Starting phenix.real_space_refine on Thu Mar 5 14:15:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x29_21997/03_2026/6x29_21997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x29_21997/03_2026/6x29_21997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x29_21997/03_2026/6x29_21997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x29_21997/03_2026/6x29_21997.map" model { file = "/net/cci-nas-00/data/ceres_data/6x29_21997/03_2026/6x29_21997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x29_21997/03_2026/6x29_21997.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.084 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 105 5.16 5 C 14580 2.51 5 N 3786 2.21 5 O 4335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22806 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Restraints were copied for chains: B, C Time building chain proxies: 7.67, per 1000 atoms: 0.34 Number of scatterers: 22806 At special positions: 0 Unit cell: (129.93, 136.32, 171.465, 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 105 16.00 O 4335 8.00 N 3786 7.00 C 14580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 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 A 985 " - pdb=" SG CYS C 383 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.01 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 936.8 milliseconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 25.7% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.638A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.764A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.209A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.501A pdb=" N LYS A 386 " --> pdb=" O CYS A 383 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.916A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.975A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.121A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.627A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.525A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.904A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.870A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.562A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 removed outlier: 3.602A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 3.862A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.783A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.184A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.638A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.765A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.209A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.501A pdb=" N LYS B 386 " --> pdb=" O CYS B 383 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.916A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.976A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.121A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.627A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.526A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.905A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.870A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.563A pdb=" N ALA B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 944 removed outlier: 3.603A pdb=" N ALA B 944 " --> pdb=" O THR B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.861A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.783A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.184A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.638A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.763A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.210A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.501A pdb=" N LYS C 386 " --> pdb=" O CYS C 383 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.915A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.977A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.121A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.627A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.525A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.904A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.870A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.562A pdb=" N ALA C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 removed outlier: 3.603A pdb=" N ALA C 944 " --> pdb=" O THR C 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 941 through 944' Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.861A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 968 Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.783A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.184A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.575A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.568A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.619A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 229 removed outlier: 5.681A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.516A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.763A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.251A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 539 removed outlier: 5.568A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.913A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.763A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.345A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.345A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.880A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.575A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.620A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.682A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.515A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.763A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.251A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'B' and resid 538 through 539 removed outlier: 5.568A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.914A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.676A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.345A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.345A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.575A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.619A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.504A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.504A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 224 through 229 removed outlier: 5.680A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.515A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.762A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AF2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.250A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.913A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.346A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.346A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF9, first strand: chain 'C' and resid 1094 through 1097 790 hydrogen bonds defined for protein. 