Starting phenix.real_space_refine on Thu Mar 5 21:39:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ddd_30651/03_2026/7ddd_30651.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ddd_30651/03_2026/7ddd_30651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ddd_30651/03_2026/7ddd_30651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ddd_30651/03_2026/7ddd_30651.map" model { file = "/net/cci-nas-00/data/ceres_data/7ddd_30651/03_2026/7ddd_30651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ddd_30651/03_2026/7ddd_30651.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.056 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 120 5.16 5 C 16260 2.51 5 N 4263 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s 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: 25503 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Chain: "B" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Chain: "C" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Time building chain proxies: 5.33, per 1000 atoms: 0.21 Number of scatterers: 25503 At special positions: 0 Unit cell: (138.72, 149.94, 175.44, 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 120 16.00 O 4860 8.00 N 4263 7.00 C 16260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 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: 1.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6108 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 51 sheets defined 23.6% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.841A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.717A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.612A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (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 758 through 783 removed outlier: 3.537A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 836 through 842 removed outlier: 3.526A pdb=" N CYS A 840 " --> pdb=" O GLN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.650A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.723A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.514A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.017A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.702A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.707A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.867A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.532A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.841A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.810A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.608A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (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 758 through 783 removed outlier: 3.504A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.523A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.638A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.722A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.507A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.050A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.708A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.624A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.851A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1031 removed outlier: 3.558A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.828A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.774A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.621A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (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 758 through 783 removed outlier: 3.545A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 836 through 842 removed outlier: 3.541A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.654A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.699A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.768A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.030A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.728A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.710A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.845A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1031 removed outlier: 3.543A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 5.320A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.678A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.882A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.882A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.537A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.860A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.672A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.611A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.813A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 595 through 598 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.872A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.750A 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: 3.612A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.612A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.268A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.609A 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 'B' and resid 29 