Starting phenix.real_space_refine on Thu Mar 5 20:25:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w92_32359/03_2026/7w92_32359.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w92_32359/03_2026/7w92_32359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w92_32359/03_2026/7w92_32359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w92_32359/03_2026/7w92_32359.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w92_32359/03_2026/7w92_32359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w92_32359/03_2026/7w92_32359.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15986 2.51 5 N 4211 2.21 5 O 4760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 255 residue(s): 0.03s 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: 25071 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8382 Classifications: {'peptide': 1072} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 6 Chain: "C" Number of atoms: 8296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8296 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 53, 'TRANS': 1007} Chain breaks: 6 Chain: "B" Number of atoms: 8393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8393 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 54, 'TRANS': 1018} Chain breaks: 7 Time building chain proxies: 5.62, per 1000 atoms: 0.22 Number of scatterers: 25071 At special positions: 0 Unit cell: (155.382, 141.987, 201.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4760 8.00 N 4211 7.00 C 15986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.04 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 A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5994 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 55 sheets defined 21.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.951A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.049A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.277A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.786A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.762A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 4.002A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.819A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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 782 removed outlier: 3.502A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.698A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.530A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 4.098A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.977A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.567A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 removed outlier: 4.056A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.013A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (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: 3.584A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 removed outlier: 3.555A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.662A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 removed outlier: 4.005A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.723A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.554A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.647A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (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 782 removed outlier: 3.754A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.532A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.549A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.760A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.885A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.047A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (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 982 removed outlier: 3.722A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 982' Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.568A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C1014 " --> pdb=" O GLN C1010 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.738A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.765A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.759A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 371' Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.593A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.808A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.592A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (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 780 removed outlier: 3.933A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.691A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.508A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.687A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.586A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.719A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.215A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (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: 3.629A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.386A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.500A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1143 through 1147' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.695A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.025A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.517A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.807A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.807A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.699A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.663A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.568A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.705A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 574 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.252A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.942A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.606A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.511A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.387A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.804A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.503A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'A' and resid 1122 through 1125 removed outlier: 5.432A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.538A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.954A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.811A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.141A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.141A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.937A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.574A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 400 through 402 Processing sheet with id=AD5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.019A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.263A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.719A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AE1, first strand: chain 'C' and resid 718 through 719 removed outlier: 3.530A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.241A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.532A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.781A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.907A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.310A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.887A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.544A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.534A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AF6, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AF7, first strand: chain 'B' and resid 718 through 719 removed outlier: 7.386A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AG1, first strand: chain 'B' and resid 1094 through 1097 657 hydrogen bonds defined for protein. 