Starting phenix.real_space_refine on Tue Feb 3 23:26:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9krk_62531/02_2026/9krk_62531.cif Found real_map, /net/cci-nas-00/data/ceres_data/9krk_62531/02_2026/9krk_62531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9krk_62531/02_2026/9krk_62531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9krk_62531/02_2026/9krk_62531.map" model { file = "/net/cci-nas-00/data/ceres_data/9krk_62531/02_2026/9krk_62531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9krk_62531/02_2026/9krk_62531.cif" } resolution = 3.29 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= 0.064 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 37 5.16 5 C 4941 2.51 5 N 1264 2.21 5 O 1333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7575 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7575 Classifications: {'peptide': 943} Link IDs: {'PTRANS': 30, 'TRANS': 912} Chain breaks: 3 Time building chain proxies: 1.72, per 1000 atoms: 0.23 Number of scatterers: 7575 At special positions: 0 Unit cell: (82.5, 103.4, 140.8, 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 37 16.00 O 1333 8.00 N 1264 7.00 C 4941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.73 Conformation dependent library (CDL) restraints added in 222.9 milliseconds 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 71.7% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.779A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 74 removed outlier: 4.290A pdb=" N GLU A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 105 removed outlier: 3.585A pdb=" N CYS A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.815A pdb=" N ILE A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 150 removed outlier: 3.617A pdb=" N PHE A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 179 removed outlier: 4.202A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.684A pdb=" N LYS A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.694A pdb=" N LYS A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP A 206 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.669A pdb=" N LEU A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 238 through 243 removed outlier: 4.208A pdb=" N VAL A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 281 removed outlier: 3.662A pdb=" N CYS A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.736A pdb=" N ILE A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 326 removed outlier: 4.415A pdb=" N PHE A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 343 removed outlier: 3.985A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 390 removed outlier: 3.852A pdb=" N ALA A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Proline residue: A 370 - end of helix removed outlier: 3.826A pdb=" N ILE A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.523A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 744 removed outlier: 3.676A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL A 726 " --> pdb=" O THR A 722 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 735 " --> pdb=" O GLN A 731 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 744 " --> pdb=" O ASN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 806 removed outlier: 4.375A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 768 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 782 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 783 " --> pdb=" O GLY A 779 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 815 removed outlier: 3.564A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 835 removed outlier: 3.926A pdb=" N ILE A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 859 Processing helix chain 'A' and resid 869 through 887 removed outlier: 3.830A pdb=" N ILE A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 876 " --> pdb=" O GLY A 872 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 877 " --> pdb=" O ILE A 873 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 910 Proline residue: A 899 - end of helix removed outlier: 3.948A pdb=" N GLN A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 910 " --> pdb=" O SER A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 4.041A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 970 removed outlier: 3.898A pdb=" N GLN A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 941 " --> pdb=" O ALA