2145 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: 5.46 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7351 1.35 - 1.47: 6097 1.47 - 1.60: 9733 1.60 - 1.73: 0 1.73 - 1.86: 129 Bond restraints: 23310 Sorted by residual: bond pdb=" CG LEU B 878 " pdb=" CD1 LEU B 878 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.22e+00 bond pdb=" CG LEU C 878 " pdb=" CD1 LEU C 878 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.13e+00 bond pdb=" CG LEU A 878 " pdb=" CD1 LEU A 878 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CB GLU B1072 " pdb=" CG GLU B1072 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.84e+00 bond pdb=" CB GLU A1072 " pdb=" CG GLU A1072 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.79e+00 ... (remaining 23305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 31541 3.81 - 7.62: 157 7.62 - 11.44: 6 11.44 - 15.25: 0 15.25 - 19.06: 3 Bond angle restraints: 31707 Sorted by residual: angle pdb=" C VAL C 83 " pdb=" N LEU C 84 " pdb=" CA LEU C 84 " ideal model delta sigma weight residual 120.94 140.00 -19.06 1.90e+00 2.77e-01 1.01e+02 angle pdb=" C VAL A 83 " pdb=" N LEU A 84 " pdb=" CA LEU A 84 " ideal model delta sigma weight residual 120.94 139.96 -19.02 1.90e+00 2.77e-01 1.00e+02 angle pdb=" C VAL B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta sigma weight residual 120.94 139.92 -18.98 1.90e+00 2.77e-01 9.98e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.64 -4.94 1.22e+00 6.72e-01 1.64e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.62 -4.92 1.22e+00 6.72e-01 1.62e+01 ... (remaining 31702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13477 17.91 - 35.82: 334 35.82 - 53.73: 79 53.73 - 71.64: 9 71.64 - 89.55: 12 Dihedral angle restraints: 13911 sinusoidal: 5421 harmonic: 8490 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -175.55 89.55 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -175.52 89.52 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -175.48 89.48 1 1.00e+01 1.00e-02 9.51e+01 ... (remaining 13908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2006 0.043 - 0.085: 1187 0.085 - 0.128: 365 0.128 - 0.170: 60 0.170 - 0.213: 15 Chirality restraints: 3633 Sorted by residual: chirality pdb=" CB THR C 581 " pdb=" CA THR C 581 " pdb=" OG1 THR C 581 " pdb=" CG2 THR C 581 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB THR B 581 " pdb=" CA THR B 581 " pdb=" OG1 THR B 581 " pdb=" CG2 THR B 581 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB THR A 581 " pdb=" CA THR A 581 " pdb=" OG1 THR A 581 " pdb=" CG2 THR A 581 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3630 not shown) Planarity restraints: 4098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 86 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C PHE B 86 " 0.060 2.00e-02 2.50e+03 pdb=" O PHE B 86 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 87 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 86 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C PHE C 86 " 0.059 2.00e-02 2.50e+03 pdb=" O PHE C 86 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN C 87 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 86 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C PHE A 86 " 0.059 2.00e-02 2.50e+03 pdb=" O PHE A 86 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 87 " -0.020 2.00e-02 2.50e+03 ... (remaining 4095 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 477 2.68 - 3.23: 20603 3.23 - 3.79: 34748 3.79 - 4.34: 46282 4.34 - 4.90: 78352 Nonbonded interactions: 180462 Sorted by model distance: nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.123 3.120 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.123 3.120 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.123 3.120 nonbonded pdb=" NZ LYS C 557 " pdb=" OD2 ASP C 574 " model vdw 2.207 3.120 nonbonded pdb=" NZ LYS B 557 " pdb=" OD2 ASP B 574 " model vdw 2.208 3.120 ... (remaining 180457 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.020 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 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 : 0.009 0.077 23349 Z= 0.389 Angle : 0.877 19.061 31785 Z= 0.480 Chirality : 0.056 0.213 3633 Planarity : 0.007 0.080 4098 Dihedral : 8.822 76.066 8310 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.12 % Allowed : 0.47 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.11 % 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: -4.56 (0.12), residues: 2844 helix: -4.57 (0.07), residues: 714 sheet: -2.33 (0.17), residues: 660 loop : -2.48 (0.13), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 815 TYR 0.025 0.003 TYR C 38 PHE 0.031 0.004 PHE B 800 TRP 0.016 0.003 TRP B 64 HIS 0.013 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00918 (23310) covalent geometry : angle 0.87308 (31707) SS BOND : bond 0.01050 ( 39) SS BOND : angle 1.88468 ( 78) hydrogen bonds : bond 0.29421 ( 772) hydrogen bonds : angle 11.24390 ( 2145) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 500 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6500 (mtp-110) REVERT: A 326 ILE cc_start: 0.5706 (mm) cc_final: 0.5486 (mp) REVERT: A 340 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7974 (mp0) REVERT: A 360 ASN cc_start: 0.7609 (m-40) cc_final: 0.7113 (t0) REVERT: A 365 TYR cc_start: 0.7186 (m-80) cc_final: 0.6751 (m-80) REVERT: A 394 ASN cc_start: 0.6804 (m-40) cc_final: 0.6588 (m-40) REVERT: A 529 LYS cc_start: 0.8219 (mttt) cc_final: 0.7582 (tmtt) REVERT: A 530 SER cc_start: 0.7694 (p) cc_final: 0.7374 (m) REVERT: A 532 ASN cc_start: 0.7398 (t0) cc_final: 0.7073 (t0) REVERT: A 537 LYS cc_start: 0.6658 (ttpt) cc_final: 0.6371 (ptmt) REVERT: A 574 ASP cc_start: 0.5792 (t70) cc_final: 0.5470 (t0) REVERT: A 588 THR cc_start: 0.6729 (m) cc_final: 0.6229 (t) REVERT: A 592 PHE cc_start: 0.6798 (p90) cc_final: 0.6508 (p90) REVERT: A 607 GLN cc_start: 0.7530 (tt0) cc_final: 0.7177 (tt0) REVERT: A 614 ASP cc_start: 0.7701 (t0) cc_final: 0.7202 (m-30) REVERT: A 656 VAL cc_start: 0.6491 (t) cc_final: 0.6257 (m) REVERT: A 661 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6884 (tt0) REVERT: A 702 GLU cc_start: 0.8166 (tt0) cc_final: 0.7914 (tp30) REVERT: A 745 ASP cc_start: 0.7544 (m-30) cc_final: 0.7085 (p0) REVERT: A 748 GLU cc_start: 0.7570 (mp0) cc_final: 0.7096 (mp0) REVERT: A 814 LYS cc_start: 0.7622 (mttt) cc_final: 0.7220 (mptp) REVERT: A 819 GLU cc_start: 0.5851 (mt-10) cc_final: 0.5413 (mt-10) REVERT: A 872 GLN cc_start: 0.6795 (mt0) cc_final: 0.6520 (tt0) REVERT: A 875 SER cc_start: 0.6229 (t) cc_final: 0.6012 (m) REVERT: A 990 GLU cc_start: 0.6272 (mt-10) cc_final: 0.5920 (mp0) REVERT: A 995 ARG cc_start: 0.6169 (mtt180) cc_final: 0.5884 (mtp180) REVERT: A 1045 LYS cc_start: 0.7565 (ttpp) cc_final: 0.7179 (tmmt) REVERT: A 1050 MET cc_start: 0.7367 (ptt) cc_final: 0.7142 (ptm) REVERT: A 1073 LYS cc_start: 0.6462 (mttt) cc_final: 0.6020 (mtpp) REVERT: A 1092 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6922 (mp0) REVERT: A 1119 ASN cc_start: 0.6929 (m-40) cc_final: 0.6635 (m110) REVERT: A 1138 TYR cc_start: 0.7040 (t80) cc_final: 0.6815 (t80) REVERT: B 224 GLU cc_start: 0.4614 (pm20) cc_final: 0.4347 (mp0) REVERT: B 237 ARG cc_start: 0.4996 (mtt90) cc_final: 0.4770 (mtp-110) REVERT: B 282 ASN cc_start: 0.6485 (m-40) cc_final: 0.5999 (m-40) REVERT: B 287 ASP cc_start: 0.5593 (t0) cc_final: 0.5306 (m-30) REVERT: B 314 GLN cc_start: 0.7428 (tt0) cc_final: 0.6952 (tp40) REVERT: B 316 SER cc_start: 0.6920 (t) cc_final: 0.6386 (p) REVERT: B 319 ARG cc_start: 0.6948 (mtm-85) cc_final: 0.6594 (mtp-110) REVERT: B 340 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7880 (mp0) REVERT: B 351 TYR cc_start: 0.6915 (p90) cc_final: 0.6031 (p90) REVERT: B 360 ASN cc_start: 0.7745 (m-40) cc_final: 0.7280 (t0) REVERT: B 365 TYR cc_start: 0.6875 (m-80) cc_final: 0.6582 (m-80) REVERT: B 394 ASN cc_start: 0.6626 (m-40) cc_final: 0.6180 (t0) REVERT: B 529 LYS cc_start: 0.8188 (mttt) cc_final: 0.7594 (tmtt) REVERT: B 532 ASN cc_start: 0.7437 (t0) cc_final: 0.6902 (t0) REVERT: B 537 LYS cc_start: 0.6774 (ttpt) cc_final: 0.6335 (ptmt) REVERT: B 574 ASP cc_start: 0.5880 (t70) cc_final: 0.5582 (t0) REVERT: B 607 GLN cc_start: 0.7363 (tt0) cc_final: 0.7079 (tt0) REVERT: B 614 ASP cc_start: 0.7634 (t0) cc_final: 0.7080 (m-30) REVERT: B 651 ILE cc_start: 0.7513 (mt) cc_final: 0.7291 (mm) REVERT: B 656 VAL cc_start: 0.6424 (t) cc_final: 0.6173 (m) REVERT: B 661 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6059 (mm-30) REVERT: B 745 ASP cc_start: 0.7334 (m-30) cc_final: 0.7133 (p0) REVERT: B 748 GLU cc_start: 0.7509 (mp0) cc_final: 0.7038 (mp0) REVERT: B 794 ILE cc_start: 0.7380 (mt) cc_final: 0.7086 (pp) REVERT: B 814 LYS cc_start: 0.7608 (mttt) cc_final: 0.7232 (mptp) REVERT: B 819 GLU cc_start: 0.5883 (mt-10) cc_final: 0.5584 (mt-10) REVERT: B 868 GLU cc_start: 0.7171 (tt0) cc_final: 0.6855 (tt0) REVERT: B 872 GLN cc_start: 0.6538 (mt0) cc_final: 0.6145 (mt0) REVERT: B 947 LYS cc_start: 0.7636 (mttt) cc_final: 0.7425 (mtmt) REVERT: B 987 PRO cc_start: 0.7774 (Cg_exo) cc_final: 0.7540 (Cg_endo) REVERT: B 995 ARG cc_start: 0.6377 (mtt180) cc_final: 0.6047 (mtp180) REVERT: B 1050 MET cc_start: 0.7396 (ptt) cc_final: 0.7040 (ptm) REVERT: B 1073 LYS cc_start: 0.6811 (mttt) cc_final: 0.6340 (mtpt) REVERT: B 1092 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6687 (mp0) REVERT: B 1100 THR cc_start: 0.7303 (p) cc_final: 0.6966 (p) REVERT: B 1101 HIS cc_start: 0.6843 (m90) cc_final: 0.6338 (m170) REVERT: C 237 ARG cc_start: 0.4936 (mtt90) cc_final: 0.4701 (mtm180) REVERT: C 287 ASP cc_start: 0.5562 (t0) cc_final: 0.5202 (m-30) REVERT: C 305 SER cc_start: 0.7997 (t) cc_final: 0.7728 (t) REVERT: C 340 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8005 (mp0) REVERT: C 360 ASN cc_start: 0.7520 (m-40) cc_final: 0.6985 (t0) REVERT: C 365 TYR cc_start: 0.6997 (m-80) cc_final: 0.6353 (m-80) REVERT: C 394 ASN cc_start: 0.6668 (m-40) cc_final: 0.6285 (m-40) REVERT: C 521 PRO cc_start: 0.7418 (Cg_exo) cc_final: 0.7113 (Cg_endo) REVERT: C 532 ASN cc_start: 0.7356 (t0) cc_final: 0.7076 (t0) REVERT: C 537 LYS cc_start: 0.6759 (ttpt) cc_final: 0.6225 (ptmt) REVERT: C 574 ASP cc_start: 0.5688 (t70) cc_final: 0.5391 (t0) REVERT: C 592 PHE cc_start: 0.6971 (p90) cc_final: 0.6709 (p90) REVERT: C 607 GLN cc_start: 0.7337 (tt0) cc_final: 0.6901 (tt0) REVERT: C 614 ASP cc_start: 0.7396 (t0) cc_final: 0.7069 (m-30) REVERT: C 651 ILE cc_start: 0.7747 (mt) cc_final: 0.7533 (mp) REVERT: C 661 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6771 (tt0) REVERT: C 697 MET cc_start: 0.7203 (ptt) cc_final: 0.6990 (ptt) REVERT: C 748 GLU cc_start: 0.7734 (mp0) cc_final: 0.7341 (mp0) REVERT: C 794 ILE cc_start: 0.7592 (mt) cc_final: 0.7205 (pp) REVERT: C 814 LYS cc_start: 0.7726 (mttt) cc_final: 0.7298 (mptp) REVERT: C 819 GLU cc_start: 0.6113 (mt-10) cc_final: 0.5675 (mt-10) REVERT: C 872 GLN cc_start: 0.6426 (mt0) cc_final: 0.6147 (tt0) REVERT: C 947 LYS cc_start: 0.7720 (mttt) cc_final: 0.7493 (mtpt) REVERT: C 987 PRO cc_start: 0.8032 (Cg_exo) cc_final: 0.7689 (Cg_endo) REVERT: C 995 ARG cc_start: 0.6213 (mtt180) cc_final: 0.5929 (mtp180) REVERT: C 1002 GLN cc_start: 0.6327 (tt0) cc_final: 0.6056 (tt0) REVERT: C 1045 LYS cc_start: 0.7563 (ttpp) cc_final: 0.7343 (ttpt) REVERT: C 1092 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6947 (mp0) outliers start: 3 outliers final: 2 residues processed: 503 average time/residue: 0.5572 time to fit residues: 321.5477 Evaluate side-chains 293 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 291 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain C residue 391 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 580 GLN A 603 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1005 GLN A1101 HIS B 66 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 536 ASN B 603 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN B1119 ASN C 66 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 580 GLN C 603 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS C1142 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.182576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.122856 restraints weight = 28265.020| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.92 r_work: 0.3493 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23349 Z= 0.137 Angle : 0.574 9.529 31785 Z= 0.305 Chirality : 0.045 0.175 3633 Planarity : 0.005 0.048 4098 Dihedral : 5.329 46.168 3101 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.80 % Allowed : 6.69 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.13), residues: 2844 helix: -2.47 (0.15), residues: 669 sheet: -1.64 (0.20), residues: 576 loop : -1.88 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.018 0.001 TYR A 396 PHE 0.021 0.002 PHE C 906 TRP 0.011 0.001 TRP C 886 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00320 (23310) covalent geometry : angle 0.57116 (31707) SS BOND : bond 0.00430 ( 39) SS BOND : angle 1.25016 ( 78) hydrogen bonds : bond 0.04133 ( 772) hydrogen bonds : angle 6.42078 ( 2145) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7424 (tp) cc_final: 0.6633 (mt) REVERT: A 202 LYS cc_start: 0.6934 (mttm) cc_final: 0.6403 (mtmt) REVERT: A 206 LYS cc_start: 0.8329 (tptt) cc_final: 0.7606 (tptp) REVERT: A 287 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: A 360 ASN cc_start: 0.8010 (m-40) cc_final: 0.7723 (t0) REVERT: A 365 TYR cc_start: 0.8161 (m-80) cc_final: 0.7950 (m-80) REVERT: A 400 PHE cc_start: 0.8317 (p90) cc_final: 0.8091 (p90) REVERT: A 529 LYS cc_start: 0.8575 (mttt) cc_final: 0.8268 (tmtt) REVERT: A 574 ASP cc_start: 0.7343 (t70) cc_final: 0.7045 (t0) REVERT: A 581 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.6986 (p) REVERT: A 588 THR cc_start: 0.8318 (m) cc_final: 0.7745 (t) REVERT: A 780 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7947 (mm-30) REVERT: B 202 LYS cc_start: 0.6703 (mttm) cc_final: 0.6062 (mtmt) REVERT: B 237 ARG cc_start: 0.5905 (mtt90) cc_final: 0.5545 (mmt90) REVERT: B 271 GLN cc_start: 0.8075 (mt0) cc_final: 0.7706 (mt0) REVERT: B 335 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7510 (mm) REVERT: B 356 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7718 (tptp) REVERT: B 360 ASN cc_start: 0.8267 (m-40) cc_final: 0.7995 (t0) REVERT: B 394 ASN cc_start: 0.7391 (m-40) cc_final: 0.6786 (m-40) REVERT: B 529 LYS cc_start: 0.8627 (mttt) cc_final: 0.8274 (tmtt) REVERT: B 532 ASN cc_start: 0.8059 (t0) cc_final: 0.7735 (t0) REVERT: B 537 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7400 (ptmt) REVERT: B 574 ASP cc_start: 0.7272 (t70) cc_final: 0.6971 (t0) REVERT: B 581 THR cc_start: 0.7079 (OUTLIER) cc_final: 0.6839 (p) REVERT: B 661 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7730 (mm-30) REVERT: B 1119 ASN cc_start: 0.8379 (m-40) cc_final: 0.8074 (m110) REVERT: C 118 LEU cc_start: 0.7463 (tp) cc_final: 0.6592 (mt) REVERT: C 202 LYS cc_start: 0.6755 (mttm) cc_final: 0.6271 (mtmt) REVERT: C 237 ARG cc_start: 0.5759 (mtt90) cc_final: 0.5558 (mtm180) REVERT: C 360 ASN cc_start: 0.8031 (m-40) cc_final: 0.7654 (t0) REVERT: C 365 TYR cc_start: 0.8122 (m-80) cc_final: 0.7825 (m-80) REVERT: C 394 ASN cc_start: 0.7379 (m-40) cc_final: 0.6948 (m-40) REVERT: C 396 TYR cc_start: 0.7132 (m-80) cc_final: 0.6924 (m-80) REVERT: C 528 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7222 (mtpm) REVERT: C 529 LYS cc_start: 0.8532 (mttt) cc_final: 0.8213 (tmtt) REVERT: C 530 SER cc_start: 0.8779 (p) cc_final: 0.8517 (m) REVERT: C 532 ASN cc_start: 0.7820 (t0) cc_final: 0.7592 (t0) REVERT: C 537 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7251 (ptmt) REVERT: C 574 ASP cc_start: 0.7232 (t70) cc_final: 0.6911 (t0) REVERT: C 581 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6974 (p) REVERT: C 607 GLN cc_start: 0.8534 (tt0) cc_final: 0.8307 (tt0) REVERT: C 661 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7796 (mm-30) REVERT: C 776 LYS cc_start: 0.8688 (tttt) cc_final: 0.8407 (ttpp) REVERT: C 794 ILE cc_start: 0.8731 (mt) cc_final: 0.8395 (pp) outliers start: 46 outliers final: 11 residues processed: 331 average time/residue: 0.5802 time to fit residues: 219.6360 Evaluate side-chains 228 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 220 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 76 optimal weight: 0.0050 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 969 ASN B1002 GLN B1101 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.178616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.120903 restraints weight = 28083.659| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.27 r_work: 0.3377 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23349 Z= 0.172 Angle : 0.569 9.303 31785 Z= 0.300 Chirality : 0.045 0.154 3633 Planarity : 0.004 0.046 4098 Dihedral : 5.058 54.041 3101 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.23 % Allowed : 9.66 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.14), residues: 2844 helix: -1.10 (0.19), residues: 678 sheet: -1.34 (0.19), residues: 615 loop : -1.61 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 403 TYR 0.018 0.002 TYR A 313 PHE 0.021 0.002 PHE C 906 TRP 0.019 0.002 TRP C 886 HIS 0.009 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00411 (23310) covalent geometry : angle 0.56678 (31707) SS BOND : bond 0.00546 ( 39) SS BOND : angle 1.07705 ( 78) hydrogen bonds : bond 0.03980 ( 772) hydrogen bonds : angle 5.95775 ( 2145) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7533 (tp) cc_final: 0.6726 (mt) REVERT: A 202 LYS cc_start: 0.7011 (mttm) cc_final: 0.6438 (mtmt) REVERT: A 206 LYS cc_start: 0.8354 (tptt) cc_final: 0.7858 (tptp) REVERT: A 287 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: A 360 ASN cc_start: 0.8044 (m-40) cc_final: 0.7688 (t0) REVERT: A 400 PHE cc_start: 0.8366 (p90) cc_final: 0.7998 (p90) REVERT: A 529 LYS cc_start: 0.8598 (mttt) cc_final: 0.8232 (tmtt) REVERT: A 558 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7879 (pmmt) REVERT: A 574 ASP cc_start: 0.7564 (t70) cc_final: 0.7205 (t0) REVERT: A 581 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6962 (p) REVERT: A 603 ASN cc_start: 0.7980 (t0) cc_final: 0.7689 (t0) REVERT: A 655 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8323 (t-170) REVERT: A 780 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7986 (mm-30) REVERT: B 202 LYS cc_start: 0.6959 (mttm) cc_final: 0.6222 (mtmt) REVERT: B 237 ARG cc_start: 0.5858 (mtt90) cc_final: 0.5461 (mtm110) REVERT: B 335 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7446 (mm) REVERT: B 360 ASN cc_start: 0.8340 (m-40) cc_final: 0.7972 (t0) REVERT: B 394 ASN cc_start: 0.7743 (m-40) cc_final: 0.7418 (m-40) REVERT: B 529 LYS cc_start: 0.8736 (mttt) cc_final: 0.8419 (tmtt) REVERT: B 532 ASN cc_start: 0.8160 (t0) cc_final: 0.7862 (t0) REVERT: B 574 ASP cc_start: 0.7323 (t70) cc_final: 0.6980 (t0) REVERT: B 581 THR cc_start: 0.7266 (OUTLIER) cc_final: 0.7030 (p) REVERT: B 661 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7807 (mm-30) REVERT: B 1119 ASN cc_start: 0.8391 (m-40) cc_final: 0.8084 (m110) REVERT: C 118 LEU cc_start: 0.7367 (tp) cc_final: 0.6709 (mt) REVERT: C 202 LYS cc_start: 0.6851 (mttm) cc_final: 0.6222 (mtmt) REVERT: C 271 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7459 (mt0) REVERT: C 353 TRP cc_start: 0.7247 (p-90) cc_final: 0.6747 (p-90) REVERT: C 360 ASN cc_start: 0.8127 (m-40) cc_final: 0.7700 (t0) REVERT: C 365 TYR cc_start: 0.8219 (m-80) cc_final: 0.7999 (m-80) REVERT: C 394 ASN cc_start: 0.7719 (m-40) cc_final: 0.7407 (m-40) REVERT: C 396 TYR cc_start: 0.7616 (m-80) cc_final: 0.6848 (m-80) REVERT: C 528 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7399 (mtpm) REVERT: C 529 LYS cc_start: 0.8587 (mttt) cc_final: 0.8219 (tmtt) REVERT: C 530 SER cc_start: 0.8732 (p) cc_final: 0.8523 (m) REVERT: C 532 ASN cc_start: 0.7992 (t0) cc_final: 0.7741 (t0) REVERT: C 537 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7525 (ptmt) REVERT: C 574 ASP cc_start: 0.7384 (t70) cc_final: 0.6941 (t0) REVERT: C 776 LYS cc_start: 0.8723 (tttt) cc_final: 0.8306 (ttpp) REVERT: C 780 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8127 (mm-30) REVERT: C 794 ILE cc_start: 0.8770 (mt) cc_final: 0.8282 (pp) REVERT: C 1144 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8238 (mp0) outliers start: 57 outliers final: 