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.683A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.851A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.851A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.517A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.598A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.677A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.640A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.846A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 595 through 598 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.874A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.765A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.599A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.599A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.250A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.521A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.681A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.889A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.889A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.533A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.533A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.620A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 595 through 598 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.878A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.615A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.615A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.283A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 888 hydrogen bonds defined for protein. 2394 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: 6.04 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8277 1.35 - 1.47: 6486 1.47 - 1.59: 11175 1.59 - 1.72: 0 1.72 - 1.84: 150 Bond restraints: 26088 Sorted by residual: bond pdb=" N LYS A 147 " pdb=" CA LYS A 147 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.23e-02 6.61e+03 9.95e+00 bond pdb=" N LYS B 147 " pdb=" CA LYS B 147 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.23e-02 6.61e+03 9.71e+00 bond pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.32e-02 5.74e+03 6.89e+00 bond pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.32e-02 5.74e+03 6.83e+00 bond pdb=" N ASP C 215 " pdb=" CA ASP C 215 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.32e-02 5.74e+03 6.77e+00 ... (remaining 26083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 34671 1.97 - 3.94: 713 3.94 - 5.91: 85 5.91 - 7.89: 13 7.89 - 9.86: 11 Bond angle restraints: 35493 Sorted by residual: angle pdb=" C ARG B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.31 131.17 -9.86 1.49e+00 4.50e-01 4.38e+01 angle pdb=" C ARG A 214 " pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 121.31 131.13 -9.82 1.49e+00 4.50e-01 4.35e+01 angle pdb=" C ARG C 214 " pdb=" N ASP C 215 " pdb=" CA ASP C 215 " ideal model delta sigma weight residual 121.31 131.13 -9.82 1.49e+00 4.50e-01 4.34e+01 angle pdb=" C HIS B 146 " pdb=" N LYS B 147 " pdb=" CA LYS B 147 " ideal model delta sigma weight residual 120.82 129.61 -8.79 1.50e+00 4.44e-01 3.43e+01 angle pdb=" C HIS A 146 " pdb=" N LYS A 147 " pdb=" CA LYS A 147 " ideal model delta sigma weight residual 120.82 129.60 -8.78 1.50e+00 4.44e-01 3.43e+01 ... (remaining 35488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 15205 17.78 - 35.56: 259 35.56 - 53.34: 88 53.34 - 71.12: 9 71.12 - 88.89: 9 Dihedral angle restraints: 15570 sinusoidal: 6072 harmonic: 9498 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -174.89 88.89 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -174.28 88.28 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -173.69 87.69 1 1.00e+01 1.00e-02 9.21e+01 ... (remaining 15567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2690 0.039 - 0.077: 837 0.077 - 0.116: 393 0.116 - 0.154: 88 0.154 - 0.193: 6 Chirality restraints: 4014 Sorted by residual: chirality pdb=" CB ILE C 197 " pdb=" CA ILE C 197 " pdb=" CG1 ILE C 197 " pdb=" CG2 ILE C 197 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CB ILE B 197 " pdb=" CA ILE B 197 " pdb=" CG1 ILE B 197 " pdb=" CG2 ILE B 197 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 4011 not shown) Planarity restraints: 4617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.046 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO C 987 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.046 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO A 987 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO B 987 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.039 5.00e-02 4.00e+02 ... (remaining 4614 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4862 2.78 - 3.31: 21691 3.31 - 3.84: 42943 3.84 - 4.37: 49964 4.37 - 4.90: 86040 Nonbonded interactions: 205500 Sorted by model distance: nonbonded pdb=" OD1 ASP A 985 " pdb=" OG1 THR C 385 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR B 385 " pdb=" OD1 ASP C 985 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 385 " pdb=" OD1 ASP B 985 " model vdw 2.251 3.040 nonbonded pdb=" O TYR A 756 " pdb=" OG SER C 968 " model vdw 2.329 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.338 3.040 ... (remaining 205495 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: 0.06 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: 7.