Starting phenix.real_space_refine on Tue Feb 3 23:42:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9krm_62533/02_2026/9krm_62533.cif Found real_map, /net/cci-nas-00/data/ceres_data/9krm_62533/02_2026/9krm_62533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9krm_62533/02_2026/9krm_62533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9krm_62533/02_2026/9krm_62533.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9krm_62533/02_2026/9krm_62533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9krm_62533/02_2026/9krm_62533.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.098 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 4981 2.51 5 N 1279 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 7641 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7608 Classifications: {'peptide': 947} Link IDs: {'PTRANS': 31, 'TRANS': 915} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MTX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.57, per 1000 atoms: 0.21 Number of scatterers: 7641 At special positions: 0 Unit cell: (80.3, 94.6, 149.6, 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 1344 8.00 N 1279 7.00 C 4981 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: 0.69 Conformation dependent library (CDL) restraints added in 173.9 milliseconds 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MTX A1401 " Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 70.0% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 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: 3.769A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.567A pdb=" N GLU A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 122 removed outlier: 3.637A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.571A pdb=" N GLY A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 150 removed outlier: 3.612A pdb=" N THR A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 178 removed outlier: 4.155A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.560A pdb=" N GLY A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.775A pdb=" N PHE A 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP A 206 " --> pdb=" O ASN A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 206' Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.682A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 280 removed outlier: 4.353A pdb=" N VAL A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.514A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.827A pdb=" N MET A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 326 removed outlier: 4.110A pdb=" N PHE A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 removed outlier: 4.234A pdb=" N GLY A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 390 removed outlier: 3.985A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Proline residue: A 370 - end of helix removed outlier: 3.937A pdb=" N ILE A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.565A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 744 removed outlier: 3.738A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 715 " --> pdb=" O TRP A 711 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL A 726 " --> pdb=" O THR A 722 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 735 " --> pdb=" O GLN A 731 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 744 " --> pdb=" O ASN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 806 removed outlier: 4.378A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 768 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 782 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 783 " --> pdb=" O GLY A 779 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 814 removed outlier: 4.059A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 834 removed outlier: 3.722A pdb=" N ILE A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.844A pdb=" N VAL A 850 " --> pdb=" O THR A 846 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 853 " --> pdb=" O GLN A 849 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 861 " --> pdb=" O ALA A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 865 removed outlier: 3.768A pdb=" N ALA A 865 " --> pdb=" O PRO A 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 862 through 865' Processing helix chain 'A' and resid 867 through 887 removed outlier: 3.743A pdb=" N ILE A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 876 " --> pdb=" O GLY A 872 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 877 " --> pdb=" O ILE A 873 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 908 Proline residue: A 899 - end of helix removed outlier: 3.765A pdb=" N LEU A 908 " --> pdb=" O LEU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.556A pdb=" N ARG A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 916 " --> pdb=" O TRP A 912 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 917' Processing helix chain 'A' and resid 921 through 969 removed outlier: 3.704A pdb=" N LEU A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 941 " --> pdb=" O ALA A 937 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 942 " --> pdb=" O TRP A 938 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A 949 " --> pdb=" O SER A 945 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 950 " --> pdb=" O ARG A 946 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 955 " --> pdb=" O ARG A 951 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 960 " --> pdb=" O CYS A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 986 removed outlier: 3.648A