A 937 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 942 " --> pdb=" O TRP A 938 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 949 " --> pdb=" O SER A 945 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 950 " --> pdb=" O ARG A 946 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 955 " --> pdb=" O ARG A 951 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 960 " --> pdb=" O CYS A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 987 removed outlier: 3.593A pdb=" N VAL A 979 " --> pdb=" O ASP A 975 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1015 removed outlier: 4.573A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A1000 " --> pdb=" O CYS A 996 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA A1001 " --> pdb=" O VAL A 997 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1109 through 1115 removed outlier: 3.689A pdb=" N LYS A1115 " --> pdb=" O HIS A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1136 removed outlier: 3.815A pdb=" N ASN A1134 " --> pdb=" O THR A1130 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1156 through 1161 removed outlier: 3.939A pdb=" N ASP A1161 " --> pdb=" O GLU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1212 through 1222 Processing helix chain 'A' and resid 1257 through 1262 removed outlier: 3.926A pdb=" N LEU A1261 " --> pdb=" O GLU A1257 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1041 through 1042 Processing sheet with id=AA2, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 3.531A pdb=" N ASP A1201 " --> pdb=" O ILE A1120 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A1231 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A1200 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A1071 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1233 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: 1.11 Time building geometry restraints manager: 0.88 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: 2378 1.35 - 1.46: 1794 1.46 - 1.58: 3511 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 7744 Sorted by residual: bond pdb=" C TRP A1035 " pdb=" N PRO A1036 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.23e-01 bond pdb=" CA SER A 898 " pdb=" C SER A 898 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.68e-01 bond pdb=" C VAL A 773 " pdb=" O VAL A 773 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.19e-02 7.06e+03 4.89e-01 bond pdb=" C SER A 898 " pdb=" N PRO A 899 " ideal model delta sigma weight residual 1.336 1.344 -0.009 1.23e-02 6.61e+03 4.88e-01 bond pdb=" C VAL A1057 " pdb=" O VAL A1057 " ideal model delta sigma weight residual 1.241 1.232 0.009 1.25e-02 6.40e+03 4.75e-01 ... (remaining 7739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 10174 1.19 - 2.38: 267 2.38 - 3.58: 37 3.58 - 4.77: 15 4.77 - 5.96: 11 Bond angle restraints: 10504 Sorted by residual: angle pdb=" C TYR A1016 " pdb=" N THR A1017 " pdb=" CA THR A1017 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.31e+00 angle pdb=" CA CYS A 19 " pdb=" CB CYS A 19 " pdb=" SG CYS A 19 " ideal model delta sigma weight residual 114.40 119.64 -5.24 2.30e+00 1.89e-01 5.19e+00 angle pdb=" C PHE A 98 " pdb=" N THR A 99 " pdb=" CA THR A 99 " ideal model delta sigma weight residual 120.31 117.31 3.00 1.52e+00 4.33e-01 3.89e+00 angle pdb=" N SER A 898 " pdb=" CA SER A 898 " pdb=" C SER A 898 " ideal model delta sigma weight residual 109.81 114.10 -4.29 2.21e+00 2.05e-01 3.77e+00 angle pdb=" C PHE A1089 " pdb=" N ARG A1090 " pdb=" CA ARG A1090 " ideal model delta sigma weight residual 122.46 125.06 -2.60 1.41e+00 5.03e-01 3.41e+00 ... (remaining 10499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4236 17.71 - 35.43: 318 35.43 - 53.14: 39 53.14 - 70.85: 10 70.85 - 88.57: 5 Dihedral angle restraints: 4608 sinusoidal: 1843 harmonic: 2765 Sorted by residual: dihedral pdb=" CA ASP A1143 " pdb=" CB ASP A1143 " pdb=" CG ASP A1143 " pdb=" OD1 ASP A1143 " ideal model delta sinusoidal sigma weight residual -30.00 -86.33 56.33 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU A1160 " pdb=" CG GLU A1160 " pdb=" CD GLU A1160 " pdb=" OE1 GLU A1160 " ideal model delta sinusoidal sigma weight residual 0.00 -87.74 87.74 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASP A 834 " pdb=" C ASP A 834 " pdb=" N LEU A 835 " pdb=" CA LEU A 835 " ideal model delta harmonic sigma weight residual -180.00 -164.44 -15.56 