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 23.370 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26130 Z= 0.172 Angle : 0.716 9.858 35577 Z= 0.431 Chirality : 0.047 0.193 4014 Planarity : 0.006 0.069 4617 Dihedral : 8.160 78.380 9336 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -3.86 (0.12), residues: 3234 helix: -4.43 (0.07), residues: 684 sheet: -1.17 (0.21), residues: 528 loop : -2.35 (0.11), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 466 TYR 0.017 0.002 TYR A 495 PHE 0.019 0.002 PHE B 888 TRP 0.015 0.002 TRP B 258 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00296 (26088) covalent geometry : angle 0.71307 (35493) SS BOND : bond 0.00349 ( 42) SS BOND : angle 1.43077 ( 84) hydrogen bonds : bond 0.29923 ( 817) hydrogen bonds : angle 11.46984 ( 2394) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 912 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7120 (p90) cc_final: 0.6191 (p90) REVERT: A 955 ASN cc_start: 0.6510 (m-40) cc_final: 0.6254 (m110) REVERT: B 302 THR cc_start: 0.7649 (m) cc_final: 0.7369 (p) REVERT: B 955 ASN cc_start: 0.6583 (m-40) cc_final: 0.6346 (m-40) REVERT: C 100 ILE cc_start: 0.7889 (mm) cc_final: 0.7655 (mm) REVERT: C 140 PHE cc_start: 0.7185 (p90) cc_final: 0.6300 (p90) outliers start: 0 outliers final: 8 residues processed: 912 average time/residue: 0.5005 time to fit residues: 543.9616 Evaluate side-chains 433 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 425 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0980 chunk 298 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 146 HIS A 239 GLN A 245 HIS A 321 GLN A 360 ASN A 388 ASN A 690 GLN A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 953 ASN A 969 ASN A1036 GLN A1083 HIS A1101 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 146 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 314 GLN B 321 GLN B 343 ASN B 360 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 953 ASN B1083 HIS B1101 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 146 HIS C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 314 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 953 ASN C 969 ASN C1005 GLN C1054 GLN C1083 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.159113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.144349 restraints weight = 48777.775| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.88 r_work: 0.3924 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26130 Z= 0.151 Angle : 0.609 7.589 35577 Z= 0.327 Chirality : 0.045 0.191 4014 Planarity : 0.005 0.049 4617 Dihedral : 5.144 83.379 3517 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 3.45 % Allowed : 13.73 % Favored : 82.82 % 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: -2.64 (0.12), residues: 3234 helix: -2.13 (0.15), residues: 690 sheet: -0.90 (0.20), residues: 594 loop : -1.94 (0.12), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.019 0.002 TYR A 660 PHE 0.026 0.002 PHE B 643 TRP 0.019 0.002 TRP C1102 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00334 (26088) covalent geometry : angle 0.60685 (35493) SS BOND : bond 0.00328 ( 42) SS BOND : angle 1.26789 ( 84) hydrogen bonds : bond 0.04779 ( 817) hydrogen bonds : angle 6.45826 ( 2394) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 443 time to evaluate : 0.885 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 304 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8088 (mptt) REVERT: A 340 GLU cc_start: 0.6564 (tp30) cc_final: 0.6348 (tp30) REVERT: A 365 TYR cc_start: 0.7757 (p90) cc_final: 0.7396 (p90) REVERT: A 403 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7336 (ttt-90) REVERT: A 964 LYS cc_start: 0.8130 (mttt) cc_final: 0.7900 (mptt) REVERT: A 1075 PHE cc_start: 0.7874 (m-80) cc_final: 0.7610 (m-80) REVERT: B 46 SER cc_start: 0.8908 (m) cc_final: 0.8688 (t) REVERT: B 287 ASP cc_start: 0.7597 (t0) cc_final: 0.7078 (t0) REVERT: B 964 LYS cc_start: 0.8285 (mttt) cc_final: 0.7879 (mptt) REVERT: C 100 ILE cc_start: 0.7989 (mm) cc_final: 0.7765 (mt) REVERT: C 451 TYR cc_start: 0.7273 (m-80) cc_final: 0.7013 (m-80) REVERT: C 796 ASP cc_start: 0.6399 (OUTLIER) cc_final: 0.6048 (m-30) REVERT: C 936 ASP cc_start: 0.8057 (m-30) cc_final: 0.7766 (m-30) REVERT: C 957 GLN cc_start: 0.7477 (tp40) cc_final: 0.7240 (tp40) REVERT: C 960 ASN cc_start: 0.8265 (m-40) cc_final: 0.7486 (m-40) REVERT: C 964 LYS cc_start: 0.8042 (mptt) cc_final: 0.7221 (mptt) REVERT: C 994 ASP cc_start: 0.8185 (t70) cc_final: 0.7973 (t0) outliers start: 98 outliers final: 36 residues processed: 519 average time/residue: 0.4578 time to fit residues: 287.8340 Evaluate side-chains 326 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 287 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 205 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 274 optimal weight: 6.9990 chunk 269 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 207 HIS A 234 ASN A 239 GLN A 314 GLN A 388 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 957 GLN A1074 ASN A1083 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN B1083 HIS B1088 HIS B1101 HIS C 69 HIS C 188 ASN C 239 GLN C 321 GLN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1083 HIS