20 residues processed: 260 average time/residue: 0.4590 time to fit residues: 141.6649 Evaluate side-chains 217 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 140 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 935 GLN B 969 ASN B1002 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 901 GLN C 935 GLN C 969 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.178050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.113452 restraints weight = 29887.612| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.20 r_work: 0.3598 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 23349 Z= 0.244 Angle : 0.609 11.270 31785 Z= 0.319 Chirality : 0.047 0.159 3633 Planarity : 0.004 0.064 4098 Dihedral : 5.160 59.988 3101 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.15 % Allowed : 10.95 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.15), residues: 2844 helix: -0.54 (0.20), residues: 657 sheet: -1.12 (0.19), residues: 645 loop : -1.43 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 403 TYR 0.027 0.002 TYR A 505 PHE 0.021 0.002 PHE B 906 TRP 0.028 0.002 TRP B 353 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00592 (23310) covalent geometry : angle 0.60705 (31707) SS BOND : bond 0.00518 ( 39) SS BOND : angle 1.19587 ( 78) hydrogen bonds : bond 0.04138 ( 772) hydrogen bonds : angle 5.90751 ( 2145) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7355 (tp) cc_final: 0.6648 (mt) REVERT: A 206 LYS cc_start: 0.8202 (tptt) cc_final: 0.7653 (tptp) REVERT: A 287 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: A 351 TYR cc_start: 0.7722 (p90) cc_final: 0.6950 (p90) REVERT: A 360 ASN cc_start: 0.8061 (m-40) cc_final: 0.7723 (t0) REVERT: A 400 PHE cc_start: 0.8419 (p90) cc_final: 0.7916 (p90) REVERT: A 529 LYS cc_start: 0.8553 (mttt) cc_final: 0.8194 (tmtt) REVERT: A 558 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7766 (pmmt) REVERT: A 574 ASP cc_start: 0.7294 (t70) cc_final: 0.6748 (t0) REVERT: A 603 ASN cc_start: 0.8028 (t0) cc_final: 0.7742 (t0) REVERT: A 780 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7762 (mm-30) REVERT: B 237 ARG cc_start: 0.5952 (mtt90) cc_final: 0.5463 (mmt90) REVERT: B 335 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7423 (mm) REVERT: B 360 ASN cc_start: 0.8385 (m-40) cc_final: 0.8029 (t0) REVERT: B 394 ASN cc_start: 0.7586 (m-40) cc_final: 0.7315 (m-40) REVERT: B 529 LYS cc_start: 0.8574 (mttt) cc_final: 0.8317 (tmtt) REVERT: B 532 ASN cc_start: 0.8135 (t0) cc_final: 0.7677 (t0) REVERT: B 574 ASP cc_start: 0.7086 (t70) cc_final: 0.6674 (t0) REVERT: B 661 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7612 (mm-30) REVERT: B 790 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8126 (ptmm) REVERT: B 1045 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8108 (tmmt) REVERT: C 202 LYS cc_start: 0.6640 (mttm) cc_final: 0.6070 (mtmt) REVERT: C 271 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7303 (mt0) REVERT: C 335 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7382 (mm) REVERT: C 353 TRP cc_start: 0.7310 (p-90) cc_final: 0.7098 (p-90) REVERT: C 360 ASN cc_start: 0.8140 (m-40) cc_final: 0.7791 (t0) REVERT: C 394 ASN cc_start: 0.7759 (m-40) cc_final: 0.7520 (m-40) REVERT: C 396 TYR cc_start: 0.7354 (m-80) cc_final: 0.6652 (m-80) REVERT: C 528 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7202 (mtpp) REVERT: C 529 LYS cc_start: 0.8587 (mttt) cc_final: 0.8279 (tmtt) REVERT: C 530 SER cc_start: 0.8700 (p) cc_final: 0.8432 (m) REVERT: C 532 ASN cc_start: 0.8093 (t0) cc_final: 0.7847 (t0) REVERT: C 537 LYS cc_start: 0.7836 (ttpt) cc_final: 0.7363 (ptmt) REVERT: C 574 ASP cc_start: 0.7109 (t70) cc_final: 0.6577 (t0) REVERT: C 776 LYS cc_start: 0.8281 (tttt) cc_final: 0.7709 (ttpp) REVERT: C 780 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7943 (mm-30) REVERT: C 794 ILE cc_start: 0.8546 (mt) cc_final: 0.7874 (pp) REVERT: C 1144 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8166 (mp0) outliers start: 55 outliers final: 33 residues processed: 237 average time/residue: 0.4305 time to fit residues: 122.3717 Evaluate side-chains 224 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 169 optimal weight: 0.9980 chunk 280 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 141 optimal weight: 0.0470 chunk 223 optimal weight: 8.9990 chunk 190 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 213 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 901 GLN A 955 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B1002 GLN B1005 GLN B1119 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.178491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118316 restraints weight = 27587.866| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.13 r_work: 0.3380 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23349 Z= 0.110 Angle : 0.507 11.737 31785 Z= 0.262 Chirality : 0.044 0.145 3633 Planarity : 0.004 0.039 4098 Dihedral : 4.689 57.273 3101 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.84 % Allowed : 11.78 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 2844 helix: 0.19 (0.20), residues: 678 sheet: -0.82 (0.19), residues: 606 loop : -1.35 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 403 TYR 0.017 0.001 TYR A 505 PHE 0.015 0.001 PHE C 32 TRP 0.026 0.001 TRP B 353 HIS 0.004 0.000 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00258 (23310) covalent geometry : angle 0.50563 (31707) SS BOND : bond 0.00313 ( 39) SS BOND : angle 0.87072 ( 78) hydrogen bonds : bond 0.03137 ( 772) hydrogen bonds : angle 5.42889 ( 2145) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.6555 (m-30) cc_final: 0.6283 (t0) REVERT: A 206 LYS cc_start: 0.8380 (tptt) cc_final: 0.7819 (tptp) REVERT: A 287 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: A 351 TYR cc_start: 0.7784 (p90) cc_final: 0.6981 (p90) REVERT: A 360 ASN cc_start: 0.8138 (m-40) cc_final: 0.7835 (t0) REVERT: A 400 PHE cc_start: 0.8521 (p90) cc_final: 0.8002 (p90) REVERT: A 529 LYS cc_start: 0.8609 (mttt) cc_final: 0.8303 (tmtt) REVERT: A 558 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7879 (pmmt) REVERT: A 574 ASP cc_start: 0.7510 (t70) cc_final: 0.7111 (t0) REVERT: A 581 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.7024 (p) REVERT: A 780 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7943 (mm-30) REVERT: A 988 GLU cc_start: 0.8481 (mp0) cc_final: 0.7987 (mp0) REVERT: B 326 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.5970 (tt) REVERT: B 335 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7482 (mm) REVERT: B 360 ASN cc_start: 0.8441 (m-40) cc_final: 0.8134 (t0) REVERT: B 532 ASN cc_start: 0.8176 (t0) cc_final: 0.7824 (t0) REVERT: B 574 ASP cc_start: 0.7291 (t70) cc_final: 0.6959 (t0) REVERT: B 592 PHE cc_start: 0.7664 (p90) cc_final: 0.7392 (p90) REVERT: B 661 