 0.8790 (mm) cc_final: 0.8511 (mt) REVERT: C 884 SER cc_start: 0.8586 (m) cc_final: 0.8120 (t) REVERT: C 935 GLN cc_start: 0.8132 (tp40) cc_final: 0.7709 (tm-30) REVERT: C 969 LYS cc_start: 0.8809 (mmtm) cc_final: 0.8466 (mmmm) REVERT: C 973 ILE cc_start: 0.9172 (pt) cc_final: 0.8611 (pt) REVERT: C 975 SER cc_start: 0.8714 (p) cc_final: 0.8475 (t) REVERT: C 980 ILE cc_start: 0.8305 (mt) cc_final: 0.7997 (mm) REVERT: C 990 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7080 (mt-10) REVERT: C 1040 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8259 (m) REVERT: C 1129 VAL cc_start: 0.9130 (t) cc_final: 0.8871 (m) REVERT: B 36 VAL cc_start: 0.8974 (t) cc_final: 0.8727 (m) REVERT: B 49 HIS cc_start: 0.7712 (t-170) cc_final: 0.7462 (t-170) REVERT: B 55 PHE cc_start: 0.7220 (m-10) cc_final: 0.6816 (m-10) REVERT: B 67 VAL cc_start: 0.6874 (OUTLIER) cc_final: 0.6524 (p) REVERT: B 106 PHE cc_start: 0.6671 (m-10) cc_final: 0.6439 (m-10) REVERT: B 119 ILE cc_start: 0.9033 (mm) cc_final: 0.8751 (mm) REVERT: B 125 ASN cc_start: 0.6290 (p0) cc_final: 0.5016 (t0) REVERT: B 129 LYS cc_start: 0.8763 (mttt) cc_final: 0.8420 (mmmm) REVERT: B 195 LYS cc_start: 0.4293 (tptt) cc_final: 0.3819 (tptt) REVERT: B 200 TYR cc_start: 0.5833 (OUTLIER) cc_final: 0.4030 (m-80) REVERT: B 229 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7968 (tp) REVERT: B 450 ASN cc_start: 0.7119 (m-40) cc_final: 0.6677 (t0) REVERT: B 515 PHE cc_start: 0.7621 (m-10) cc_final: 0.7192 (m-10) REVERT: B 603 ASN cc_start: 0.8295 (p0) cc_final: 0.7792 (p0) REVERT: B 615 VAL cc_start: 0.8979 (p) cc_final: 0.8735 (m) REVERT: B 673 SER cc_start: 0.8867 (t) cc_final: 0.8439 (p) REVERT: B 748 GLU cc_start: 0.8289 (pm20) cc_final: 0.7789 (pt0) REVERT: B 751 ASN cc_start: 0.8443 (m-40) cc_final: 0.8169 (m110) REVERT: B 773 GLU cc_start: 0.8201 (tt0) cc_final: 0.7731 (tm-30) REVERT: B 776 LYS cc_start: 0.8808 (tttt) cc_final: 0.8597 (ttpp) REVERT: B 808 ASP cc_start: 0.7531 (t70) cc_final: 0.6999 (p0) REVERT: B 869 MET cc_start: 0.8888 (mtp) cc_final: 0.8654 (mtt) REVERT: B 884 SER cc_start: 0.8779 (m) cc_final: 0.8223 (t) REVERT: B 921 LYS cc_start: 0.8606 (mttt) cc_final: 0.8395 (mmmm) REVERT: B 978 ASN cc_start: 0.8229 (p0) cc_final: 0.7735 (p0) REVERT: B 979 ASP cc_start: 0.8215 (m-30) cc_final: 0.7549 (m-30) REVERT: B 984 LEU cc_start: 0.7883 (mt) cc_final: 0.7425 (tp) REVERT: B 988 GLU cc_start: 0.7795 (mp0) cc_final: 0.7551 (mp0) REVERT: B 1002 GLN cc_start: 0.7685 (tp40) cc_final: 0.7430 (tp40) REVERT: B 1005 GLN cc_start: 0.8117 (tp40) cc_final: 0.7910 (mm-40) REVERT: B 1017 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 1030 SER cc_start: 0.9121 (m) cc_final: 0.8474 (t) REVERT: B 1125 ASN cc_start: 0.8118 (p0) cc_final: 0.7872 (p0) REVERT: b 49 LYS cc_start: 0.7629 (mttt) cc_final: 0.7357 (mttt) REVERT: b 59 GLU cc_start: 0.7418 (tp30) cc_final: 0.7103 (tm-30) REVERT: b 185 LEU cc_start: 0.2881 (tp) cc_final: 0.1662 (pp) outliers start: 78 outliers final: 62 residues processed: 687 average time/residue: 0.2050 time to fit residues: 221.5381 Evaluate side-chains 693 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 626 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 34 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 28 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 223 optimal weight: 0.0270 chunk 307 optimal weight: 0.7980 chunk 378 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 222 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 381 optimal weight: 6.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.170795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.129463 restraints weight = 74684.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133114 restraints weight = 36942.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.135620 restraints weight = 22348.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.137177 restraints weight = 15705.