C1088 HIS C1101 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.137667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.121386 restraints weight = 48401.213| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.86 r_work: 0.3602 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 26130 Z= 0.255 Angle : 0.731 10.916 35577 Z= 0.384 Chirality : 0.049 0.246 4014 Planarity : 0.005 0.067 4617 Dihedral : 5.445 51.829 3505 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 4.75 % Allowed : 14.57 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.13), residues: 3234 helix: -0.92 (0.18), residues: 696 sheet: -0.84 (0.20), residues: 558 loop : -1.67 (0.12), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 158 TYR 0.029 0.003 TYR A 495 PHE 0.030 0.003 PHE B 347 TRP 0.030 0.003 TRP A 64 HIS 0.009 0.002 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00590 (26088) covalent geometry : angle 0.72871 (35493) SS BOND : bond 0.00512 ( 42) SS BOND : angle 1.34728 ( 84) hydrogen bonds : bond 0.04841 ( 817) hydrogen bonds : angle 6.06183 ( 2394) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 367 time to evaluate : 0.789 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 271 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: A 387 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 727 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8718 (pp) REVERT: A 904 TYR cc_start: 0.8124 (m-10) cc_final: 0.7276 (m-80) REVERT: A 922 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8329 (tp) REVERT: A 926 GLN cc_start: 0.7827 (mt0) cc_final: 0.7589 (mt0) REVERT: A 964 LYS cc_start: 0.8328 (mttt) cc_final: 0.8007 (mptt) REVERT: A 1017 GLU cc_start: 0.8516 (tt0) cc_final: 0.8248 (tp30) REVERT: A 1050 MET cc_start: 0.8409 (ptp) cc_final: 0.8203 (ptp) REVERT: B 96 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: B 97 LYS cc_start: 0.6489 (ptpt) cc_final: 0.5909 (pptt) REVERT: B 100 ILE cc_start: 0.8382 (mm) cc_final: 0.8040 (mt) REVERT: B 153 MET cc_start: 0.2773 (OUTLIER) cc_final: 0.2441 (pp-130) REVERT: B 287 ASP cc_start: 0.8272 (t0) cc_final: 0.8008 (t0) REVERT: B 305 SER cc_start: 0.8318 (t) cc_final: 0.8009 (p) REVERT: B 675 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: B 936 ASP cc_start: 0.7717 (m-30) cc_final: 0.7492 (m-30) REVERT: B 964 LYS cc_start: 0.8508 (mttt) cc_final: 0.8208 (mptt) REVERT: B 1106 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: C 96 GLU cc_start: 0.7326 (mp0) cc_final: 0.6985 (mp0) REVERT: C 357 ARG cc_start: 0.7838 (tpp-160) cc_final: 0.7564 (tpm170) REVERT: C 403 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7607 (ttm-80) REVERT: C 727 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8639 (pp) REVERT: C 936 ASP cc_start: 0.8276 (m-30) cc_final: 0.7917 (m-30) REVERT: C 957 GLN cc_start: 0.7852 (tp40) cc_final: 0.7505 (tp40) REVERT: C 1002 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8288 (tm-30) outliers start: 135 outliers final: 54 residues processed: 470 average time/residue: 0.4370 time to fit residues: 250.9299 Evaluate side-chains 317 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 253 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 292 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 122 optimal weight: 0.0170 chunk 80 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 309 optimal weight: 3.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B1005 GLN B1083 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 540 ASN C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1074 ASN C1083 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.135470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.119279 restraints weight = 48306.908| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.87 r_work: 0.3586 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26130 Z= 0.173 Angle : 0.618 8.207 35577 Z= 0.320 Chirality : 0.046 0.195 4014 Planarity : 0.004 0.057 4617 Dihedral : 5.106 60.225 3503 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 3.91 % Allowed : 16.54 % Favored : 79.55 % 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: -1.71 (0.13), residues: 3234 helix: -0.43 (0.19), residues: 699 sheet: -0.86 (0.20), residues: 618 loop : -1.52 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.020 0.002 TYR C 495 PHE 0.028 0.002 PHE B 140 TRP 0.025 0.002 TRP B 64 HIS 0.009 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00402 (26088) covalent geometry : angle 0.61288 (35493) SS BOND : bond 0.00546 ( 42) SS BOND : angle 1.73965 ( 84) hydrogen bonds : bond 0.03946 ( 817) hydrogen bonds : angle 5.83337 ( 2394) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 301 time to evaluate : 0.923 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 96 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: A 118 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7707 (tm) REVERT: A 207 HIS cc_start: 0.6480 (OUTLIER) cc_final: 0.6179 (t-90) REVERT: A 378 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8366 (ptmm) REVERT: A 392 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: A 904 TYR cc_start: 0.8099 (m-10) cc_final: 0.7092 (m-80) REVERT: A 922 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8309 (tp) REVERT: A 926 GLN