1830 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: 4.97 Time building geometry restraints manager: 2.63 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: 8123 1.35 - 1.47: 6422 1.47 - 1.60: 10961 1.60 - 1.72: 0 1.72 - 1.84: 144 Bond restraints: 25650 Sorted by residual: bond pdb=" C GLN C 23 " pdb=" N LEU C 24 " ideal model delta sigma weight residual 1.331 1.373 -0.042 2.07e-02 2.33e+03 4.10e+00 bond pdb=" CA THR B 630 " pdb=" C THR B 630 " ideal model delta sigma weight residual 1.525 1.565 -0.040 2.10e-02 2.27e+03 3.56e+00 bond pdb=" CA GLU B 516 " pdb=" CB GLU B 516 " ideal model delta sigma weight residual 1.526 1.554 -0.028 1.70e-02 3.46e+03 2.64e+00 bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.334 1.346 -0.013 8.40e-03 1.42e+04 2.35e+00 bond pdb=" CB ASP B 198 " pdb=" CG ASP B 198 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.09e+00 ... (remaining 25645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 34318 2.33 - 4.67: 504 4.67 - 7.00: 51 7.00 - 9.33: 12 9.33 - 11.66: 4 Bond angle restraints: 34889 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" N VAL C1128 " pdb=" CA VAL C1128 " pdb=" C VAL C1128 " ideal model delta sigma weight residual 112.96 108.96 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" C ALA B 570 " pdb=" N ASP B 571 " pdb=" CA ASP B 571 " ideal model delta sigma weight residual 122.46 128.03 -5.57 1.41e+00 5.03e-01 1.56e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.08 127.37 -5.29 1.47e+00 4.63e-01 1.30e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.92 -4.22 1.22e+00 6.72e-01 1.20e+01 ... (remaining 34884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13992 18.00 - 35.99: 1058 35.99 - 53.99: 181 53.99 - 71.99: 39 71.99 - 89.98: 27 Dihedral angle restraints: 15297 sinusoidal: 5979 harmonic: 9318 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -3.44 -82.56 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 175.38 -82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -6.18 -79.82 1 1.00e+01 1.00e-02 7.90e+01 ... (remaining 15294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2911 0.046 - 0.092: 711 0.092 - 0.138: 282 0.138 - 0.183: 30 0.183 - 0.229: 4 Chirality restraints: 3938 Sorted by residual: chirality pdb=" CA ASP B 198 " pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CB ASP B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE A 434 " pdb=" CA ILE A 434 " pdb=" CG1 ILE A 434 " pdb=" CG2 ILE A 434 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE A 472 " pdb=" CA ILE A 472 " pdb=" CG1 ILE A 472 " pdb=" CG2 ILE A 472 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 3935 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.057 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO C 987 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.50e+00 pdb=" N PRO B 987 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.048 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO A 987 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.041 5.00e-02 4.00e+02 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 8060 2.82 - 3.34: 18859 3.34 - 3.86: 39193 3.86 - 4.38: 42873 4.38 - 4.90: 76730 Nonbonded interactions: 185715 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.306 3.040 nonbonded pdb=" O SER B 438 " pdb=" OG SER B 438 " model vdw 2.316 3.040 nonbonded pdb=" O SER B 151 " pdb=" OG SER B 151 " model vdw 2.334 3.040 nonbonded pdb=" O SER C 689 " pdb=" OG SER C 689 " model vdw 2.334 3.040 nonbonded pdb=" OG SER C 591 " pdb=" OE1 GLU C 619 " model vdw 2.336 3.040 ... (remaining 185710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 621 or resid 641 through 1147)) selection = (chain 'B' and (resid 14 through 621 or resid 641 through 1147)) 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: 4.970 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.730 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 0.046 25689 Z= 0.150 Angle : 0.667 11.663 34967 Z= 0.363 Chirality : 0.047 0.229 3938 Planarity : 0.006 0.084 4530 Dihedral : 13.050 89.983 9186 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % 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: -4.34 (0.11), residues: 3163 helix: -4.94 (0.05), residues: 602 sheet: -1.21 (0.19), residues: 597 loop : -2.87 (0.11), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 408 TYR 0.014 0.001 TYR C 707 PHE 0.018 0.001 PHE B 400 TRP 0.009 0.001 TRP A 152 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00303 (25650) covalent geometry : angle 0.66503 (34889) SS BOND : bond 0.00361 ( 39) SS BOND : angle 1.19110 ( 78) hydrogen bonds : bond 0.35006 ( 645) hydrogen bonds : angle 10.57107 ( 1830) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 603 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 86 PHE cc_start: 0.7493 (t80) cc_final: 0.7127 (t80) REVERT: A 153 MET cc_start: -0.4908 (tpt) cc_final: -0.5183 (tpt) REVERT: A 296 LEU cc_start: 0.8293 (tp) cc_final: 0.7955 (tp) REVERT: A 515 PHE cc_start: 0.6586 (p90) cc_final: 0.6033 (p90) REVERT: A 539 VAL cc_start: 0.7778 (t) cc_final: 0.7526 (m) REVERT: A 580 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7379 (mm-40) REVERT: A 606 ASN cc_start: 0.8525 (m-40) cc_final: 0.8272 (t0) REVERT: A 790 LYS cc_start: 0.8397 (mttt) cc_final: 0.7689 (mttm) REVERT: C 140 PHE cc_start: 0.7705 (p90) cc_final: 0.7462 (p90) REVERT: C 206 LYS cc_start: 0.8222 (tptt) cc_final: 0.7860 (tppt) REVERT: C 603 ASN cc_start: 0.7866 (p0) cc_final: 0.7533 (p0) REVERT: C 702 GLU cc_start: 0.6734 (tp30) cc_final: 0.6502 (mm-30) REVERT: C 1073 LYS cc_start: 0.8325 (tttt) cc_final: 0.8066 (tttm) REVERT: C 1118 ASP cc_start: 0.6397 (p0) cc_final: 0.6193 (p0) REVERT: B 191 GLU cc_start: 0.5954 (tt0) cc_final: 0.4023 (mt-10) REVERT: B 296 LEU cc_start: 0.8506 (tp) cc_final: 0.8071 (tp) REVERT: B 368 LEU cc_start: 0.8580 (mt) cc_final: 0.8304 (mp) REVERT: B 369 TYR cc_start: 0.4795 (m-80) cc_final: 0.4347 (m-80) REVERT: B 383 SER cc_start: 0.7785 (t) cc_final: 0.7452 (p) REVERT: B 449 TYR cc_start: 0.6887 (m-80) cc_final: 0.6566 (m-80) REVERT: B 453 TYR cc_start: 0.7257 (p90) cc_final: 0.6796 (p90) REVERT: B 455 LEU cc_start: 0.7222 (tp) cc_final: 0.6846 (tp) REVERT: B 826 VAL cc_start: 0.7507 (m) cc_final: 0.7290 (t) REVERT: B 883 THR cc_start: 0.8405 (m) cc_final: 0.8166 (p) REVERT: B 994 ASP cc_start: 0.7445 (t0) cc_final: 0.6941 (t0) outliers start: 3 outliers final: 2 residues processed: 606 average time/residue: 0.1857 time to fit residues: 168.9999 Evaluate side-chains 490 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 488 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain B residue 130 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 196 ASN A 207 HIS A 239 GLN A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 519 HIS A 536 ASN A 658 ASN A 762 GLN A 901 GLN A 949 GLN A 955 ASN A1002 GLN A1005 GLN A1071 GLN A1088 HIS C 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 207 HIS C 211 ASN C 245 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 563 GLN C 613 GLN C 955 ASN C1071 GLN B 137 ASN B 474 GLN B 493 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B1005 GLN B1106 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.152521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121551 restraints weight = 48436.823| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.22 r_work: 0.3569 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25689 Z= 0.210 Angle : 0.643 13.469 34967 Z= 0.334 Chirality : 0.046 0.204 3938 Planarity : 0.005 0.056 4530 Dihedral : 4.239 20.832 3439 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.82 % Allowed : 11.83 % Favored : 86.35 % 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: -3.06 (0.13), residues: 3163 helix: -2.50 (0.15), residues: 630 sheet: -0.68 (0.19), residues: 690 loop : -2.50 (0.12), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.021 0.002 TYR B 396 PHE 0.023 0.002 PHE B 374 TRP 0.047 0.002 TRP B 353 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00489 (25650) covalent geometry : angle 0.63830 (34889) SS BOND : bond 0.00372 ( 39) SS BOND : angle 1.72101 ( 78) hydrogen bonds : bond 0.06709 ( 645) hydrogen bonds : angle 5.99738 ( 1830) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 495 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8092 (tm-30) REVERT: A 86 PHE cc_start: 0.7689 (t80) cc_final: 0.7268 (t80) REVERT: A 140 PHE cc_start: 0.5594 (p90) cc_final: 0.5383 (p90) REVERT: A 153 MET cc_start: -0.4537 (tpt) cc_final: -0.4810 (tpt) REVERT: A 177 MET cc_start: 0.0624 (mtt) cc_final: 0.0235 (mtt) REVERT: A 190 ARG cc_start: 0.5616 (ttt180) cc_final: 0.4168 (mmm160) REVERT: A 206 LYS cc_start: 0.9102 (tptt) cc_final: 0.8603 (tptm) REVERT: A 457 ARG cc_start: 0.5745 (OUTLIER) cc_final: 0.5373 (mtp85) REVERT: A 462 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8552 (mmtm) REVERT: A 539 VAL cc_start: 0.7930 (t) cc_final: 0.7699 (m) REVERT: A 580 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7863 (mm-40) REVERT: A 690 GLN cc_start: 0.7987 (mt0) cc_final: 0.7530 (mm-40) REVERT: A 790 LYS cc_start: 0.8985 (mttt) cc_final: 0.8646 (mttm) REVERT: A 964 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8692 (ttmm) REVERT: A 1138 TYR cc_start: 0.8342 (t80) cc_final: 0.7947 (t80) REVERT: C 48 LEU cc_start: 0.8534 (mm) cc_final: 0.8306 (mp) REVERT: C 99 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8492 (p0) REVERT: C 224 GLU cc_start: 0.7342 (mp0) cc_final: 0.7039 (mp0) REVERT: C 273 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7713 (mmm-85) REVERT: C 290 ASP cc_start: 0.8286 (t0) cc_final: 0.7733 (m-30) REVERT: C 324 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7568 (mp0) REVERT: C 351 TYR cc_start: 0.4271 (p90) cc_final: 0.4044 (p90) REVERT: C 603 ASN cc_start: 0.8571 (p0) cc_final: 0.8356 (p0) REVERT: C 787 GLN cc_start: 0.7944 (mt0) cc_final: 0.7710 (mp10) REVERT: C 825 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8420 (mttp) REVERT: C 933 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7967 (ttmm) REVERT: C 1073 LYS cc_start: 0.8760 (tttt) cc_final: 0.8429 (tttm) REVERT: C 1107 ARG cc_start: 0.8406 (mtm110) cc_final: 0.6332 (tpt90) REVERT: C 1118 ASP cc_start: 0.7394 (p0) cc_final: 0.7154 (p0) REVERT: B 41 LYS cc_start: 0.7963 (mttm) cc_final: 0.7696 (mtpt) REVERT: B 133 PHE cc_start: 0.6282 (m-80) cc_final: 0.5944 (m-80) REVERT: B 140 PHE cc_start: 0.7706 (m-80) cc_final: 0.7395 (m-80) REVERT: B 191 GLU cc_start: 0.5788 (tt0) cc_final: 0.3261 (mt-10) REVERT: B 192 PHE cc_start: 0.7387 (m-80) cc_final: 0.7114 (m-10) REVERT: B 202 LYS cc_start: 0.7727 (tptt) cc_final: 0.7304 (tptt) REVERT: B 225 PRO cc_start: 0.8083 (Cg_exo) cc_final: 0.7687 (Cg_endo) REVERT: B 296 LEU cc_start: 0.8214 (tp) cc_final: 0.7956 (tt) REVERT: B 298 GLU cc_start: 0.8158 (tp30) cc_final: 0.7920 (tp30) REVERT: B 360 ASN cc_start: 0.7824 (m-40) cc_final: 0.7602 (m-40) REVERT: B 383 SER cc_start: 0.8212 (t) cc_final: 0.7763 (p) REVERT: B 515 PHE cc_start: 0.7852 (m-10) cc_final: 0.7624 (m-80) REVERT: B 796 ASP cc_start: 0.7261 (p0) cc_final: 0.6996 (p0) REVERT: B 883 THR cc_start: 0.8563 (m) cc_final: 0.6778 (t) REVERT: B 896 ILE cc_start: 0.7598 (mt) cc_final: 0.7341 (tt) REVERT: B 994 ASP cc_start: 0.7989 (t0) cc_final: 0.7730 (t0) REVERT: B 995 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8342 (mtt-85) REVERT: B 1138 TYR cc_start: 0.8017 (m-10) cc_final: 0.7761 (m-10) outliers start: 51 outliers final: 23 residues processed: 522 average time/residue: 0.1851 time to fit residues: 146.0356 Evaluate side-chains 491 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 466 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 820 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 67 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 317 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 312 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 493 GLN C 955 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1088 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.149823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119040 restraints weight = 48232.037| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.18 r_work: 0.3537 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25689 Z= 0.191 Angle : 0.605 15.649 34967 Z= 0.308 Chirality : 0.045 0.174 3938 Planarity : 0.004 0.049 4530 Dihedral : 4.349 22.604 3438 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.18 % Allowed : 14.83 % Favored : 82.99 % 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: -2.34 (0.13), residues: 3163 helix: -0.89 (0.20), residues: 638 sheet: -0.58 (0.19), residues: 666 loop : -2.26 (0.12), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 983 TYR 0.020 0.001 TYR C 170 PHE 0.021 0.002 PHE B 238 TRP 0.029 0.002 TRP B 353 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00452 (25650) covalent geometry : angle 0.59875 (34889) SS BOND : bond 0.00467 ( 39) SS BOND : angle 1.91416 ( 78) hydrogen bonds : bond 0.06377 ( 645) hydrogen bonds : angle 5.40747 ( 1830) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 496 time to evaluate : 1.061 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 