0 5.00e+00 4.00e-02 9.68e+00 ... (remaining 4605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 790 0.033 - 0.065: 323 0.065 - 0.098: 87 0.098 - 0.131: 22 0.131 - 0.163: 3 Chirality restraints: 1225 Sorted by residual: chirality pdb=" CB VAL A1153 " pdb=" CA VAL A1153 " pdb=" CG1 VAL A1153 " pdb=" CG2 VAL A1153 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA ILE A1231 " pdb=" N ILE A1231 " pdb=" C ILE A1231 " pdb=" CB ILE A1231 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB ILE A1100 " pdb=" CA ILE A1100 " pdb=" CG1 ILE A1100 " pdb=" CG2 ILE A1100 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 1222 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 365 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C VAL A 365 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL A 365 " -0.008 2.00e-02 2.50e+03 pdb=" N THR A 366 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1123 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO A1124 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A1124 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1124 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 218 " -0.016 5.00e-02 4.00e+02 2.36e-02 8.91e-01 pdb=" N PRO A 219 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " -0.013 5.00e-02 4.00e+02 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2337 2.83 - 3.34: 7264 3.34 - 3.86: 11463 3.86 - 4.38: 12508 4.38 - 4.90: 22103 Nonbonded interactions: 55675 Sorted by model distance: nonbonded pdb=" O LEU A1126 " pdb=" OG SER A1173 " model vdw 2.306 3.040 nonbonded pdb=" O LYS A 9 " pdb=" OG SER A 46 " model vdw 2.311 3.040 nonbonded pdb=" NH1 ARG A1090 " pdb=" O THR A1105 " model vdw 2.346 3.120 nonbonded pdb=" ND2 ASN A 740 " pdb=" OD2 ASP A 975 " model vdw 2.359 3.120 nonbonded pdb=" OG1 THR A 756 " pdb=" OE1 GLU A 757 " model vdw 2.363 3.040 ... (remaining 55670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.350 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.002 0.021 7744 Z= 0.108 Angle : 0.496 5.960 10504 Z= 0.275 Chirality : 0.039 0.163 1225 Planarity : 0.003 0.028 1296 Dihedral : 12.465 88.567 2810 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: -2.14 (0.25), residues: 935 helix: -0.75 (0.19), residues: 625 sheet: -1.32 (0.71), residues: 47 loop : -2.83 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1189 TYR 0.010 0.001 TYR A 768 PHE 0.008 0.001 PHE A 98 TRP 0.006 0.001 TRP A 763 HIS 0.002 0.000 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 7744) covalent geometry : angle 0.49594 (10504) hydrogen bonds : bond 0.13076 ( 417) hydrogen bonds : angle 4.00461 ( 1233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8164 (tp40) cc_final: 0.7867 (tp-100) REVERT: A 175 TYR cc_start: 0.8354 (t80) cc_final: 0.7547 (t80) REVERT: A 184 MET cc_start: 0.8060 (tmm) cc_final: 0.7838 (tmm) REVERT: A 186 MET cc_start: 0.8255 (tpt) cc_final: 0.7987 (tpt) REVERT: A 200 ASN cc_start: 0.8763 (t0) cc_final: 0.8562 (t0) REVERT: A 706 ARG cc_start: 0.8431 (ptt90) cc_final: 0.7965 (tpp-160) REVERT: A 805 ILE cc_start: 0.7571 (tt) cc_final: 0.7351 (tp) REVERT: A 827 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7903 (ttpp) REVERT: A 887 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8415 (ptp-110) REVERT: A 936 GLU cc_start: 0.7520 (tt0) cc_final: 0.7153 (tt0) REVERT: A 1042 ILE cc_start: 0.8247 (pt) cc_final: 0.7828 (tp) REVERT: A 1123 GLU cc_start: 0.8655 (pp20) cc_final: 0.8343 (pp20) REVERT: A 1166 MET cc_start: 0.5824 (mmm) cc_final: 0.5442 (mmm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1195 time to fit residues: 24.1970 Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 GLN A 725 GLN A 994 GLN A1047 ASN A1111 HIS A1139 ASN A1141 HIS A1183 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.143546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102533 restraints weight = 12678.494| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.12 r_work: 0.3348 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7744 Z= 0.106 Angle : 0.516 7.741 10504 Z= 0.256 Chirality : 0.039 0.139 1225 Planarity : 0.003 0.026 1296 Dihedral : 3.329 18.062 1016 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.81 % Allowed : 10.84 % Favored : 87.35 % 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: -0.86 (0.27), residues: 935 helix: 0.28 (0.21), residues: 646 sheet: -0.80 (0.84), residues: 