cc_start: 0.8047 (mt0) cc_final: 0.7820 (mt0) REVERT: A 964 LYS cc_start: 0.8391 (mttt) cc_final: 0.8098 (mptt) REVERT: A 1017 GLU cc_start: 0.8492 (tt0) cc_final: 0.8259 (tp30) REVERT: B 287 ASP cc_start: 0.8154 (t0) cc_final: 0.7949 (t0) REVERT: B 305 SER cc_start: 0.8463 (t) cc_final: 0.8173 (p) REVERT: B 319 ARG cc_start: 0.7785 (mmt-90) cc_final: 0.7444 (mmt-90) REVERT: B 365 TYR cc_start: 0.8736 (p90) cc_final: 0.8483 (p90) REVERT: B 675 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7771 (mp10) REVERT: B 710 ASN cc_start: 0.8125 (p0) cc_final: 0.7897 (p0) REVERT: B 954 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: C 96 GLU cc_start: 0.7144 (mp0) cc_final: 0.6872 (mp0) REVERT: C 378 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8342 (ttpp) REVERT: C 727 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8765 (pp) REVERT: C 850 ILE cc_start: 0.9157 (mm) cc_final: 0.8909 (mp) REVERT: C 912 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8706 (p) REVERT: C 936 ASP cc_start: 0.8113 (m-30) cc_final: 0.7836 (m-30) REVERT: C 957 GLN cc_start: 0.8056 (tp40) cc_final: 0.7755 (tp40) outliers start: 111 outliers final: 47 residues processed: 383 average time/residue: 0.4457 time to fit residues: 209.0096 Evaluate side-chains 302 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 314 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 231 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1083 HIS C 207 HIS C 540 ASN C 607 GLN C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1083 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.135735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.121152 restraints weight = 47076.146| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.45 r_work: 0.3617 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26130 Z= 0.153 Angle : 0.586 8.532 35577 Z= 0.302 Chirality : 0.045 0.186 4014 Planarity : 0.004 0.053 4617 Dihedral : 4.841 22.391 3501 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.05 % Allowed : 17.35 % Favored : 78.60 % 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: -1.52 (0.14), residues: 3234 helix: -0.21 (0.20), residues: 699 sheet: -0.57 (0.21), residues: 522 loop : -1.47 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 273 TYR 0.018 0.002 TYR C 495 PHE 0.024 0.001 PHE B 140 TRP 0.022 0.002 TRP B 64 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00355 (26088) covalent geometry : angle 0.58227 (35493) SS BOND : bond 0.00412 ( 42) SS BOND : angle 1.46365 ( 84) hydrogen bonds : bond 0.03791 ( 817) hydrogen bonds : angle 5.67124 ( 2394) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 291 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: A 97 LYS cc_start: 0.6419 (ptpt) cc_final: 0.6021 (pptt) REVERT: A 298 GLU cc_start: 0.8656 (tt0) cc_final: 0.8347 (mt-10) REVERT: A 727 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8555 (pp) REVERT: A 900 MET cc_start: 0.8338 (mtt) cc_final: 0.7704 (mtt) REVERT: A 904 TYR cc_start: 0.7871 (m-10) cc_final: 0.6798 (m-80) REVERT: A 922 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8497 (tp) REVERT: A 964 LYS cc_start: 0.8314 (mttt) cc_final: 0.8034 (mptt) REVERT: A 1017 GLU cc_start: 0.8506 (tt0) cc_final: 0.8216 (tp30) REVERT: B 287 ASP cc_start: 0.8249 (t0) cc_final: 0.8041 (t0) REVERT: B 298 GLU cc_start: 0.8544 (tt0) cc_final: 0.8327 (mt-10) REVERT: B 305 SER cc_start: 0.8476 (t) cc_final: 0.8191 (p) REVERT: B 510 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8698 (m) REVERT: B 675 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7692 (mp10) REVERT: B 727 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8719 (pp) REVERT: B 964 LYS cc_start: 0.8288 (mptt) cc_final: 0.7544 (mptt) REVERT: B 995 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8887 (mtm-85) REVERT: C 96 GLU cc_start: 0.7071 (mp0) cc_final: 0.6811 (mp0) REVERT: C 305 SER cc_start: 0.8450 (t) cc_final: 0.8167 (p) REVERT: C 378 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8394 (ttpp) REVERT: C 727 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8739 (pp) REVERT: C 780 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7145 (mm-30) REVERT: C 850 ILE cc_start: 0.9134 (mm) cc_final: 0.8903 (mp) REVERT: C 936 ASP cc_start: 0.8018 (m-30) cc_final: 0.7788 (m-30) REVERT: C 957 GLN cc_start: 0.7979 (tp40) cc_final: 0.7473 (tp40) REVERT: C 961 THR cc_start: 0.8959 (m) cc_final: 0.8607 (p) REVERT: C 964 LYS cc_start: 0.8101 (mptt) cc_final: 0.7326 (mptt) REVERT: C 1119 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7689 (t160) REVERT: C 1142 GLN cc_start: 0.7740 (tp40) cc_final: 0.7496 (tp40) outliers start: 115 outliers final: 49 residues processed: 377 average time/residue: 0.4302 time to fit residues: 199.5187 Evaluate side-chains 311 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 253 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 162 optimal weight: 7.9990 chunk 193 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 262 optimal weight: 0.7980 chunk 240 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 207 HIS C 540 ASN C 607 GLN C 755 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.137063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122694 restraints weight = 47621.843| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.42 r_work: 0.3632 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26130 Z= 0.129 Angle : 0.562 9.134 35577 Z= 0.290 Chirality : 0.044 0.155 4014 Planarity : 0.004 0.046 4617 Dihedral : 4.742 26.253 3501 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.63 % Allowed : 18.37 % Favored : 78.00 % 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: -1.38 (0.14), residues: 3234 helix: -0.07 (0.20), residues: 714 sheet: -0.48 (0.21), residues: 540 loop : -1.40 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 466 TYR 0.017 0.001 TYR C 495 PHE 0.019 0.001 PHE B 140 TRP 0.021 0.002 TRP B 64 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00296 (26088) covalent geometry : angle 0.55861 (35493) SS BOND : bond 0.00556 ( 42) SS BOND : angle 1.36193 ( 84) hydrogen bonds : bond 0.03645 ( 817) hydrogen bonds : angle 5.55177 ( 2394) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 286 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.6432 (ptpt) cc_final: 0.6073 (pptt) REVERT: A 138 ASP cc_start: 0.7019 (p0) cc_final: 0.6568 (p0) REVERT: A 306 PHE cc_start: 0.7956 (m-10) cc_final: 0.7715 (m-10) REVERT: A 510 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8771 (m) REVERT: A 612 TYR cc_start: 0.7861 (m-80) cc_final: 0.7624 (m-80) REVERT: A 900 MET cc_start: 0.8345 (mtt) cc_final: 0.7713 (mtt) REVERT: A 904 TYR cc_start: 0.7848 (m-80) cc_final: 0.6783 (m-80) REVERT: A 964 LYS cc_start: 0.8360 (mttt) cc_final: 0.7975 (mptt) REVERT: A 1002 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 1017 GLU cc_start: 0.8445 (tt0) cc_final: 0.8219 (tp30) REVERT: B 97 LYS cc_start: 0.6400 (ptpt) cc_final: 0.5774 (pptt) REVERT: B 100 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7750 (mp) REVERT: B 118 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7162 (tm) REVERT: B 287 ASP cc_start: 0.8202 (t0) cc_final: 0.7985 (t0) REVERT: B 305 SER cc_start: 0.8524 (t) cc_final: 0.8274 (p) REVERT: B 319 ARG cc_start: 0.7637 (mmt-90) cc_final: 0.7333 (mmt-90) REVERT: B 510 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8719 (m) REVERT: B 675 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: B 727 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8759 (pp) REVERT: B 995 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8835 (mtm-85) REVERT: C 153 MET cc_start: 0.4239 (OUTLIER) cc_final: 0.3944 (ppp) REVERT: C 305 SER cc_start: 0.8508 (t) cc_final: 0.8242 (p) REVERT: C 378 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8397 (ttpp) REVERT: C 461 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5875 (pp) REVERT: C 612 TYR cc_start: 0.8388 (m-80) cc_final: 0.8174 (m-80) REVERT: C 727 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8743 (pp) REVERT: C 850 ILE cc_start: 0.9128 (mm) cc_final: 0.8893 (mp) REVERT: C 957 GLN cc_start: 0.7993 (tp40) cc_final: 0.7502 (tp40) REVERT: C 1119 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7729 (t160) outliers start: 103 outliers final: 47 residues processed: 360 average time/residue: 0.3989 time to fit residues: 179.2642 Evaluate side-chains 317 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 259 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 288 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 297 optimal weight: 0.5980 chunk 285 optimal weight: 5.9990 chunk 316 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 207 HIS C 501 ASN C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1083 HIS C1135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.129675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115865 restraints weight = 47744.750| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.23 r_work: 0.3537 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.7283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 26130 Z= 0.263 Angle : 0.703 14.039 35577 Z= 0.363 Chirality : 0.048 0.202 4014 Planarity : 0.005 0.081 4617 Dihedral : 5.300 31.692 3501 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.15 % Allowed : 18.41 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.49 (0.14), residues: 3234 helix: -0.19 (0.20), residues: 702 sheet: -0.84 (0.21), residues: 513 loop : -1.35 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 466 TYR 0.030 0.002 TYR C 495 PHE 0.026 0.002 PHE B 140 TRP 0.033 0.003 TRP B 64 HIS 0.008 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00610 (26088) covalent geometry : angle 0.69801 (35493) SS BOND : bond 0.00567 ( 42) SS BOND : angle 1.82062 ( 84) hydrogen bonds : bond 0.04248 ( 817) hydrogen bonds : angle 5.93356 ( 2394) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 267 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.6698 (ptpt) cc_final: 0.6441 (pptt) REVERT: A 138 ASP cc_start: 0.7159 (p0) cc_final: 0.6898 (p0) REVERT: A 305 SER cc_start: 0.8794 (t) cc_final: 0.8566 (p) REVERT: A 1002 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8584 (tm-30) REVERT: B 41 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7881 (mmmt) REVERT: B 97 LYS cc_start: 0.6642 (ptpt) cc_final: 0.6233 (pptt) REVERT: B 100 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7917 (mp) REVERT: B 271 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: B 305 SER cc_start: 0.8848 (t) cc_final: 0.8617 (p) REVERT: B 353 TRP cc_start: 0.8762 (OUTLIER) cc_final: 0.7518 (p-90) REVERT: B 675 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: B 995 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8829 (mtm-85) REVERT: B 1072 GLU cc_start: 0.6416 (mp0) cc_final: 0.6190 (mp0) REVERT: C 41 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7634 (mmmt) REVERT: C 100 ILE cc_start: 0.8318 (mt) cc_final: 0.8036 (mm) REVERT: C 271 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: C 305 SER cc_start: 0.8847 (t) cc_final: 0.8627 (p) REVERT: C 319 ARG cc_start: 0.7957 (mmt-90) cc_final: 0.7662 (mmt90) REVERT: C 727 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8935 (pp) REVERT: C 850 ILE cc_start: 0.9227 (mm) cc_final: 0.9024 (mp) REVERT: C 957 GLN cc_start: 0.8447 (tp40) cc_final: 0.8205 (tp40) outliers start: 118 outliers final: 58 residues processed: 359 average time/residue: 0.4630 time to fit residues: 202.0026 Evaluate side-chains 305 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 238 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 62 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1058 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.118331 restraints weight = 47941.513| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.17 r_work: 0.3570 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.7371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26130 Z= 0.168 Angle : 0.629 11.696 35577 Z= 0.324 Chirality : 0.046 0.199 4014 Planarity : 0.004 0.060 4617 Dihedral : 5.129 35.739 3501 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.34 % Allowed : 20.49 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.37 (0.14), residues: 3234 helix: -0.17 (0.20), residues: 723 sheet: -0.68 (0.22), residues: 504 loop : -1.27 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 466 TYR 0.019 0.002 TYR C 495 PHE 0.022 0.002 PHE B 140 TRP 0.025 0.002 TRP B 64 HIS 0.009 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00391 (26088) covalent geometry : angle 0.62253 (35493) SS BOND : bond 0.00474 ( 42) SS BOND : angle 1.94886 ( 84) hydrogen bonds : bond 0.03860 ( 817) hydrogen bonds : angle 5.82125 ( 2394) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 276 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8727 (tp40) REVERT: A 97 LYS cc_start: 0.6578 (ptpt) cc_final: 0.6272 (pptt) REVERT: A 138 ASP cc_start: 0.7143 (p0) cc_final: 0.6752 (p0) REVERT: A 740 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8492 (ttm) REVERT: A 1002 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 1107 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7534 (mpp-170) REVERT: B 41 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7720 (mmmt) REVERT: B 97 LYS cc_start: 0.6614 (ptpt) cc_final: 0.6210 (pptt) REVERT: B 100 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7867 (mp) REVERT: B 200 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6193 (t80) REVERT: B 305 SER cc_start: 0.8722 (t) cc_final: 0.8508 (p) REVERT: B 675 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: B 995 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8835 (mtm-85) REVERT: B 1072 GLU cc_start: 0.6315 (mp0) cc_final: 0.6063 (mp0) REVERT: C 319 ARG cc_start: 0.7891 (mmt-90) cc_final: 0.7562 (mmt90) REVERT: C 727 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8952 (pp) REVERT: C 850 ILE cc_start: 0.9225 (mm) cc_final: 0.9023 (mp) outliers start: 95 outliers final: 54 residues processed: 342 average time/residue: 0.4690 time to fit residues: 194.1556 Evaluate side-chains 301 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 41 optimal weight: 3.9990 chunk 284 optimal weight: 0.2980 chunk 137 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1058 HIS A1083 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 207 HIS C 354 ASN C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1054 GLN C1083 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.130954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117948 restraints weight = 48118.193| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.11 r_work: 0.3595 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26130 Z= 0.177 Angle : 0.636 10.932 35577 Z= 0.326 Chirality : 0.046 0.202 4014 Planarity : 0.004 0.058 4617 Dihedral : 5.091 35.004 3501 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.92 % Allowed : 21.44 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.24 (0.14), residues: 3234 helix: -0.04 (0.20), residues: 711 sheet: -0.66 (0.22), residues: 513 loop : -1.18 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 466 TYR 0.022 0.002 TYR B 660 PHE 0.022 0.002 PHE A 140 TRP 0.027 0.002 TRP B 64 HIS 0.009 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00417 (26088) covalent geometry : angle 0.63054 (35493) SS BOND : bond 0.00516 ( 42) SS BOND : angle 1.82541 ( 84) hydrogen bonds : bond 0.03868 ( 817) hydrogen bonds : angle 5.77976 ( 2394) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 252 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8696 (tp40) REVERT: A 97 LYS cc_start: 0.6617 (ptpt) cc_final: 0.6295 (pptt) REVERT: A 138 ASP cc_start: 0.6866 (p0) cc_final: 0.6576 (p0) REVERT: A 