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.138117 restraints weight = 12441.230| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.561 32154 Z= 0.234 Angle : 0.804 59.100 43788 Z= 0.430 Chirality : 0.046 0.503 4935 Planarity : 0.005 0.147 5629 Dihedral : 4.631 29.467 4311 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.52 % Rotamer: Outliers : 2.14 % Allowed : 18.53 % Favored : 79.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 3961 helix: 0.85 (0.22), residues: 642 sheet: 0.39 (0.15), residues: 1078 loop : -0.89 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG C1019 TYR 0.021 0.002 TYR C1138 PHE 0.074 0.002 PHE C 135 TRP 0.079 0.002 TRP A 104 HIS 0.034 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00625 (32108) covalent geometry : angle 0.79690 (43696) SS BOND : bond 0.00522 ( 46) SS BOND : angle 2.39362 ( 92) hydrogen bonds : bond 0.03749 ( 901) hydrogen bonds : angle 5.43497 ( 2469) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 630 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8444 (m) cc_final: 0.8213 (p) REVERT: A 291 CYS cc_start: 0.6770 (t) cc_final: 0.6423 (t) REVERT: A 304 LYS cc_start: 0.8338 (mttt) cc_final: 0.8051 (mptt) REVERT: A 338 PHE cc_start: 0.5994 (m-80) cc_final: 0.5519 (m-80) REVERT: A 346 ARG cc_start: 0.8106 (mmp-170) cc_final: 0.7873 (mmp-170) REVERT: A 386 LYS cc_start: 0.8244 (mttt) cc_final: 0.7791 (ptpt) REVERT: A 537 LYS cc_start: 0.8806 (tptp) cc_final: 0.8542 (tmtt) REVERT: A 546 LEU cc_start: 0.8544 (tt) cc_final: 0.8231 (tt) REVERT: A 654 GLU cc_start: 0.7582 (tt0) cc_final: 0.7349 (tt0) REVERT: A 750 SER cc_start: 0.9264 (m) cc_final: 0.8845 (p) REVERT: A 764 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8347 (ttmm) REVERT: A 780 GLU cc_start: 0.7673 (tt0) cc_final: 0.7420 (tt0) REVERT: A 814 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8593 (mmmt) REVERT: A 819 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7290 (mp0) REVERT: A 821 LEU cc_start: 0.8433 (mt) cc_final: 0.8154 (mp) REVERT: A 823 PHE cc_start: 0.8409 (t80) cc_final: 0.7900 (t80) REVERT: A 884 SER cc_start: 0.8507 (m) cc_final: 0.8190 (t) REVERT: A 900 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7980 (mtt) REVERT: A 926 GLN cc_start: 0.8057 (mt0) cc_final: 0.7765 (mt0) REVERT: A 969 LYS cc_start: 0.8982 (mttt) cc_final: 0.8531 (mtpp) REVERT: A 1073 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8461 (mtpp) REVERT: A 1097 SER cc_start: 0.8944 (t) cc_final: 0.8706 (p) REVERT: C 49 HIS cc_start: 0.7640 (t70) cc_final: 0.7289 (t70) REVERT: C 170 TYR cc_start: 0.7821 (t80) cc_final: 0.7578 (t80) REVERT: C 190 ARG cc_start: 0.3646 (tpt170) cc_final: 0.2996 (tpt-90) REVERT: C 200 TYR cc_start: 0.6983 (m-80) cc_final: 0.6712 (m-80) REVERT: C 277 LEU cc_start: 0.9002 (mm) cc_final: 0.8758 (mp) REVERT: C 365 TYR cc_start: 0.7157 (m-10) cc_final: 0.6824 (m-10) REVERT: C 392 PHE cc_start: 0.8271 (m-80) cc_final: 0.8020 (m-80) REVERT: C 421 TYR cc_start: 0.6542 (m-10) cc_final: 0.5204 (m-10) REVERT: C 509 ARG cc_start: 0.5031 (tmt170) cc_final: 0.4517 (ptm160) REVERT: C 613 GLN cc_start: 0.7907 (pt0) cc_final: 0.7613 (pt0) REVERT: C 819 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7717 (mt-10) REVERT: C 861 LEU cc_start: 0.8786 (mm) cc_final: 0.8505 (mt) REVERT: C 884 SER cc_start: 0.8595 (m) cc_final: 0.8133 (t) REVERT: C 935 GLN cc_start: 0.8111 (tp40) cc_final: 0.7701 (tm-30) REVERT: C 969 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8402 (mmmm) REVERT: C 973 ILE cc_start: 0.9154 (pt) cc_final: 0.8578 (pt) REVERT: C 980 ILE cc_start: 0.8299 (mt) cc_final: 0.7995 (mm) REVERT: C 1040 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8258 (m) REVERT: C 1129 VAL cc_start: 0.9104 (t) cc_final: 0.8871 (m) REVERT: C 1139 ASP cc_start: 0.8295 (t0) cc_final: 0.7968 (t0) REVERT: B 36 VAL cc_start: 0.8969 (t) cc_final: 0.8726 (m) REVERT: B 49 HIS cc_start: 0.7689 (t-170) cc_final: 0.7451 (t-170) REVERT: B 55 PHE cc_start: 0.7218 (m-10) cc_final: 0.6809 (m-10) REVERT: B 67 VAL cc_start: 0.6869 (OUTLIER) cc_final: 0.6518 (p) REVERT: B 106 PHE cc_start: 0.6697 (m-10) cc_final: 0.6456 (m-10) REVERT: B 119 ILE cc_start: 0.9043 (mm) cc_final: 0.8761 (mm) REVERT: B 125 ASN cc_start: 0.6283 (p0) cc_final: 0.5007 (t0) REVERT: B 129 LYS cc_start: 0.8776 (mttt) cc_final: 0.8420 (mmmm) REVERT: B 195 LYS cc_start: 0.4290 (tptt) cc_final: 0.3580 (tppt) REVERT: B 200 TYR cc_start: 0.5836 (OUTLIER) cc_final: 0.4034 (m-80) REVERT: B 229 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7963 (tp) REVERT: B 450 ASN cc_start: 0.7082 (m-40) cc_final: 0.6685 (t0) REVERT: B 515 PHE cc_start: 0.7621 (m-10) cc_final: 0.7201 (m-10) REVERT: B 603 ASN cc_start: 0.8262 (p0) cc_final: 0.7759 (p0) REVERT: B 615 VAL cc_start: 0.8985 (p) cc_final: 0.8735 (m) REVERT: B 673 SER cc_start: 0.8863 (t) cc_final: 0.8437 (p) REVERT: B 748 GLU cc_start: 0.8256 (pm20) cc_final: 0.7752 (pt0) REVERT: B 751 ASN cc_start: 0.8415 (m-40) cc_final: 0.8146 (m110) REVERT: B 765 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7642 (ttp-170) REVERT: B 773 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: B 776 LYS cc_start: 0.8809 (tttt) cc_final: 0.8607 (ttpp) REVERT: B 808 ASP cc_start: 0.7544 (t70) cc_final: 0.7004 (p0) REVERT: B 869 MET cc_start: 0.8886 (mtp) cc_final: 0.8650 (mtt) REVERT: B 884 SER cc_start: 0.8776 (m) cc_final: 0.8223 (t) REVERT: B 921 LYS cc_start: 0.8594 (mttt) cc_final: 0.8389 (mmmm) REVERT: B 978 ASN cc_start: 0.8186 (p0) cc_final: 0.7725 (p0) REVERT: B 979 ASP cc_start: 0.8194 (m-30) cc_final: 0.7523 (m-30) REVERT: B 984 LEU cc_start: 0.7875 (mt) cc_final: 0.7442 (tp) REVERT: B 988 GLU cc_start: 0.7726 (mp0) cc_final: 0.7499 (mp0) REVERT: B 1002 GLN cc_start: 0.7645 (tp40) cc_final: 0.7407 (tp40) REVERT: B 1017 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 1030 SER cc_start: 0.9135 (m) cc_final: 0.8481 (t) REVERT: B 1125 ASN cc_start: 0.8115 (p0) cc_final: 0.7873 (p0) REVERT: b 49 LYS cc_start: 0.7599 (mttt) cc_final: 0.7330 (mttt) REVERT: b 59 GLU cc_start: 0.7403 (tp30) cc_final: 0.7093 (tm-30) REVERT: b 185 LEU cc_start: 0.2865 (tp) cc_final: 0.1641 (pp) outliers start: 75 outliers final: 65 residues processed: 664 average time/residue: 0.2103 time to fit residues: 219.1029 Evaluate side-chains 700 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 629 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 34 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 293 optimal weight: 8.9990 chunk 239 optimal weight: 0.2980 chunk 222 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 398 optimal weight: 9.9990 chunk 340 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 324 optimal weight: 0.0030 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.170901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128978 restraints weight = 74347.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132367 restraints weight = 37030.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.134783 restraints weight = 22558.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.136009 restraints weight = 16039.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.136951 restraints weight = 12891.326| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.7327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.561 32154 Z= 0.243 Angle : 0.809 59.098 43788 Z= 0.432 Chirality : 0.046 0.503 4935 Planarity : 0.005 0.147 5629 Dihedral : 4.631 29.467 4311 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.52 % Rotamer: Outliers : 2.08 % Allowed : 18.67 % Favored : 79.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 3961 helix: 0.85 (0.22), residues: 642 sheet: 0.39 (0.15), residues: 1078 loop : -0.89 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG C1019 TYR 0.021 0.002 TYR C1138 PHE 0.074 0.002 PHE C 135 TRP 0.079 0.002 TRP A 104 HIS 0.034 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00625 (32108) covalent geometry : angle 0.79690 (43696) SS BOND : bond 0.03618 ( 46) SS BOND : angle 3.08271 ( 92) hydrogen bonds : bond 0.03749 ( 901) hydrogen bonds : angle 5.43497 ( 2469) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8477.94 seconds wall clock time: 145 minutes 49.84 seconds (8749.84 seconds total)