52 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 86 PHE cc_start: 0.7683 (t80) cc_final: 0.7220 (t80) REVERT: A 153 MET cc_start: -0.4355 (tpt) cc_final: -0.4654 (tpt) REVERT: A 177 MET cc_start: 0.0813 (mtt) cc_final: -0.2273 (mtt) REVERT: A 190 ARG cc_start: 0.5616 (ttt180) cc_final: 0.4094 (ttt180) REVERT: A 353 TRP cc_start: 0.8408 (p90) cc_final: 0.8151 (p90) REVERT: A 422 ASN cc_start: 0.7808 (m-40) cc_final: 0.6885 (m-40) REVERT: A 462 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8582 (mmtt) REVERT: A 495 TYR cc_start: 0.5559 (m-80) cc_final: 0.5314 (m-80) REVERT: A 580 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7895 (mm-40) REVERT: A 690 GLN cc_start: 0.8087 (mt0) cc_final: 0.7687 (tp40) REVERT: A 790 LYS cc_start: 0.9061 (mttt) cc_final: 0.8829 (mttm) REVERT: A 935 GLN cc_start: 0.8074 (mt0) cc_final: 0.7780 (mt0) REVERT: A 964 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8761 (ttmm) REVERT: A 1138 TYR cc_start: 0.8286 (t80) cc_final: 0.7890 (t80) REVERT: C 177 MET cc_start: -0.2986 (mmt) cc_final: -0.3983 (mmt) REVERT: C 224 GLU cc_start: 0.7587 (mp0) cc_final: 0.7175 (mp0) REVERT: C 495 TYR cc_start: 0.5860 (m-80) cc_final: 0.5603 (m-80) REVERT: C 537 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8143 (mmtm) REVERT: C 574 ASP cc_start: 0.8235 (p0) cc_final: 0.7275 (t0) REVERT: C 745 ASP cc_start: 0.7208 (t0) cc_final: 0.6905 (t0) REVERT: C 823 PHE cc_start: 0.8269 (t80) cc_final: 0.8006 (t80) REVERT: C 825 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8527 (mttm) REVERT: C 933 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7901 (ttmm) REVERT: C 976 VAL cc_start: 0.9003 (m) cc_final: 0.8791 (p) REVERT: C 1107 ARG cc_start: 0.8546 (mtm110) cc_final: 0.6333 (tpt170) REVERT: B 140 PHE cc_start: 0.7953 (m-80) cc_final: 0.7493 (m-80) REVERT: B 202 LYS cc_start: 0.7650 (tptt) cc_final: 0.7365 (tptt) REVERT: B 203 ILE cc_start: 0.8414 (mt) cc_final: 0.8212 (mp) REVERT: B 225 PRO cc_start: 0.8088 (Cg_exo) cc_final: 0.7722 (Cg_endo) REVERT: B 298 GLU cc_start: 0.8193 (tp30) cc_final: 0.7985 (tp30) REVERT: B 383 SER cc_start: 0.8261 (t) cc_final: 0.7738 (p) REVERT: B 429 PHE cc_start: 0.8117 (t80) cc_final: 0.7414 (t80) REVERT: B 532 ASN cc_start: 0.8056 (t0) cc_final: 0.7831 (t0) REVERT: B 896 ILE cc_start: 0.7693 (mt) cc_final: 0.7354 (tt) REVERT: B 995 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8102 (mtt-85) outliers start: 61 outliers final: 38 residues processed: 530 average time/residue: 0.1854 time to fit residues: 148.6554 Evaluate side-chains 511 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 473 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 223 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 185 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 493 GLN C 955 ASN B 134 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.147182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.115897 restraints weight = 48161.984| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.23 r_work: 0.3517 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25689 Z= 0.185 Angle : 0.602 15.499 34967 Z= 0.306 Chirality : 0.045 0.220 3938 Planarity : 0.004 0.048 4530 Dihedral : 4.423 23.789 3438 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.61 % Allowed : 16.51 % Favored : 80.88 % 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: -2.03 (0.14), residues: 3163 helix: -0.37 (0.21), residues: 646 sheet: -0.46 (0.19), residues: 679 loop : -2.15 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.025 0.001 TYR A 351 PHE 0.026 0.002 PHE B 374 TRP 0.024 0.002 TRP B 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00442 (25650) covalent geometry : angle 0.59458 (34889) SS BOND : bond 0.00499 ( 39) SS BOND : angle 2.07109 ( 78) hydrogen bonds : bond 0.05676 ( 645) hydrogen bonds : angle 5.19214 ( 1830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 482 time to evaluate : 1.002 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 40 ASP cc_start: 0.8226 (p0) cc_final: 0.8011 (p0) REVERT: A 52 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 153 MET cc_start: -0.4262 (tpt) cc_final: -0.4581 (tpt) REVERT: A 177 MET cc_start: 0.0741 (mtt) cc_final: -0.1281 (mtt) REVERT: A 462 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8629 (mmtm) REVERT: A 580 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7956 (mm-40) REVERT: A 690 GLN cc_start: 0.8012 (mt0) cc_final: 0.7559 (mm-40) REVERT: A 697 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8618 (ptm) REVERT: A 790 LYS cc_start: 0.9055 (mttt) cc_final: 0.8810 (mttm) REVERT: A 935 GLN cc_start: 0.7978 (mt0) cc_final: 0.7766 (mt0) REVERT: A 964 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8744 (ttmm) REVERT: A 1138 TYR cc_start: 0.8321 (t80) cc_final: 0.7985 (t80) REVERT: C 177 MET cc_start: -0.2716 (mmt) cc_final: -0.3986 (mmt) REVERT: C 224 GLU cc_start: 0.7698 (mp0) cc_final: 0.7448 (mp0) REVERT: C 290 ASP cc_start: 0.8420 (t0) cc_final: 0.8207 (t0) REVERT: C 537 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8224 (mmtm) REVERT: C 556 ASN cc_start: 0.8724 (t0) cc_final: 0.8521 (t0) REVERT: C 574 ASP cc_start: 0.8151 (p0) cc_final: 0.7323 (t0) REVERT: C 745 ASP cc_start: 0.7338 (t0) cc_final: 0.7108 (t0) REVERT: C 823 PHE cc_start: 0.8245 (t80) cc_final: 0.7993 (t80) REVERT: C 1107 ARG cc_start: 0.8556 (mtm110) cc_final: 0.6553 (tpt170) REVERT: B 140 PHE cc_start: 0.7953 (m-80) cc_final: 0.7494 (m-80) REVERT: B 192 PHE cc_start: 0.7488 (m-80) cc_final: 0.7234 (m-10) REVERT: B 203 ILE cc_start: 0.8419 (mt) cc_final: 0.8111 (mp) REVERT: B 225 PRO cc_start: 0.8058 (Cg_exo) cc_final: 0.7657 (Cg_endo) REVERT: B 429 PHE cc_start: 0.8149 (t80) cc_final: 0.7468 (t80) REVERT: B 532 ASN cc_start: 0.8206 (t0) cc_final: 0.7930 (t0) REVERT: B 654 GLU cc_start: 0.7501 (pm20) cc_final: 0.7229 (pm20) REVERT: B 896 ILE cc_start: 0.7903 (mt) cc_final: 0.7598 (tt) REVERT: B 995 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8124 (mtt-85) REVERT: B 1107 ARG cc_start: 0.7519 (mtt180) cc_final: 0.5754 (tpt170) outliers start: 73 outliers final: 43 residues processed: 519 average time/residue: 0.1732 time to fit residues: 136.8986 Evaluate side-chains 509 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 465 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 53 optimal weight: 0.4980 chunk 163 optimal weight: 0.8980 chunk 257 optimal weight: 7.9990 chunk 288 optimal weight: 2.9990 chunk 109 optimal weight: 0.0980 chunk 150 optimal weight: 0.3980 chunk 38 optimal weight: 0.0010 chunk 219 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 207 HIS C 542 ASN C 955 ASN C 978 ASN B 30 ASN B 965 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.149624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118134 restraints weight = 47618.499| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.32 r_work: 0.3560 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25689 Z= 0.104 Angle : 0.549 12.806 34967 Z= 