pdb=" N TYR A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1015 removed outlier: 4.206A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A1000 " --> pdb=" O CYS A 996 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A1001 " --> pdb=" O VAL A 997 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1089 removed outlier: 3.768A pdb=" N LEU A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A1089 " --> pdb=" O ILE A1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1084 through 1089' Processing helix chain 'A' and resid 1110 through 1115 Processing helix chain 'A' and resid 1130 through 1135 removed outlier: 3.598A pdb=" N LEU A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1153 removed outlier: 3.799A pdb=" N TRP A1147 " --> pdb=" O ASP A1143 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A1153 " --> pdb=" O ALA A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1162 removed outlier: 4.071A pdb=" N GLU A1160 " --> pdb=" O LYS A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1193 Processing helix chain 'A' and resid 1210 through 1222 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 1118 through 1120 removed outlier: 6.420A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE A1231 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A1200 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A1071 " --> pdb=" O THR A1230 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1137 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: 0.86 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2397 1.34 - 1.46: 1784 1.46 - 1.58: 3572 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 7814 Sorted by residual: bond pdb=" C MTX A1401 " pdb=" O MTX A1401 " ideal model delta sigma weight residual 1.230 1.410 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C7 MTX A1401 " pdb=" N8 MTX A1401 " ideal model delta sigma weight residual 1.309 1.379 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C6 MTX A1401 " pdb=" N5 MTX A1401 " ideal model delta sigma weight residual 1.313 1.380 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C4 MTX A1401 " pdb=" N3 MTX A1401 " ideal model delta sigma weight residual 1.313 1.380 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C4 MTX A1401 " pdb=" C4A MTX A1401 " ideal model delta sigma weight residual 1.444 1.390 0.054 2.00e-02 2.50e+03 7.25e+00 ... (remaining 7809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10348 1.64 - 3.28: 204 3.28 - 4.92: 34 4.92 - 6.56: 12 6.56 - 8.20: 5 Bond angle restraints: 10603 Sorted by residual: angle pdb=" N ILE A 864 " pdb=" CA ILE A 864 " pdb=" C ILE A 864 " ideal model delta sigma weight residual 111.91 108.45 3.46 8.90e-01 1.26e+00 1.51e+01 angle pdb=" C GLY A1164 " pdb=" N LYS A1165 " pdb=" CA LYS A1165 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.30e+00 angle pdb=" N ASP A1208 " pdb=" CA ASP A1208 " pdb=" C ASP A1208 " ideal model delta sigma weight residual 109.81 116.08 -6.27 2.21e+00 2.05e-01 8.06e+00 angle pdb=" O1 MTX A1401 " pdb=" CT MTX A1401 " pdb=" O2 MTX A1401 " ideal model delta sigma weight residual 127.30 119.10 8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" N GLY A1250 " pdb=" CA GLY A1250 " pdb=" C GLY A1250 " ideal model delta sigma weight residual 113.18 119.55 -6.37 2.37e+00 1.78e-01 7.24e+00 ... (remaining 10598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 4263 16.38 - 32.75: 316 32.75 - 49.13: 56 49.13 - 65.50: 6 65.50 - 81.88: 4 Dihedral angle restraints: 4645 sinusoidal: 1867 harmonic: 2778 Sorted by residual: dihedral pdb=" CA CYS A1226 " pdb=" C CYS A1226 " pdb=" N THR A1227 " pdb=" CA THR A1227 " ideal model delta harmonic sigma weight residual 180.00 150.10 29.90 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA PRO A1209 " pdb=" C PRO A1209 " pdb=" N ARG A1210 " pdb=" CA ARG A1210 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA LYS A1059 " pdb=" C LYS A1059 " pdb=" N HIS A1060 " pdb=" CA HIS A1060 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 4642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 855 0.040 - 0.079: 305 0.079 - 0.119: 66 0.119 - 0.159: 4 0.159 - 0.198: 1 Chirality restraints: 1231 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 -2.43 -0.20 2.00e-01 2.50e+01 9.82e-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 2.49 0.15 2.00e-01 2.50e+01 5.87e-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 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1228 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 MTX A1401 " -0.017 2.00e-02 2.50e+03 8.01e-02 2.08e+02 pdb=" C4 MTX A1401 " -0.102 2.00e-02 2.50e+03 pdb=" C4A MTX A1401 " -0.053 2.00e-02 2.50e+03 pdb=" C6 MTX A1401 " -0.018 2.00e-02 2.50e+03 pdb=" C7 MTX A1401 " 0.051 2.00e-02 2.50e+03 pdb=" C8A MTX A1401 " 0.017 2.00e-02 2.50e+03 pdb=" C9 MTX A1401 " -0.038 2.00e-02 2.50e+03 pdb=" N1 MTX A1401 " 0.034 2.00e-02 2.50e+03 pdb=" N3 MTX A1401 " -0.086 2.00e-02 2.50e+03 pdb=" N5 MTX A1401 " -0.071 2.00e-02 2.50e+03 pdb=" N8 MTX A1401 " 0.068 2.00e-02 2.50e+03 pdb=" NA2 MTX A1401 " 0.000 2.00e-02 2.50e+03 pdb=" NA4 MTX A1401 " 0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 MTX A1401 " 0.035 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C9 MTX A1401 " 0.034 2.00e-02 2.50e+03 pdb=" CM MTX A1401 " 0.034 2.00e-02 2.50e+03 pdb=" N10 MTX A1401 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MTX A1401 " -0.031 2.00e-02 2.50e+03 4.03e-02 3.24e+01 pdb=" C11 MTX A1401 " -0.023 2.00e-02 2.50e+03 pdb=" C12 MTX A1401 " 0.013 2.00e-02 2.50e+03 pdb=" C13 MTX A1401 " 