40 loop : -2.70 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 274 TYR 0.016 0.001 TYR A 123 PHE 0.024 0.001 PHE A 258 TRP 0.014 0.001 TRP A1099 HIS 0.002 0.000 HIS A1111 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 7744) covalent geometry : angle 0.51614 (10504) hydrogen bonds : bond 0.04618 ( 417) hydrogen bonds : angle 3.34595 ( 1233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.9015 (mmm) cc_final: 0.8528 (mmt) REVERT: A 184 MET cc_start: 0.8580 (tmm) cc_final: 0.8302 (tmm) REVERT: A 186 MET cc_start: 0.7870 (tpt) cc_final: 0.7627 (tpt) REVERT: A 200 ASN cc_start: 0.8690 (t0) cc_final: 0.8446 (t0) REVERT: A 389 PHE cc_start: 0.8296 (t80) cc_final: 0.8065 (t80) REVERT: A 706 ARG cc_start: 0.9034 (ptt90) cc_final: 0.7958 (tpp-160) REVERT: A 936 GLU cc_start: 0.7978 (tt0) cc_final: 0.7583 (tt0) REVERT: A 1020 GLU cc_start: 0.7750 (mp0) cc_final: 0.7541 (mp0) REVERT: A 1042 ILE cc_start: 0.8266 (pt) cc_final: 0.7869 (tp) REVERT: A 1123 GLU cc_start: 0.8714 (pp20) cc_final: 0.8318 (pp20) REVERT: A 1183 GLN cc_start: 0.9200 (mp10) cc_final: 0.8629 (mp10) REVERT: A 1245 MET cc_start: 0.8334 (mtp) cc_final: 0.8018 (mtp) outliers start: 15 outliers final: 9 residues processed: 126 average time/residue: 0.0811 time to fit residues: 14.3520 Evaluate side-chains 115 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.140552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100051 restraints weight = 12618.528| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.17 r_work: 0.3281 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7744 Z= 0.129 Angle : 0.530 7.818 10504 Z= 0.267 Chirality : 0.040 0.139 1225 Planarity : 0.003 0.028 1296 Dihedral : 3.444 19.157 1016 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.17 % Allowed : 14.22 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.28), residues: 935 helix: 0.70 (0.21), residues: 640 sheet: -0.87 (0.87), residues: 42 loop : -2.31 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.017 0.001 TYR A 123 PHE 0.019 0.001 PHE A 258 TRP 0.014 0.001 TRP A 711 HIS 0.002 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7744) covalent geometry : angle 0.53048 (10504) hydrogen bonds : bond 0.05322 ( 417) hydrogen bonds : angle 3.37204 ( 1233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.9016 (mmm) cc_final: 0.8508 (mmt) REVERT: A 184 MET cc_start: 0.8627 (tmm) cc_final: 0.8346 (tmm) REVERT: A 186 MET cc_start: 0.7777 (tpt) cc_final: 0.7541 (tpt) REVERT: A 200 ASN cc_start: 0.8699 (t0) cc_final: 0.8427 (t0) REVERT: A 363 LEU cc_start: 0.9033 (tt) cc_final: 0.8820 (tp) REVERT: A 706 ARG cc_start: 0.9053 (ptt90) cc_final: 0.7965 (tpp-160) REVERT: A 1020 GLU cc_start: 0.7741 (mp0) cc_final: 0.7495 (mp0) REVERT: A 1042 ILE cc_start: 0.8246 (pt) cc_final: 0.7862 (tp) REVERT: A 1123 GLU cc_start: 0.8757 (pp20) cc_final: 0.8390 (pp20) REVERT: A 1166 MET cc_start: 0.5486 (mmm) cc_final: 0.5152 (mmm) REVERT: A 1245 MET cc_start: 0.8337 (mtp) cc_final: 0.8102 (mtp) outliers start: 18 outliers final: 14 residues processed: 124 average time/residue: 0.0786 time to fit residues: 13.8472 Evaluate side-chains 117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1246 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 GLN A1225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.141508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101166 restraints weight = 12676.770| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.20 r_work: 0.3304 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7744 Z= 0.112 Angle : 0.516 8.921 10504 Z= 0.255 Chirality : 0.039 0.131 1225 Planarity : 0.003 0.030 1296 Dihedral : 3.432 19.875 1016 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.05 % Allowed : 15.42 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.28), residues: 935 helix: 0.98 (0.21), residues: 640 sheet: -0.37 (0.91), residues: 40 loop : -2.18 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 274 TYR 0.018 0.001 TYR A 123 PHE 0.017 0.001 PHE A 324 TRP 0.016 0.001 TRP A 711 HIS 0.001 0.000 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7744) covalent geometry : angle 0.51642 (10504) hydrogen bonds : bond 0.04894 ( 417) hydrogen bonds : angle 3.28190 ( 1233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 TYR cc_start: 0.8630 (t80) cc_final: 0.8351 (t80) REVERT: A 184 MET cc_start: 0.8638 (tmm) cc_final: 0.8334 (tmm) REVERT: A 186 MET cc_start: 0.7891 (tpt) cc_final: 0.7679 (tpt) REVERT: A 200 ASN cc_start: 0.8697 (t0) cc_final: 0.8468 (t0) REVERT: A 363 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8865 (tp) REVERT: A 706 ARG cc_start: 0.9018 (ptt90) cc_final: 0.7965 (tpp-160) REVERT: A 757 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7390 (pm20) REVERT: A 1020 GLU cc_start: 0.7785 (mp0) cc_final: 0.7539 (mp0) REVERT: A 1042 ILE cc_start: 0.8298 (pt) cc_final: 0.7933 (tp) REVERT: A 1123 GLU cc_start: 0.8726 (pp20) cc_final: 0.8330 (pp20) REVERT: A 1166 MET cc_start: 0.6116 (mmm) cc_final: 0.5436 (mmm) outliers start: 17 outliers final: 12 residues processed: 120 average time/residue: 0.0785 time to fit residues: 13.3480 Evaluate side-chains 120 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1246 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.141600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099489 restraints weight = 12615.155| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.16 r_work: 0.3294 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7744 Z= 0.113 Angle : 0.522 9.406 10504 Z= 0.258 Chirality : 0.039 0.131 1225 Planarity : 0.003 0.034 1296 Dihedral : 3.407 19.608 1016 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.41 % Allowed : 16.51 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.29), residues: 935 helix: 1.22 (0.22), residues: 634 sheet: -0.29 (0.90), residues: 40 loop : -2.12 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.019 0.001 TYR A 123 PHE 0.014 0.001 PHE A 258 TRP 0.017 0.001 TRP A 711 HIS 0.002 0.000 HIS A1225 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7744) covalent geometry : angle 0.52169 (10504) hydrogen bonds : bond 0.04852 ( 417) hydrogen bonds : angle 3.23504 ( 1233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 TYR cc_start: 0.8566 (t80) cc_final: 0.8225 (t80) REVERT: A 184 MET cc_start: 0.8667 (tmm) cc_final: 0.8337 (tmm) REVERT: A 186 MET cc_start: 0.7792 (tpt) cc_final: 0.7575 (tpt) REVERT: A 200 ASN cc_start: 0.8691 (t0) cc_final: 0.8434 (t0) REVERT: A 358 TYR cc_start: 0.8652 (m-80) cc_final: 0.8273 (m-80) REVERT: A 706 ARG cc_start: 0.9016 (ptt90) cc_final: 0.7924 (tpp-160) REVERT: A 757 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: A 936 GLU cc_start: 0.7929 (tt0) cc_final: 0.7661 (tt0) REVERT: A 1020 GLU cc_start: 0.7743 (mp0) cc_final: 0.7488 (mp0) REVERT: A 1042 ILE cc_start: 0.8281 (pt) cc_final: 0.7935 (tp) REVERT: A 1123 GLU cc_start: 0.8721 (pp20) cc_final: 0.8310 (pp20) outliers start: 20 outliers final: 16 residues processed: 120 average time/residue: 0.0826 time to fit residues: 13.8879 Evaluate side-chains 123 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1246 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.0050 chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.140338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098034 restraints weight = 12814.730| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.14 r_work: 0.3285 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7744 Z= 0.124 Angle : 0.523 8.327 10504 Z= 0.262 Chirality : 0.039 0.130 1225 Planarity : 0.003 0.034 1296 Dihedral : 3.449 19.505 1016 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.53 % Allowed : 16.75 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.29), residues: 935 helix: 1.31 (0.22), residues: 633 sheet: -0.32 (0.90), residues: 40 loop : -1.92 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.013 0.001 TYR A 175 PHE 0.018 0.001 PHE A 324 TRP 0.019 0.001 TRP A 711 HIS 0.002 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7744) covalent geometry : angle 0.52265 (10504) hydrogen bonds : bond 0.05156 ( 417) hydrogen bonds : angle 3.26991 ( 1233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 TYR cc_start: 0.8596 (t80) cc_final: 0.8264 (t80) REVERT: A 184 MET cc_start: 0.8676 (tmm) cc_final: 0.8334 (tmm) REVERT: A 186 MET cc_start: 0.7702 (tpt) cc_final: 0.7478 (tpt) REVERT: A 200 ASN cc_start: 0.8703 (t0) cc_final: 0.8438 (t0) REVERT: A 706 ARG cc_start: 0.9029 (ptt90) cc_final: 0.7958 (tpp-160) REVERT: A 757 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: A 936 GLU cc_start: 0.7951 (tt0) cc_final: 0.7720 (tt0) REVERT: A 1020 GLU cc_start: 0.7748 (mp0) cc_final: 0.7505 (mp0) REVERT: A 1042 ILE cc_start: 0.8221 (pt) cc_final: 0.7890 (tp) REVERT: A 1166 MET cc_start: 0.5154 (mmm) cc_final: 0.4669 (mmm) outliers start: 21 outliers final: 16 residues processed: 123 average time/residue: 0.0842 time to fit residues: 14.3227 Evaluate side-chains 117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1246 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 38 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.141750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.099816 restraints weight = 12732.417| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.12 r_work: 0.3307 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7744 Z= 0.112 Angle : 0.535 11.015 10504 Z= 0.263 Chirality : 0.040 0.231 1225 Planarity : 0.003 0.037 1296 Dihedral : 3.427 19.608 1016 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.41 % Allowed : 17.47 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.29), residues: 935 helix: 1.40 (0.22), residues: 634 sheet: -0.17 (0.90), residues: 40 loop : -1.87 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 891 TYR 0.015 0.001 TYR A 123 PHE 0.012 0.001 PHE A 258 TRP 0.020 0.001 TRP A 711 HIS 0.001 0.000 HIS A1225 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7744) covalent geometry : angle 0.53539 (10504) hydrogen bonds : bond 0.04755 ( 417) hydrogen bonds : angle 3.20267 ( 1233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 TYR cc_start: 0.8579 (t80) cc_final: 0.8220 (t80) REVERT: A 184 MET cc_start: 0.8671 (tmm) cc_final: 0.8325 (tmm) REVERT: A 200 ASN cc_start: 0.8686 (t0) cc_final: 0.8430 (t0) REVERT: A 358 TYR cc_start: 0.8649 (m-80) cc_final: 0.8272 (m-80) REVERT: A 706 ARG cc_start: 0.9040 (ptt90) cc_final: 0.7939 (tpp-160) REVERT: A 757 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: A 936 GLU cc_start: 0.7940 (tt0) cc_final: 0.7704 (tt0) REVERT: A 1020 GLU cc_start: 0.7733 (mp0) cc_final: 0.7503 (mp0) REVERT: A 1123 GLU cc_start: 0.8718 (pp20) cc_final: 0.8306 (pp20) REVERT: A 1131 MET cc_start: 0.7936 (tpp) cc_final: 0.7719 (tpp) REVERT: A 1166 MET cc_start: 0.5530 (mmm) cc_final: 0.5118 (mmm) outliers start: 20 outliers final: 18 residues processed: 115 average time/residue: 0.0783 time to fit residues: 12.6885 Evaluate side-chains 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1246 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.139005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096876 restraints weight = 12875.619| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.16 r_work: 0.3254 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7744 Z= 0.135 Angle : 0.553 9.527 10504 Z= 0.274 Chirality : 0.040 0.234 1225 Planarity : 0.003 0.039 1296 Dihedral : 3.501 18.936 1016 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.29 % Allowed : 17.95 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.29), residues: 935 helix: 1.37 (0.22), residues: 634 sheet: 0.06 (0.86), residues: 42 loop : -1.81 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 891 TYR 0.013 0.001 TYR A 728 PHE 0.019 0.001 PHE A 324 TRP 0.022 0.001 TRP A 711 HIS 0.002 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7744) covalent geometry : angle 0.55299 (10504) hydrogen bonds : bond 0.05473 ( 417) hydrogen bonds : angle 3.33952 ( 1233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8707 (tmm) cc_final: 0.8382 (tmm) REVERT: A 200 ASN cc_start: 0.8648 (t0) cc_final: 0.8360 (t0) REVERT: A 706 ARG cc_start: 0.9055 (ptt90) cc_final: 0.8028 (tpp-160) REVERT: A 757 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: A 990 MET cc_start: 0.4088 (mmt) cc_final: 0.3821 (mmt) REVERT: A 1020 GLU cc_start: 0.7738 (mp0) cc_final: 0.7503 (mp0) REVERT: A 1131 MET cc_start: 0.7892 (tpp) cc_final: 0.7678 (tpp) REVERT: A 1166 MET cc_start: 0.5607 (mmm) cc_final: 0.5043 (mmm) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 0.0802 time to fit residues: 12.8275 Evaluate side-chains 113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1246 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 HIS ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.133659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093215 restraints weight = 12810.407| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.09 r_work: 0.3223 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7744 Z= 0.176 Angle : 0.601 9.038 10504 Z= 0.302 Chirality : 0.042 0.227 1225 Planarity : 0.003 0.042 1296 Dihedral : 3.755 18.912 1016 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.05 % Allowed : 19.04 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.29), residues: 935 helix: 1.12 (0.22), residues: 641 sheet: 0.03 (0.87), residues: 42 loop : -1.76 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 891 TYR 0.017 0.001 TYR A 123 PHE 0.014 0.001 PHE A 258 TRP 0.020 0.001 TRP A 711 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 7744) covalent geometry : angle 0.60102 (10504) hydrogen bonds : bond 0.06488 ( 417) hydrogen bonds : angle 3.61647 ( 1233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8666 (tmm) cc_final: 0.8394 (tmm) REVERT: A 200 ASN cc_start: 0.8778 (t0) cc_final: 0.8498 (t0) REVERT: A 706 ARG cc_start: 0.9068 (ptt90) cc_final: 0.8258 (tpp-160) REVERT: A 936 GLU cc_start: 0.8114 (tt0) cc_final: 0.7830 (tt0) REVERT: A 990 MET cc_start: 0.4419 (mmt) cc_final: 0.4206 (mmt) REVERT: A 1020 GLU cc_start: 0.7761 (mp0) cc_final: 0.7549 (mp0) REVERT: A 1131 MET cc_start: 0.8085 (tpp) cc_final: 0.7802 (tpp) REVERT: A 1166 MET cc_start: 0.5704 (mmm) cc_final: 0.5174 (mmm) outliers start: 17 outliers final: 16 residues processed: 109 average time/residue: 0.0784 time to fit residues: 12.1683 Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1246 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 91 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 82 optimal weight: 0.0020 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 0.0370 chunk 68 optimal weight: 0.6980 overall best weight: 0.3466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A1183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.139362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099550 restraints weight = 12739.189| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.11 r_work: 0.3327 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7744 Z= 0.110 Angle : 0.549 8.920 10504 Z= 0.270 Chirality : 0.040 0.244 1225 Planarity : 0.003 0.038 1296 Dihedral : 3.539 20.245 1016 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.57 % Allowed : 19.88 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.29), residues: 935 helix: 1.45 (0.22), residues: 638 sheet: 0.06 (0.87), residues: 42 loop : -1.77 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 891 TYR 0.017 0.001 TYR A 123 PHE 0.011 0.001 PHE A 258 TRP 0.022 0.001 TRP A 711 HIS 0.001 0.000 HIS A1225 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 7744) covalent geometry : angle 0.54914 (10504) hydrogen bonds : bond 0.04500 ( 417) hydrogen bonds : angle 3.25864 ( 1233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7664 (pttm) REVERT: A 175 TYR cc_start: 0.8597 (t80) cc_final: 0.8314 (t80) REVERT: A 184 MET cc_start: 0.8632 (tmm) cc_final: 0.8348 (tmm) REVERT: A 706 ARG cc_start: 0.8986 (ptt90) cc_final: 0.7949 (tpp-160) REVERT: A 1020 GLU cc_start: 0.7693 (mp0) cc_final: 0.7480 (mp0) REVERT: A 1064 LEU cc_start: 0.8645 (mt) cc_final: 0.8215 (tp) REVERT: A 1123 GLU cc_start: 0.8741 (pp20) cc_final: 0.8356 (pp20) REVERT: A 1166 MET cc_start: 0.5704 (mmm) cc_final: 0.5106 (mmm) outliers start: 13 outliers final: 11 residues processed: 112 average time/residue: 0.0730 time to fit residues: 11.3057 Evaluate side-chains 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1183 GLN Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1246 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.140087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.100226 restraints weight = 12389.581| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.85 r_work: 0.3302 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7744 Z= 0.134 Angle : 0.565 8.687 10504 Z= 0.282 Chirality : 0.040 0.231 1225 Planarity : 0.003 0.043 1296 Dihedral : 3.529 19.876 1016 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.57 % Allowed : 20.24 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.29), residues: 935 helix: 1.43 (0.22), residues: 636 sheet: 0.04 (0.87), residues: 42 loop : -1.74 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 891 TYR 0.013 0.001 TYR A 728 PHE 0.011 0.001 PHE A 258 TRP 0.021 0.001 TRP A 711 HIS 0.002 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7744) covalent geometry : angle 0.56488 (10504) hydrogen bonds : bond 0.05218 ( 417) hydrogen bonds : angle 3.32569 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1746.73 seconds wall clock time: 30 minutes 39.45 seconds (1839.45 seconds total)