0.277 Chirality : 0.043 0.185 3938 Planarity : 0.004 0.046 4530 Dihedral : 4.101 23.846 3438 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.47 % Allowed : 17.73 % Favored : 79.81 % 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: -1.69 (0.14), residues: 3163 helix: 0.16 (0.22), residues: 646 sheet: -0.27 (0.19), residues: 667 loop : -2.02 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.014 0.001 TYR C 28 PHE 0.041 0.001 PHE A 342 TRP 0.016 0.001 TRP A 436 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00237 (25650) covalent geometry : angle 0.54316 (34889) SS BOND : bond 0.00321 ( 39) SS BOND : angle 1.75146 ( 78) hydrogen bonds : bond 0.04557 ( 645) hydrogen bonds : angle 4.86100 ( 1830) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 472 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 153 MET cc_start: -0.4304 (tpt) cc_final: -0.4678 (tpt) REVERT: A 177 MET cc_start: 0.0902 (mtt) cc_final: -0.0977 (mtt) REVERT: A 191 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8225 (mt-10) REVERT: A 403 ARG cc_start: 0.4734 (mmt-90) cc_final: 0.4513 (mmt180) REVERT: A 422 ASN cc_start: 0.7870 (m-40) cc_final: 0.6807 (m-40) REVERT: A 462 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8622 (mmtm) REVERT: A 473 TYR cc_start: 0.8032 (t80) cc_final: 0.7786 (t80) REVERT: A 508 TYR cc_start: 0.7109 (m-80) cc_final: 0.6231 (m-80) REVERT: A 580 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7899 (mm-40) REVERT: A 690 GLN cc_start: 0.8081 (mt0) cc_final: 0.7535 (mm-40) REVERT: A 697 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8553 (ptm) REVERT: A 790 LYS cc_start: 0.9085 (mttt) cc_final: 0.8786 (mttm) REVERT: A 964 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8659 (ttmm) REVERT: A 1017 GLU cc_start: 0.7227 (mm-30) cc_final: 0.7009 (tp30) REVERT: A 1134 ASN cc_start: 0.6553 (m-40) cc_final: 0.6179 (m110) REVERT: A 1138 TYR cc_start: 0.8275 (t80) cc_final: 0.7844 (t80) REVERT: C 99 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8459 (p0) REVERT: C 177 MET cc_start: -0.2873 (mmt) cc_final: -0.3982 (mmt) REVERT: C 202 LYS cc_start: 0.8479 (mptt) cc_final: 0.7927 (mptt) REVERT: C 224 GLU cc_start: 0.7640 (mp0) cc_final: 0.7208 (mp0) REVERT: C 290 ASP cc_start: 0.8518 (t0) cc_final: 0.8287 (t0) REVERT: C 294 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6812 (t0) REVERT: C 549 THR cc_start: 0.8784 (m) cc_final: 0.8506 (m) REVERT: C 574 ASP cc_start: 0.8032 (p0) cc_final: 0.7262 (t0) REVERT: C 745 ASP cc_start: 0.7366 (t0) cc_final: 0.7086 (t0) REVERT: C 790 LYS cc_start: 0.9153 (mtpp) cc_final: 0.8813 (mmtm) REVERT: C 823 PHE cc_start: 0.8260 (t80) cc_final: 0.7996 (t80) REVERT: C 933 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7962 (ttmm) REVERT: C 1107 ARG cc_start: 0.8537 (mtm110) cc_final: 0.6378 (tpt170) REVERT: B 41 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7596 (mtpt) REVERT: B 140 PHE cc_start: 0.7928 (m-80) cc_final: 0.7468 (m-80) REVERT: B 168 PHE cc_start: 0.7314 (t80) cc_final: 0.6983 (t80) REVERT: B 202 LYS cc_start: 0.7444 (tptt) cc_final: 0.6889 (tptt) REVERT: B 225 PRO cc_start: 0.8064 (Cg_exo) cc_final: 0.7700 (Cg_endo) REVERT: B 429 PHE cc_start: 0.8067 (t80) cc_final: 0.7399 (t80) REVERT: B 455 LEU cc_start: 0.8005 (tt) cc_final: 0.7738 (tt) REVERT: B 532 ASN cc_start: 0.8215 (t0) cc_final: 0.7932 (t0) REVERT: B 559 PHE cc_start: 0.7426 (t80) cc_final: 0.7080 (t80) REVERT: B 564 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7534 (mm-40) REVERT: B 779 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8138 (mm-40) REVERT: B 790 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8664 (mtmt) REVERT: B 896 ILE cc_start: 0.7690 (mt) cc_final: 0.7345 (tt) outliers start: 69 outliers final: 37 residues processed: 513 average time/residue: 0.1750 time to fit residues: 137.4531 Evaluate side-chains 499 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 458 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 68 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 309 optimal weight: 0.3980 chunk 202 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 211 optimal weight: 0.0870 chunk 30 optimal weight: 0.0370 chunk 143 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 207 HIS C 493 GLN C 607 GLN C 955 ASN B 498 GLN B 965 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.151078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120359 restraints weight = 47923.872| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.15 r_work: 0.3571 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25689 Z= 0.109 Angle : 0.550 11.662 34967 Z= 0.278 Chirality : 0.043 0.186 3938 Planarity : 0.004 0.046 4530 Dihedral : 4.033 24.372 3438 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.43 % Allowed : 18.37 % Favored : 79.20 % 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: -1.48 (0.14), residues: 3163 helix: 0.46 (0.22), residues: 644 sheet: -0.16 (0.19), residues: 689 loop : -1.94 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.011 0.001 TYR B1067 PHE 0.043 0.001 PHE C 374 TRP 0.024 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00252 (25650) covalent geometry : angle 0.54359 (34889) SS BOND : bond 0.00465 ( 39) SS BOND : angle 1.80634 ( 78) hydrogen bonds : bond 0.04358 ( 645) hydrogen bonds : angle 4.73432 ( 1830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 466 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8196 (tm-30) REVERT: A 153 MET cc_start: -0.4373 (tpt) cc_final: -0.4705 (tpt) REVERT: A 177 MET cc_start: 0.1128 (mtt) cc_final: -0.0770 (mtt) REVERT: A 191 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8228 (mt-10) REVERT: A 462 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8654 (mmtm) REVERT: A 473 TYR cc_start: 0.8025 (t80) cc_final: 0.7810 (t80) REVERT: A 508 TYR cc_start: 0.7031 (m-80) cc_final: 0.6166 (m-80) REVERT: A 544 ASN cc_start: 0.8138 (t0) cc_final: 0.7802 (p0) REVERT: A 580 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7941 (mm-40) REVERT: A 690 GLN cc_start: 0.8058 (mt0) cc_final: 0.7571 (mm-40) REVERT: A 697 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8569 (ptm) REVERT: A 790 LYS cc_start: 0.9078 (mttt) cc_final: 0.8787 (mttm) REVERT: A 964 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8646 (ttmm) REVERT: A 1134 ASN cc_start: 0.6562 (m-40) cc_final: 0.6097 (m110) REVERT: A 1138 TYR cc_start: 0.8261 (t80) cc_final: 0.7823 (t80) REVERT: C 99 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8532 (p0) REVERT: C 177 MET cc_start: -0.2882 (mmt) cc_final: -0.4016 (mmt) REVERT: C 224 GLU cc_start: 0.7654 (mp0) cc_final: 0.7228 (mp0) REVERT: C 294 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6905 (t0) REVERT: C 549 THR cc_start: 0.8785 (m) cc_final: 0.8522 (m) REVERT: C 574 ASP cc_start: 0.7996 (p0) cc_final: 0.7240 (t0) REVERT: C 745 ASP cc_start: 0.7388 (t0) cc_final: 0.7130 (t0) REVERT: C 790 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8798 (mmtm) REVERT: C 823 PHE cc_start: 