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8022 (mm-30) REVERT: B 969 ASN cc_start: 0.8224 (m110) cc_final: 0.7980 (m-40) REVERT: B 1045 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8329 (tmmt) REVERT: C 202 LYS cc_start: 0.6909 (mttm) cc_final: 0.6341 (mtmt) REVERT: C 206 LYS cc_start: 0.8386 (tptt) cc_final: 0.7926 (tptm) REVERT: C 335 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7515 (mm) REVERT: C 353 TRP cc_start: 0.7517 (p-90) cc_final: 0.7232 (p-90) REVERT: C 357 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7743 (mmm-85) REVERT: C 360 ASN cc_start: 0.8219 (m-40) cc_final: 0.7906 (t0) REVERT: C 396 TYR cc_start: 0.7262 (m-80) cc_final: 0.6801 (m-80) REVERT: C 528 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7353 (mtpm) REVERT: C 529 LYS cc_start: 0.8622 (mttt) cc_final: 0.8336 (tmtt) REVERT: C 532 ASN cc_start: 0.8174 (t0) cc_final: 0.7898 (t0) REVERT: C 537 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7461 (ptmt) REVERT: C 574 ASP cc_start: 0.7404 (t70) cc_final: 0.6926 (t0) REVERT: C 780 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8076 (mm-30) REVERT: C 787 GLN cc_start: 0.8570 (mt0) cc_final: 0.8359 (mt0) REVERT: C 791 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8282 (p) REVERT: C 794 ILE cc_start: 0.8855 (mt) cc_final: 0.8244 (pp) REVERT: C 1144 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8099 (mp0) outliers start: 47 outliers final: 24 residues processed: 244 average time/residue: 0.4013 time to fit residues: 118.5799 Evaluate side-chains 231 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 204 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 124 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.175975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.114797 restraints weight = 27681.307| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.08 r_work: 0.3341 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23349 Z= 0.171 Angle : 0.542 11.087 31785 Z= 0.281 Chirality : 0.045 0.149 3633 Planarity : 0.004 0.038 4098 Dihedral : 4.768 59.674 3101 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.58 % Allowed : 11.85 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.15), residues: 2844 helix: 0.44 (0.20), residues: 675 sheet: -0.97 (0.19), residues: 618 loop : -1.19 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 403 TYR 0.018 0.001 TYR B 396 PHE 0.017 0.002 PHE A 168 TRP 0.026 0.002 TRP B 353 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00412 (23310) covalent geometry : angle 0.54042 (31707) SS BOND : bond 0.00399 ( 39) SS BOND : angle 1.03511 ( 78) hydrogen bonds : bond 0.03575 ( 772) hydrogen bonds : angle 5.54134 ( 2145) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 205 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7529 (mm) REVERT: A 351 TYR cc_start: 0.7650 (p90) cc_final: 0.6904 (p90) REVERT: A 360 ASN cc_start: 0.8193 (m-40) cc_final: 0.7896 (t0) REVERT: A 400 PHE cc_start: 0.8525 (p90) cc_final: 0.8069 (p90) REVERT: A 529 LYS cc_start: 0.8603 (mttt) cc_final: 0.8252 (tmtt) REVERT: A 574 ASP cc_start: 0.7542 (t70) cc_final: 0.7074 (t0) REVERT: A 661 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: A 780 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7983 (mm-30) REVERT: A 988 GLU cc_start: 0.8567 (mp0) cc_final: 0.7884 (mp0) REVERT: B 190 ARG cc_start: 0.7063 (mtm180) cc_final: 0.6790 (mtt-85) REVERT: B 326 ILE cc_start: 0.6220 (OUTLIER) cc_final: 0.5912 (tt) REVERT: B 360 ASN cc_start: 0.8434 (m-40) cc_final: 0.8113 (t0) REVERT: B 506 GLN cc_start: 0.7674 (mt0) cc_final: 0.7299 (mp10) REVERT: B 532 ASN cc_start: 0.8205 (t0) cc_final: 0.7828 (t0) REVERT: B 574 ASP cc_start: 0.7316 (t70) cc_final: 0.6952 (t0) REVERT: B 592 PHE cc_start: 0.7700 (p90) cc_final: 0.7328 (p90) REVERT: B 661 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8043 (mm-30) REVERT: B 790 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8475 (ptmm) REVERT: B 1045 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8335 (tmmt) REVERT: B 1142 GLN cc_start: 0.8013 (tp40) cc_final: 0.7710 (tp-100) REVERT: C 206 LYS cc_start: 0.8398 (tptt) cc_final: 0.7989 (tptm) REVERT: C 335 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7495 (mm) REVERT: C 357 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7706 (mmm-85) REVERT: C 360 ASN cc_start: 0.8198 (m-40) cc_final: 0.7888 (t0) REVERT: C 396 TYR cc_start: 0.7218 (m-80) cc_final: 0.6895 (m-80) REVERT: C 400 PHE cc_start: 0.8191 (p90) cc_final: 0.7964 (p90) REVERT: C 528 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7340 (mtpm) REVERT: C 529 LYS cc_start: 0.8682 (mttt) cc_final: 0.8376 (tmtt) REVERT: C 532 ASN cc_start: 0.8189 (t0) cc_final: 0.7605 (t0) REVERT: C 574 ASP cc_start: 0.7380 (t70) cc_final: 0.6885 (t0) REVERT: C 780 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8124 (mm-30) REVERT: C 794 ILE cc_start: 0.8874 (mt) cc_final: 0.8222 (pp) REVERT: C 916 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8424 (tp) outliers start: 66 outliers final: 36 residues processed: 248 average time/residue: 0.4062 time to fit residues: 121.8386 Evaluate side-chains 238 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 955 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 969 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C1142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.174124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112899 restraints weight = 27701.315| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.11 r_work: 0.3312 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23349 Z= 0.221 Angle : 0.580 11.569 31785 Z= 0.300 Chirality : 0.047 0.178 3633 Planarity : 0.004 0.073 4098 Dihedral : 4.896 56.492 3101 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.31 % Allowed : 12.64 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.15), residues: 2844 helix: 0.35 (0.20), residues: 696 sheet: -0.73 (0.19), residues: 639 loop : -1.24 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 403 TYR 0.018 0.002 TYR B 396 PHE 0.015 0.002 PHE C 32 TRP 0.030 0.002 TRP B 353 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00538 (23310) covalent geometry : angle 0.57818 (31707) SS BOND : bond 0.00470 ( 39) SS BOND : angle 1.15544 ( 78) hydrogen bonds : bond 0.03827 ( 772) hydrogen bonds : angle 5.64517 ( 2145) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7459 (mm) REVERT: A 351 TYR cc_start: 0.7733 (p90) cc_final: 0.7018 (p90) REVERT: A 360 ASN cc_start: 0.8215 (m-40) cc_final: 0.7952 (t0) REVERT: A 400 PHE cc_start: 0.8554 (p90) cc_final: 0.8235 (p90) REVERT: A 529 LYS cc_start: 0.8592 (mttt) cc_final: 0.8248 (tmtt) REVERT: A 574 ASP cc_start: 0.7615 (t70) cc_final: 0.7159 (t0) REVERT: A 661 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: A 780 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7975 (mm-30) REVERT: A 988 GLU cc_start: 0.8658 (mp0) cc_final: 0.7878 (mp0) REVERT: B 190 ARG cc_start: 0.7102 (mtm180) cc_final: 0.6783 (mtt-85) REVERT: B 326 ILE cc_start: 0.6353 (OUTLIER) cc_final: 0.6059 (tt) REVERT: B 335 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7605 (mm) REVERT: B 532 ASN cc_start: 0.8156 (t0) cc_final: 0.7928 (m-40) REVERT: B 574 ASP cc_start: 0.7354 (t70) cc_final: 0.6978 (t0) REVERT: B 661 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8067 (mm-30) REVERT: B 790 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8465 (ptmm) REVERT: B 1045 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8299 (tmmt) REVERT: B 1142 GLN cc_start: 0.8043 (tp40) cc_final: 0.7755 (tp-100) REVERT: C 335 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7593 (mm) REVERT: C 360 ASN cc_start: 0.8252 (m-40) cc_final: 0.7940 (t0) REVERT: C 365 TYR cc_start: 0.8167 (m-80) cc_final: 0.7885 (m-80) REVERT: C 400 PHE cc_start: 0.8250 (p90) cc_final: 0.7980 (p90) REVERT: C 528 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7344 (mtpm) REVERT: C 529 LYS cc_start: 0.8668 (mttt) cc_final: 0.8375 (tmtt) REVERT: C 532 ASN cc_start: 0.8227 (t0) cc_final: 0.7746 (m-40) REVERT: C 574 ASP cc_start: 0.7382 (t70) cc_final: 0.6904 (t0) REVERT: C 780 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8171 (mm-30) REVERT: C 794 ILE cc_start: 0.8875 (mt) cc_final: 0.8204 (pp) REVERT: C 916 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8449 (tp) outliers start: 59 outliers final: 38 residues processed: 246 average time/residue: 0.3970 time to fit residues: 119.0198 Evaluate side-chains 232 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 4 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A1142 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B1135 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.175503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115988 restraints weight = 27524.363| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.97 r_work: 0.3348 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23349 Z= 0.160 Angle : 0.548 12.109 31785 Z= 0.280 Chirality : 0.045 0.176 3633 Planarity : 0.004 0.042 4098 Dihedral : 4.728 54.683 3101 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.00 % Allowed : 13.46 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 2844 helix: 0.64 (0.20), residues: 696 sheet: -0.87 (0.19), residues: 657 loop : -1.12 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 403 TYR 0.019 0.001 TYR B 170 PHE 0.022 0.002 PHE A 32 TRP 0.019 0.001 TRP A 353 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00387 (23310) covalent geometry : angle 0.54649 (31707) SS BOND : bond 0.00388 ( 39) SS BOND : angle 1.01354 ( 78) hydrogen bonds : bond 0.03409 ( 772) hydrogen bonds : angle 5.48855 ( 2145) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7436 (mm) REVERT: A 351 TYR cc_start: 0.7740 (p90) cc_final: 0.7047 (p90) REVERT: A 353 TRP cc_start: 0.7351 (p-90) cc_final: 0.6616 (p-90) REVERT: A 360 ASN cc_start: 0.8202 (m-40) cc_final: 0.7994 (t0) REVERT: A 529 LYS cc_start: 0.8626 (mttt) cc_final: 0.8400 (tmtt) REVERT: A 574 ASP cc_start: 0.7519 (t70) cc_final: 0.7087 (t0) REVERT: A 780 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7935 (mm-30) REVERT: A 988 GLU cc_start: 0.8648 (mp0) cc_final: 0.7959 (mp0) REVERT: B 169 GLU cc_start: 0.7934 (tt0) cc_final: 0.7032 (tm-30) REVERT: B 190 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6813 (mtt-85) REVERT: B 326 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.6023 (tt) REVERT: B 335 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7571 (mm) REVERT: B 532 ASN cc_start: 0.8139 (t0) cc_final: 0.7911 (m-40) REVERT: B 574 ASP cc_start: 0.7322 (t70) cc_final: 0.6963 (t0) REVERT: B 661 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8099 (mm-30) REVERT: B 1045 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8283 (tmmt) REVERT: B 1142 GLN cc_start: 0.8075 (tp40) cc_final: 0.7787 (tp-100) REVERT: C 287 ASP cc_start: 0.7503 (t0) cc_final: 0.7043 (m-30) REVERT: C 335 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7549 (mm) REVERT: C 360 ASN cc_start: 0.8253 (m-40) cc_final: 0.7964 (t0) REVERT: C 365 TYR cc_start: 0.8063 (m-80) cc_final: 0.7738 (m-80) REVERT: C 396 TYR cc_start: 0.7575 (m-80) cc_final: 0.7314 (m-10) REVERT: C 400 PHE cc_start: 0.8254 (p90) cc_final: 0.8010 (p90) REVERT: C 528 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7314 (mtpm) REVERT: C 529 LYS cc_start: 0.8675 (mttt) cc_final: 0.8395 (tmtt) REVERT: C 574 ASP cc_start: 0.7366 (t70) cc_final: 0.6880 (t0) REVERT: C 747 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8189 (t) REVERT: C 780 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8133 (mm-30) REVERT: C 794 ILE cc_start: 0.8894 (mt) cc_final: 0.8239 (pp) REVERT: C 916 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8388 (tp) outliers start: 51 outliers final: 31 residues processed: 239 average time/residue: 0.4090 time to fit residues: 119.1331 Evaluate side-chains 232 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 28 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 219 optimal weight: 0.0000 chunk 55 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 209 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 200 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 247 optimal weight: 0.4980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 613 GLN B 969 ASN B1119 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C1142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.177100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.117237 restraints weight = 27729.143| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.13 r_work: 0.3370 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23349 Z= 0.111 Angle : 0.521 12.092 31785 Z= 0.263 Chirality : 0.044 0.160 3633 Planarity : 0.004 0.040 4098 Dihedral : 4.482 54.293 3101 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.64 % Allowed : 13.85 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2844 helix: 1.05 (0.21), residues: 702 sheet: -0.73 (0.20), residues: 624 loop : -1.06 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 403 TYR 0.020 0.001 TYR A 170 PHE 0.021 0.001 PHE A 32 TRP 0.018 0.001 TRP A 353 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00262 (23310) covalent geometry : angle 0.51994 (31707) SS BOND : bond 0.00306 ( 39) SS BOND : angle 0.87330 ( 78) hydrogen bonds : bond 0.03030 ( 772) hydrogen bonds : angle 5.27172 ( 2145) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6238 (mtm180) cc_final: 0.5540 (mpt-90) REVERT: A 351 TYR cc_start: 0.7696 (p90) cc_final: 0.6967 (p90) REVERT: A 400 PHE cc_start: 0.8420 (p90) cc_final: 0.8012 (p90) REVERT: A 529 LYS cc_start: 0.8651 (mttt) cc_final: 0.8385 (tmtt) REVERT: A 574 ASP cc_start: 0.7491 (t70) cc_final: 0.7053 (t0) REVERT: A 581 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.6967 (p) REVERT: A 780 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7920 (mm-30) REVERT: A 988 GLU cc_start: 0.8631 (mp0) cc_final: 0.7932 (mp0) REVERT: B 169 GLU cc_start: 0.7890 (tt0) cc_final: 0.6896 (tm-30) REVERT: B 190 ARG cc_start: 0.7195 (mtm180) cc_final: 0.6768 (mtt-85) REVERT: B 206 LYS cc_start: 0.8344 (tptt) cc_final: 0.7818 (tmtt) REVERT: B 326 ILE cc_start: 0.6009 (OUTLIER) cc_final: 0.5759 (tt) REVERT: B 351 TYR cc_start: 0.7745 (p90) cc_final: 0.6734 (p90) REVERT: B 574 ASP cc_start: 0.7251 (t70) cc_final: 0.6884 (t0) REVERT: B 661 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8062 (mm-30) REVERT: B 780 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7925 (mm-30) REVERT: B 969 ASN cc_start: 0.8255 (m110) cc_final: 0.8013 (m-40) REVERT: B 1045 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8324 (tmmt) REVERT: B 1142 GLN cc_start: 0.8051 (tp40) cc_final: 0.7751 (tp-100) REVERT: C 287 ASP cc_start: 0.7495 (t0) cc_final: 0.7035 (m-30) REVERT: C 360 ASN cc_start: 0.8183 (m-40) cc_final: 0.7854 (t0) REVERT: C 365 TYR cc_start: 0.8146 (m-80) cc_final: 0.7787 (m-80) REVERT: C 400 PHE cc_start: 0.8283 (p90) cc_final: 0.8023 (p90) REVERT: C 528 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7262 (mtpm) REVERT: C 529 LYS cc_start: 0.8614 (mttt) cc_final: 0.8254 (tmtt) REVERT: C 574 ASP cc_start: 0.7300 (t70) cc_final: 0.6812 (t0) REVERT: C 747 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8130 (t) REVERT: C 791 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8322 (p) REVERT: C 794 ILE cc_start: 0.8884 (mt) cc_final: 0.8246 (pp) REVERT: C 916 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8286 (tt) REVERT: C 1119 ASN cc_start: 0.8432 (m110) cc_final: 0.8114 (m-40) outliers start: 42 outliers final: 28 residues processed: 240 average time/residue: 0.3960 time to fit residues: 115.5629 Evaluate side-chains 236 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 108 optimal weight: 10.0000 chunk 143 optimal weight: 0.0270 chunk 18 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 chunk 233 optimal weight: 8.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.177101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.117821 restraints weight = 27679.518| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.14 r_work: 0.3373 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23349 Z= 0.112 Angle : 0.521 11.510 31785 Z= 0.263 Chirality : 0.044 0.166 3633 Planarity : 0.004 0.050 4098 Dihedral : 4.421 53.784 3101 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.37 % Allowed : 14.51 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2844 helix: 1.33 (0.21), residues: 684 sheet: -0.62 (0.20), residues: 618 loop : -1.06 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 403 TYR 0.013 0.001 TYR C 396 PHE 0.025 0.001 PHE C 168 TRP 0.015 0.001 TRP A 353 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00264 (23310) covalent geometry : angle 0.51978 (31707) SS BOND : bond 0.00305 ( 39) SS BOND : angle 0.87556 ( 78) hydrogen bonds : bond 0.03027 ( 772) hydrogen bonds : angle 5.21606 ( 2145) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7852 (tt0) cc_final: 0.7105 (tm-30) REVERT: A 237 ARG cc_start: 0.6223 (mtm180) cc_final: 0.5528 (mpt-90) REVERT: A 351 TYR cc_start: 0.7679 (p90) cc_final: 0.6958 (p90) REVERT: A 353 TRP cc_start: 0.7352 (p-90) cc_final: 0.6478 (p-90) REVERT: A 400 PHE cc_start: 0.8402 (p90) cc_final: 0.8043 (p90) REVERT: A 529 LYS cc_start: 0.8660 (mttt) cc_final: 0.8384 (tmtt) REVERT: A 574 ASP cc_start: 0.7481 (t70) cc_final: 0.7082 (t0) REVERT: A 581 THR cc_start: 0.7331 (OUTLIER) cc_final: 0.6969 (p) REVERT: A 780 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7898 (mm-30) REVERT: A 988 GLU cc_start: 0.8616 (mp0) cc_final: 0.7906 (mp0) REVERT: B 190 ARG cc_start: 0.7263 (mtm180) cc_final: 0.6833 (mtt-85) REVERT: B 206 LYS cc_start: 0.8339 (tptt) cc_final: 0.7822 (tmtt) REVERT: B 326 ILE cc_start: 0.6045 (OUTLIER) cc_final: 0.5816 (tt) REVERT: B 351 TYR cc_start: 0.7732 (p90) cc_final: 0.6751 (p90) REVERT: B 574 ASP cc_start: 0.7242 (t70) cc_final: 0.6921 (t0) REVERT: B 661 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8070 (mm-30) REVERT: B 780 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7899 (mm-30) REVERT: B 969 ASN cc_start: 0.8227 (m110) cc_final: 0.7993 (m-40) REVERT: B 1142 GLN cc_start: 0.8048 (tp40) cc_final: 0.7745 (tp-100) REVERT: C 287 ASP cc_start: 0.7472 (t0) cc_final: 0.7033 (m-30) REVERT: C 360 ASN cc_start: 0.8234 (m-40) cc_final: 0.7904 (t0) REVERT: C 365 TYR cc_start: 0.8140 (m-80) cc_final: 0.7803 (m-80) REVERT: C 400 PHE cc_start: 0.8298 (p90) cc_final: 0.8028 (p90) REVERT: C 528 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7257 (mtpm) REVERT: C 529 LYS cc_start: 0.8618 (mttt) cc_final: 0.8255 (tmtt) REVERT: C 574 ASP cc_start: 0.7298 (t70) cc_final: 0.6790 (t0) REVERT: C 747 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8118 (t) REVERT: C 791 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8305 (p) REVERT: C 794 ILE cc_start: 0.8881 (mt) cc_final: 0.8240 (pp) REVERT: C 916 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8316 (tt) REVERT: C 1119 ASN cc_start: 0.8437 (m110) cc_final: 0.8110 (m-40) outliers start: 35 outliers final: 28 residues processed: 235 average time/residue: 0.3791 time to fit residues: 108.9879 Evaluate side-chains 235 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 55 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 282 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 266 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.176106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117891 restraints weight = 27658.380| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.33 r_work: 0.3339 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23349 Z= 0.141 Angle : 0.538 11.582 31785 Z= 0.272 Chirality : 0.045 0.183 3633 Planarity : 0.004 0.053 4098 Dihedral : 4.511 53.232 3101 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.37 % Allowed : 14.71 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2844 helix: 1.33 (0.21), residues: 681 sheet: -0.59 (0.20), residues: 621 loop : -0.94 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 403 TYR 0.018 0.001 TYR B 170 PHE 0.023 0.001 PHE C 168 TRP 0.016 0.001 TRP A 353 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00340 (23310) covalent geometry : angle 0.53629 (31707) SS BOND : bond 0.00349 ( 39) SS BOND : angle 0.95695 ( 78) hydrogen bonds : bond 0.03224 ( 772) hydrogen bonds : angle 5.28679 ( 2145) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8994.40 seconds wall clock time: 153 minutes 21.41 seconds (9201.41 seconds total)