1002 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8478 (tm-30) REVERT: A 1107 ARG cc_start: 0.7808 (mtt90) cc_final: 0.7536 (mpp-170) REVERT: B 41 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7790 (mmmt) REVERT: B 97 LYS cc_start: 0.6582 (ptpt) cc_final: 0.6275 (pptt) REVERT: B 100 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8081 (mp) REVERT: B 141 LEU cc_start: 0.7842 (mp) cc_final: 0.6980 (mp) REVERT: B 200 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: B 305 SER cc_start: 0.8689 (t) cc_final: 0.8445 (p) REVERT: B 675 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: B 1072 GLU cc_start: 0.6325 (mp0) cc_final: 0.6095 (mp0) REVERT: C 319 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.7665 (mmt90) REVERT: C 727 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8923 (pp) REVERT: C 850 ILE cc_start: 0.9207 (mm) cc_final: 0.9002 (mp) outliers start: 83 outliers final: 53 residues processed: 306 average time/residue: 0.4334 time to fit residues: 162.6375 Evaluate side-chains 291 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 150 optimal weight: 0.4980 chunk 305 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 160 optimal weight: 0.0970 chunk 20 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1083 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 207 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1054 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113196 restraints weight = 48656.926| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.66 r_work: 0.3518 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.7592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26130 Z= 0.172 Angle : 0.639 10.724 35577 Z= 0.328 Chirality : 0.046 0.202 4014 Planarity : 0.004 0.057 4617 Dihedral : 5.073 35.501 3501 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.60 % Allowed : 22.07 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.28 (0.14), residues: 3234 helix: -0.11 (0.19), residues: 738 sheet: -0.65 (0.22), residues: 507 loop : -1.21 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 466 TYR 0.024 0.002 TYR B 660 PHE 0.022 0.002 PHE A 140 TRP 0.025 0.002 TRP B 64 HIS 0.009 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00407 (26088) covalent geometry : angle 0.63368 (35493) SS BOND : bond 0.00477 ( 42) SS BOND : angle 1.83709 ( 84) hydrogen bonds : bond 0.03828 ( 817) hydrogen bonds : angle 5.77499 ( 2394) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 243 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.6571 (ptpt) cc_final: 0.6176 (pptt) REVERT: A 1002 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8475 (tm-30) REVERT: A 1107 ARG cc_start: 0.7823 (mtt90) cc_final: 0.7534 (mpp-170) REVERT: B 97 LYS cc_start: 0.6516 (ptpt) cc_final: 0.6076 (pptt) REVERT: B 141 LEU cc_start: 0.7747 (mp) cc_final: 0.6874 (mp) REVERT: B 144 TYR cc_start: 0.4982 (p90) cc_final: 0.4611 (p90) REVERT: B 200 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: B 305 SER cc_start: 0.8704 (t) cc_final: 0.8356 (p) REVERT: B 675 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: C 141 LEU cc_start: 0.7613 (mp) cc_final: 0.7030 (mt) REVERT: C 303 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8652 (mp) REVERT: C 319 ARG cc_start: 0.7881 (mmt-90) cc_final: 0.7547 (mmt90) REVERT: C 727 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8837 (pp) REVERT: C 850 ILE cc_start: 0.9151 (mm) cc_final: 0.8933 (mp) outliers start: 74 outliers final: 51 residues processed: 293 average time/residue: 0.4458 time to fit residues: 159.7453 Evaluate side-chains 288 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 233 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 235 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 273 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 157 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 0.0000 chunk 81 optimal weight: 0.5980 chunk 274 optimal weight: 0.8980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1054 GLN C1083 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.130925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.115879 restraints weight = 48528.996| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.66 r_work: 0.3553 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.7540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26130 Z= 0.127 Angle : 0.623 15.553 35577 Z= 0.316 Chirality : 0.046 0.189 4014 Planarity : 0.004 0.063 4617 Dihedral : 4.984 34.916 3501 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.11 % Allowed : 22.84 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.08 (0.14), residues: 3234 helix: 0.03 (0.20), residues: 741 sheet: -0.58 (0.23), residues: 465 loop : -1.05 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 466 TYR 0.024 0.001 TYR C 904 PHE 0.019 0.001 PHE A 140 TRP 0.019 0.002 TRP B 64 HIS 0.020 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00293 (26088) covalent geometry : angle 0.61833 (35493) SS BOND : bond 0.00420 ( 42) SS BOND : angle 1.61187 ( 84) hydrogen bonds : bond 0.03647 ( 817) hydrogen bonds : angle 5.65866 ( 2394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7199.78 seconds wall clock time: 123 minutes 52.15 seconds (7432.15 seconds total)