0.8259 (t80) cc_final: 0.8007 (t80) REVERT: C 933 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7936 (ttmm) REVERT: C 1073 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8443 (mtpp) REVERT: C 1107 ARG cc_start: 0.8531 (mtm110) cc_final: 0.6396 (tpt170) REVERT: B 41 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7569 (mtpt) REVERT: B 140 PHE cc_start: 0.7801 (m-80) cc_final: 0.7418 (m-80) REVERT: B 190 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6566 (mtp180) REVERT: B 202 LYS cc_start: 0.7578 (tptt) cc_final: 0.7241 (tptt) REVERT: B 225 PRO cc_start: 0.8100 (Cg_exo) cc_final: 0.7733 (Cg_endo) REVERT: B 429 PHE cc_start: 0.7985 (t80) cc_final: 0.7362 (t80) REVERT: B 532 ASN cc_start: 0.8252 (t0) cc_final: 0.7972 (t0) REVERT: B 559 PHE cc_start: 0.7481 (t80) cc_final: 0.7097 (t80) REVERT: B 564 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7507 (mm-40) REVERT: B 779 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8054 (mm-40) REVERT: B 896 ILE cc_start: 0.7695 (mt) cc_final: 0.7377 (tt) REVERT: B 1107 ARG cc_start: 0.7509 (mtt180) cc_final: 0.5688 (tpt170) outliers start: 68 outliers final: 51 residues processed: 504 average time/residue: 0.1840 time to fit residues: 141.2266 Evaluate side-chains 509 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 454 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 203 optimal weight: 0.6980 chunk 247 optimal weight: 4.9990 chunk 235 optimal weight: 0.0170 chunk 101 optimal weight: 0.9990 chunk 208 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 192 optimal weight: 0.0030 chunk 151 optimal weight: 2.9990 overall best weight: 0.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 207 HIS C 955 ASN B 493 GLN B 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.152113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121548 restraints weight = 48058.878| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.20 r_work: 0.3552 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25689 Z= 0.101 Angle : 0.542 11.695 34967 Z= 0.274 Chirality : 0.043 0.207 3938 Planarity : 0.004 0.046 4530 Dihedral : 3.949 25.746 3438 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.36 % Allowed : 18.55 % Favored : 79.09 % 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: -1.27 (0.14), residues: 3163 helix: 0.75 (0.22), residues: 642 sheet: -0.00 (0.19), residues: 670 loop : -1.84 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1019 TYR 0.011 0.001 TYR B1067 PHE 0.037 0.001 PHE C 374 TRP 0.047 0.001 TRP B 436 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00229 (25650) covalent geometry : angle 0.53710 (34889) SS BOND : bond 0.00332 ( 39) SS BOND : angle 1.66924 ( 78) hydrogen bonds : bond 0.04027 ( 645) hydrogen bonds : angle 4.60472 ( 1830) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 465 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 153 MET cc_start: -0.4355 (tpt) cc_final: -0.4682 (tpt) REVERT: A 177 MET cc_start: 0.1003 (mtt) cc_final: -0.0799 (mtt) REVERT: A 191 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 422 ASN cc_start: 0.7836 (m-40) cc_final: 0.6885 (m-40) REVERT: A 508 TYR cc_start: 0.7220 (m-80) cc_final: 0.6124 (m-80) REVERT: A 544 ASN cc_start: 0.8228 (t0) cc_final: 0.7872 (p0) REVERT: A 580 GLN cc_start: 0.8248 (mm110) cc_final: 0.7952 (mm-40) REVERT: A 690 GLN cc_start: 0.8084 (mt0) cc_final: 0.7528 (mm-40) REVERT: A 697 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8586 (ptm) REVERT: A 790 LYS cc_start: 0.9094 (mttt) cc_final: 0.8800 (mttm) REVERT: A 964 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8613 (ttmm) REVERT: A 1017 GLU cc_start: 0.7240 (tp30) cc_final: 0.6786 (tp30) REVERT: A 1091 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7908 (ttp-170) REVERT: A 1134 ASN cc_start: 0.6470 (m-40) cc_final: 0.6050 (m110) REVERT: A 1138 TYR cc_start: 0.8254 (t80) cc_final: 0.7794 (t80) REVERT: C 99 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8585 (p0) REVERT: C 177 MET cc_start: -0.3216 (mmt) cc_final: -0.4375 (mmt) REVERT: C 224 GLU cc_start: 0.7622 (mp0) cc_final: 0.7189 (mp0) REVERT: C 294 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6929 (t0) REVERT: C 549 THR cc_start: 0.8781 (m) cc_final: 0.8540 (m) REVERT: C 574 ASP cc_start: 0.7943 (p0) cc_final: 0.7503 (t0) REVERT: C 586 ASP cc_start: 0.7995 (t0) cc_final: 0.7569 (t0) REVERT: C 607 GLN cc_start: 0.8591 (mt0) cc_final: 0.8391 (mt0) REVERT: C 745 ASP cc_start: 0.7403 (t0) cc_final: 0.7130 (t0) REVERT: C 790 LYS cc_start: 0.9156 (mtpp) cc_final: 0.8813 (mmtm) REVERT: C 823 PHE cc_start: 0.8242 (t80) cc_final: 0.8001 (t80) REVERT: C 933 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7951 (ttmm) REVERT: C 964 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8581 (ttmm) REVERT: C 1073 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8408 (mtpp) REVERT: C 1107 ARG cc_start: 0.8535 (mtm110) cc_final: 0.6372 (tpt170) REVERT: B 140 PHE cc_start: 0.7885 (m-80) cc_final: 0.7416 (m-80) REVERT: B 190 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6600 (mtp180) REVERT: B 202 LYS cc_start: 0.7594 (tptt) cc_final: 0.7217 (tptt) REVERT: B 225 PRO cc_start: 0.8114 (Cg_exo) cc_final: 0.7744 (Cg_endo) REVERT: B 374 PHE cc_start: 0.5078 (m-10) cc_final: 0.4623 (m-10) REVERT: B 429 PHE cc_start: 0.7963 (t80) cc_final: 0.7333 (t80) REVERT: B 515 PHE cc_start: 0.7993 (m-80) cc_final: 0.7628 (m-80) REVERT: B 532 ASN cc_start: 0.8293 (t0) cc_final: 0.8000 (t0) REVERT: B 559 PHE cc_start: 0.7603 (t80) cc_final: 0.7136 (t80) REVERT: B 564 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7524 (mm-40) REVERT: B 779 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8096 (mm-40) REVERT: B 896 ILE cc_start: 0.7449 (mt) cc_final: 0.7110 (tt) REVERT: B 995 ARG cc_start: 0.8398 (mtp85) cc_final: 0.8018 (mtt-85) REVERT: B 1107 ARG cc_start: 0.7516 (mtt180) cc_final: 0.5671 (tpt170) outliers start: 66 outliers final: 50 residues processed: 503 average time/residue: 0.1838 time to fit residues: 140.9318 Evaluate side-chains 508 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 455 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 145 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 271 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 17 optimal weight: 0.0050 chunk 172 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 207 HIS C 607 GLN C 955 ASN B 30 ASN B 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.148651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117981 restraints weight = 48172.885| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.28 r_work: 0.3555 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25689 Z= 0.139 Angle : 0.565 11.661 34967 Z= 0.287 Chirality : 0.044 0.202 3938 Planarity : 0.004 0.048 4530 Dihedral : 4.071 29.838 3438 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.61 % Allowed : 18.37 % Favored : 79.02 % 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: -1.23 (0.14), residues: 3163 helix: 0.79 (0.22), residues: 644 sheet: 0.07 (0.20), residues: 671 loop : -1.85 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.016 0.001 TYR B 170 PHE 0.034 0.001 PHE A 342 TRP 0.060 0.002 TRP B 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00331 (25650) covalent geometry : angle 0.55799 (34889) SS BOND : bond 0.00374 ( 39) SS BOND : angle 1.90561 ( 78) hydrogen bonds : bond 0.04638 ( 645) hydrogen bonds : angle 4.67017 ( 1830) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 465 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8180 (tm-30) REVERT: A 153 MET cc_start: -0.4266 (tpt) cc_final: -0.4605 (tpt) REVERT: A 177 MET cc_start: 0.0686 (mtt) cc_final: -0.0582 (mtt) REVERT: A 508 TYR cc_start: 0.7159 (m-80) cc_final: 0.6134 (m-80) REVERT: A 564 GLN cc_start: 0.7674 (mp10) cc_final: 0.7398 (mp10) REVERT: A 580 GLN cc_start: 0.8266 (mm110) cc_final: 0.7989 (mm-40) REVERT: A 697 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8623 (ptm) REVERT: A 790 LYS cc_start: 0.9091 (mttt) cc_final: 0.8810 (mttm) REVERT: A 964 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8683 (ttmm) REVERT: A 1017 GLU cc_start: 0.7431 (tp30) cc_final: 0.6982 (tp30) REVERT: A 1091 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7800 (ttp-170) REVERT: A 1134 ASN cc_start: 0.6582 (m-40) cc_final: 0.6187 (m110) REVERT: A 1138 TYR cc_start: 0.8331 (t80) cc_final: 0.7945 (t80) REVERT: C 52 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 99 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8604 (p0) REVERT: C 177 MET cc_start: -0.3131 (mmt) cc_final: -0.4293 (mmt) REVERT: C 200 TYR cc_start: 0.7312 (m-10) cc_final: 0.7108 (m-10) REVERT: C 202 LYS cc_start: 0.8517 (mptt) cc_final: 0.7873 (mptt) REVERT: C 224 GLU cc_start: 0.7679 (mp0) cc_final: 0.7277 (mp0) REVERT: C 290 ASP cc_start: 0.8273 (t0) cc_final: 0.7866 (m-30) REVERT: C 294 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7098 (t0) REVERT: C 549 THR cc_start: 0.8783 (m) cc_final: 0.8554 (m) REVERT: C 574 ASP cc_start: 0.7894 (p0) cc_final: 0.7508 (t0) REVERT: C 586 ASP cc_start: 0.7972 (t0) cc_final: 0.7605 (t0) REVERT: C 745 ASP cc_start: 0.7534 (t0) cc_final: 0.7300 (t0) REVERT: C 790 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8768 (mmtm) REVERT: C 823 PHE cc_start: 0.8250 (t80) cc_final: 0.8028 (t80) REVERT: C 933 LYS cc_start: 0.8290 (ttmt) cc_final: 0.8075 (ttmm) REVERT: C 964 LYS cc_start: 0.8898 (ttpp) cc_final: 0.8646 (ttmm) REVERT: C 1073 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8473 (mtpp) REVERT: C 1107 ARG cc_start: 0.8566 (mtm110) cc_final: 0.6478 (tpt170) REVERT: B 140 PHE cc_start: 0.7927 (m-80) cc_final: 0.7468 (m-80) REVERT: B 190 ARG cc_start: 0.7256 (mtp180) cc_final: 0.6685 (mtp180) REVERT: B 225 PRO cc_start: 0.8099 (Cg_exo) cc_final: 0.7737 (Cg_endo) REVERT: B 374 PHE cc_start: 0.5447 (m-10) cc_final: 0.5240 (m-10) REVERT: B 429 PHE cc_start: 0.8024 (t80) cc_final: 0.7394 (t80) REVERT: B 462 LYS cc_start: 0.7420 (tptp) cc_final: 0.7219 (tptp) REVERT: B 559 PHE cc_start: 0.7700 (t80) cc_final: 0.7393 (t80) REVERT: B 560 LEU cc_start: 0.8580 (mt) cc_final: 0.8367 (tp) REVERT: B 779 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8155 (mm-40) REVERT: B 780 GLU cc_start: 0.7780 (tt0) cc_final: 0.7561 (tt0) REVERT: B 896 ILE cc_start: 0.7566 (mt) cc_final: 0.7266 (tt) REVERT: B 1107 ARG cc_start: 0.7512 (mtt180) cc_final: 0.5764 (tpt170) outliers start: 73 outliers final: 57 residues processed: 506 average time/residue: 0.1875 time to fit residues: 144.5697 Evaluate side-chains 511 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 451 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 113 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 207 HIS C 607 GLN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.147706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.117098 restraints weight = 48413.394| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.30 r_work: 0.3545 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25689 Z= 0.155 Angle : 0.594 12.339 34967 Z= 0.303 Chirality : 0.045 0.334 3938 Planarity : 0.004 0.049 4530 Dihedral : 4.184 28.948 3438 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.50 % Allowed : 18.94 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3163 helix: 0.82 (0.22), residues: 645 sheet: 0.05 (0.20), residues: 672 loop : -1.87 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.021 0.001 TYR A 351 PHE 0.033 0.001 PHE A 342 TRP 0.079 0.002 TRP B 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00371 (25650) covalent geometry : angle 0.58399 (34889) SS BOND : bond 0.00388 ( 39) SS BOND : angle 2.39423 ( 78) hydrogen bonds : bond 0.04805 ( 645) hydrogen bonds : angle 4.68541 ( 1830) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 455 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 153 MET cc_start: -0.4259 (tpt) cc_final: -0.4581 (tpt) REVERT: A 177 MET cc_start: 0.0766 (mtt) cc_final: -0.0537 (mtt) REVERT: A 508 TYR cc_start: 0.7236 (m-80) cc_final: 0.6159 (m-80) REVERT: A 515 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.5596 (p90) REVERT: A 564 GLN cc_start: 0.7753 (mp10) cc_final: 0.7385 (mp10) REVERT: A 580 GLN cc_start: 0.8271 (mm110) cc_final: 0.8001 (mm-40) REVERT: A 690 GLN cc_start: 0.8032 (mt0) cc_final: 0.7560 (mm-40) REVERT: A 697 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8625 (ptm) REVERT: A 790 LYS cc_start: 0.9094 (mttt) cc_final: 0.8803 (mttm) REVERT: A 964 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8673 (ttmm) REVERT: A 1017 GLU cc_start: 0.7490 (tp30) cc_final: 0.7058 (tp30) REVERT: A 1091 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7851 (ttp-170) REVERT: A 1134 ASN cc_start: 0.6599 (m-40) cc_final: 0.6199 (m110) REVERT: A 1138 TYR cc_start: 0.8293 (t80) cc_final: 0.7930 (t80) REVERT: C 52 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7520 (tm-30) REVERT: C 99 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8711 (p0) REVERT: C 177 MET cc_start: -0.3056 (mmt) cc_final: -0.4239 (mmt) REVERT: C 202 LYS cc_start: 0.8499 (mptt) cc_final: 0.7896 (mptt) REVERT: C 224 GLU cc_start: 0.7706 (mp0) cc_final: 0.7303 (mp0) REVERT: C 290 ASP cc_start: 0.8240 (t0) cc_final: 0.7864 (m-30) REVERT: C 294 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7156 (t0) REVERT: C 533 LEU cc_start: 0.8612 (tt) cc_final: 0.8323 (tt) REVERT: C 574 ASP cc_start: 0.7859 (p0) cc_final: 0.7539 (t0) REVERT: C 586 ASP cc_start: 0.7960 (t0) cc_final: 0.7578 (t0) REVERT: C 745 ASP cc_start: 0.7585 (t0) cc_final: 0.7372 (t0) REVERT: C 790 LYS cc_start: 0.9136 (mtpp) cc_final: 0.8790 (mmtm) REVERT: C 823 PHE cc_start: 0.8258 (t80) cc_final: 0.8032 (t80) REVERT: C 933 LYS cc_start: 0.8296 (ttmt) cc_final: 0.8085 (ttmm) REVERT: C 964 LYS cc_start: 0.8917 (ttpp) cc_final: 0.8694 (ttmm) REVERT: C 1073 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8463 (mtpp) REVERT: C 1107 ARG cc_start: 0.8594 (mtm110) cc_final: 0.6509 (tpt170) REVERT: B 41 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7476 (mtpt) REVERT: B 140 PHE cc_start: 0.7935 (m-80) cc_final: 0.7441 (m-80) REVERT: B 190 ARG cc_start: 0.7230 (mtp180) cc_final: 0.6653 (mtp180) REVERT: B 225 PRO cc_start: 0.8031 (Cg_exo) cc_final: 0.7824 (Cg_endo) REVERT: B 429 PHE cc_start: 0.8089 (t80) cc_final: 0.7409 (t80) REVERT: B 462 LYS cc_start: 0.7449 (tptp) cc_final: 0.7243 (tptp) REVERT: B 559 PHE cc_start: 0.7720 (t80) cc_final: 0.7448 (t80) REVERT: B 560 LEU cc_start: 0.8568 (mt) cc_final: 0.8351 (tp) REVERT: B 564 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7669 (mm110) REVERT: B 779 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8174 (mm-40) REVERT: B 780 GLU cc_start: 0.7847 (tt0) cc_final: 0.7628 (tt0) REVERT: B 896 ILE cc_start: 0.7593 (mt) cc_final: 0.7285 (tt) REVERT: B 1107 ARG cc_start: 0.7524 (mtt180) cc_final: 0.5778 (tpt170) outliers start: 70 outliers final: 61 residues processed: 493 average time/residue: 0.1775 time to fit residues: 134.1522 Evaluate side-chains 516 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 450 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 39 optimal weight: 0.8980 chunk 182 optimal weight: 0.0270 chunk 37 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 50 optimal weight: 0.0040 chunk 131 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 318 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 overall best weight: 0.5452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 607 GLN C 955 ASN B 675 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.148934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.118358 restraints weight = 48234.081| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.28 r_work: 0.3561 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25689 Z= 0.118 Angle : 0.587 11.757 34967 Z= 0.298 Chirality : 0.044 0.276 3938 Planarity : 0.004 0.050 4530 Dihedral : 4.156 28.226 3438 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.25 % Allowed : 19.66 % Favored : 78.09 % 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: -1.15 (0.14), residues: 3163 helix: 1.00 (0.22), residues: 650 sheet: 0.09 (0.20), residues: 663 loop : -1.84 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.015 0.001 TYR B 170 PHE 0.034 0.001 PHE A 342 TRP 0.088 0.002 TRP B 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00277 (25650) covalent geometry : angle 0.57774 (34889) SS BOND : bond 0.00349 ( 39) SS BOND : angle 2.30729 ( 78) hydrogen bonds : bond 0.04314 ( 645) hydrogen bonds : angle 4.58747 ( 1830) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 458 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 153 MET cc_start: -0.4425 (tpt) cc_final: -0.4808 (tpt) REVERT: A 177 MET cc_start: 0.0759 (mtt) cc_final: -0.0578 (mtt) REVERT: A 508 TYR cc_start: 0.7147 (m-80) cc_final: 0.6077 (m-80) REVERT: A 564 GLN cc_start: 0.7753 (mp10) cc_final: 0.7408 (mp10) REVERT: A 580 GLN cc_start: 0.8253 (mm110) cc_final: 0.7998 (mm-40) REVERT: A 690 GLN cc_start: 0.7999 (mt0) cc_final: 0.7540 (mm-40) REVERT: A 697 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8617 (ptm) REVERT: A 790 LYS cc_start: 0.9093 (mttt) cc_final: 0.8813 (mttm) REVERT: A 804 GLN cc_start: 0.8624 (mt0) cc_final: 0.8389 (mt0) REVERT: A 964 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8678 (ttmm) REVERT: A 1017 GLU cc_start: 0.7452 (tp30) cc_final: 0.6978 (tp30) REVERT: A 1091 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7831 (ttp-170) REVERT: A 1134 ASN cc_start: 0.6623 (m-40) cc_final: 0.6306 (m110) REVERT: A 1138 TYR cc_start: 0.8278 (t80) cc_final: 0.7917 (t80) REVERT: C 52 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7527 (tm-30) REVERT: C 177 MET cc_start: -0.3133 (mmt) cc_final: -0.4257 (mmt) REVERT: C 202 LYS cc_start: 0.8513 (mptt) cc_final: 0.7891 (mptt) REVERT: C 224 GLU cc_start: 0.7639 (mp0) cc_final: 0.7243 (mp0) REVERT: C 290 ASP cc_start: 0.8215 (t0) cc_final: 0.7824 (m-30) REVERT: C 294 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7163 (t0) REVERT: C 586 ASP cc_start: 0.7958 (t0) cc_final: 0.7625 (t0) REVERT: C 745 ASP cc_start: 0.7528 (t0) cc_final: 0.7324 (t0) REVERT: C 790 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8784 (mmtm) REVERT: C 823 PHE cc_start: 0.8230 (t80) cc_final: 0.8011 (t80) REVERT: C 933 LYS cc_start: 0.8298 (ttmt) cc_final: 0.8086 (ttmm) REVERT: C 1073 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8463 (mtpp) REVERT: C 1107 ARG cc_start: 0.8560 (mtm110) cc_final: 0.6476 (tpt170) REVERT: B 140 PHE cc_start: 0.7940 (m-80) cc_final: 0.7449 (m-80) REVERT: B 168 PHE cc_start: 0.7348 (t80) cc_final: 0.6985 (t80) REVERT: B 190 ARG cc_start: 0.7228 (mtp180) cc_final: 0.6683 (mtp180) REVERT: B 429 PHE cc_start: 0.8007 (t80) cc_final: 0.7338 (t80) REVERT: B 462 LYS cc_start: 0.7542 (tptp) cc_final: 0.7319 (tptp) REVERT: B 559 PHE cc_start: 0.7669 (t80) cc_final: 0.7468 (t80) REVERT: B 560 LEU cc_start: 0.8510 (mt) cc_final: 0.8299 (tp) REVERT: B 779 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8183 (mm-40) REVERT: B 780 GLU cc_start: 0.7808 (tt0) cc_final: 0.7583 (tt0) REVERT: B 896 ILE cc_start: 0.7524 (mt) cc_final: 0.7220 (tt) REVERT: B 985 ASP cc_start: 0.7248 (p0) cc_final: 0.6705 (p0) REVERT: B 1107 ARG cc_start: 0.7517 (mtt180) cc_final: 0.5817 (tpt170) outliers start: 63 outliers final: 57 residues processed: 495 average time/residue: 0.1726 time to fit residues: 130.9408 Evaluate side-chains 509 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 450 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 4 optimal weight: 0.9980 chunk 319 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 270 optimal weight: 1.9990 chunk 295 optimal weight: 0.9980 chunk 216 optimal weight: 0.8980 chunk 211 optimal weight: 0.0570 chunk 35 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 207 HIS C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.150943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.120389 restraints weight = 48089.085| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.21 r_work: 0.3564 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25689 Z= 0.115 Angle : 0.592 11.698 34967 Z= 0.299 Chirality : 0.044 0.250 3938 Planarity : 0.004 0.061 4530 Dihedral : 4.129 34.945 3438 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.22 % Allowed : 19.80 % Favored : 77.98 % 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: -1.07 (0.15), residues: 3163 helix: 1.12 (0.22), residues: 650 sheet: 0.09 (0.20), residues: 676 loop : -1.81 (0.13), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 357 TYR 0.019 0.001 TYR A 351 PHE 0.034 0.001 PHE A 342 TRP 0.051 0.002 TRP A 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00270 (25650) covalent geometry : angle 0.58345 (34889) SS BOND : bond 0.00316 ( 39) SS BOND : angle 2.24464 ( 78) hydrogen bonds : bond 0.04146 ( 645) hydrogen bonds : angle 4.50577 ( 1830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6692.50 seconds wall clock time: 115 minutes 2.35 seconds (6902.35 seconds total)