0.024 2.00e-02 2.50e+03 pdb=" C14 MTX A1401 " -0.016 2.00e-02 2.50e+03 pdb=" C15 MTX A1401 " -0.051 2.00e-02 2.50e+03 pdb=" C16 MTX A1401 " 0.088 2.00e-02 2.50e+03 pdb=" N10 MTX A1401 " -0.004 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1643 2.78 - 3.31: 7229 3.31 - 3.84: 11332 3.84 - 4.37: 13119 4.37 - 4.90: 22656 Nonbonded interactions: 55979 Sorted by model distance: nonbonded pdb=" O GLU A1152 " pdb=" NZ LYS A1218 " model vdw 2.249 3.120 nonbonded pdb=" NH2 ARG A 37 " pdb=" OD2 ASP A 43 " model vdw 2.270 3.120 nonbonded pdb=" O TYR A1016 " pdb=" OG1 THR A1017 " model vdw 2.316 3.040 nonbonded pdb=" O ALA A 138 " pdb=" OG1 THR A 142 " model vdw 2.333 3.040 nonbonded pdb=" O THR A 281 " pdb=" OG1 THR A 281 " model vdw 2.403 3.040 ... (remaining 55974 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: 1.310 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.250 Find NCS groups from input model: 0.030 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:9.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.004 0.180 7814 Z= 0.190 Angle : 0.615 8.202 10603 Z= 0.336 Chirality : 0.040 0.198 1231 Planarity : 0.005 0.080 1310 Dihedral : 11.806 81.881 2839 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.11 % 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: -3.35 (0.24), residues: 941 helix: -1.62 (0.18), residues: 619 sheet: -1.69 (0.78), residues: 32 loop : -3.36 (0.30), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1182 TYR 0.011 0.001 TYR A 768 PHE 0.008 0.001 PHE A 336 TRP 0.008 0.001 TRP A 763 HIS 0.002 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7814) covalent geometry : angle 0.61461 (10603) hydrogen bonds : bond 0.15161 ( 380) hydrogen bonds : angle 5.35537 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.204 Fit side-chains REVERT: A 44 MET cc_start: 0.7437 (ptt) cc_final: 0.7175 (ptp) REVERT: A 1123 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6949 (tm-30) REVERT: A 1245 MET cc_start: 0.7418 (mtm) cc_final: 0.7076 (mmp) outliers start: 0 outliers final: 1 residues processed: 126 average time/residue: 0.5399 time to fit residues: 71.2490 Evaluate side-chains 76 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 742 GLN A 798 HIS A 823 ASN A 909 GLN A 934 HIS A 978 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN A1139 ASN A1183 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.187862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130309 restraints weight = 9293.952| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.50 r_work: 0.3379 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7814 Z= 0.128 Angle : 0.579 9.521 10603 Z= 0.298 Chirality : 0.041 0.144 1231 Planarity : 0.004 0.074 1310 Dihedral : 5.752 53.053 1037 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.64 % Allowed : 10.43 % Favored : 86.93 % Cbeta Deviations : 0.11 % 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: -1.92 (0.26), residues: 941 helix: -0.48 (0.20), residues: 627 sheet: -1.21 (0.86), residues: 34 loop : -2.98 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.017 0.001 TYR A 768 PHE 0.013 0.001 PHE A 352 TRP 0.009 0.001 TRP A 733 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7814) covalent geometry : angle 0.57919 (10603) hydrogen bonds : bond 0.05374 ( 380) hydrogen bonds : angle 3.62667 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 262 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6935 (ttm170) REVERT: A 276 MET cc_start: 0.7981 (mmt) cc_final: 0.7677 (mmt) REVERT: A 319 MET cc_start: 0.8116 (mmm) cc_final: 0.7603 (tpp) REVERT: A 1104 LEU cc_start: 0.8042 (mm) cc_final: 0.7658 (mm) REVERT: A 1245 MET cc_start: 0.7820 (mtm) cc_final: 0.7457 (mtp) outliers start: 22 outliers final: 6 residues processed: 98 average time/residue: 0.4419 time to fit residues: 45.8487 Evaluate side-chains 74 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 803 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 823 ASN A 909 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 GLN 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 = 0.177902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127656 restraints weight = 9091.756| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.13 r_work: 0.3324 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7814 Z= 0.135 Angle : 0.572 9.874 10603 Z= 0.294 Chirality : 0.042 0.132 1231 Planarity : 0.004 0.072 1310 Dihedral : 5.599 53.943 1037 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.64 % Allowed : 14.39 % Favored : 82.97 % Cbeta Deviations : 0.11 % 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 (0.27), residues: 941 helix: 0.01 (0.21), residues: 633 sheet: -0.74 (0.84), residues: 36 loop : -2.80 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1090 TYR 0.016 0.001 TYR A 768 PHE 0.025 0.001 PHE A 324 TRP 0.008 0.001 TRP A 733 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7814) covalent geometry : angle 0.57158 (10603) hydrogen bonds : bond 0.05968 ( 380) hydrogen bonds : angle 3.51128 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7385 (mp) REVERT: A 262 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7154 (ttm170) REVERT: A 276 MET cc_start: 0.8530 (mmt) cc_final: 0.8259 (mmt) REVERT: A 319 MET cc_start: 0.8328 (mmm) cc_final: 0.7823 (tpp) REVERT: A 840 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: A 1245 MET cc_start: 0.8028 (mtm) cc_final: 0.7606 (mtp) outliers start: 22 outliers final: 9 residues processed: 92 average time/residue: 0.4918 time to fit residues: 47.9291 Evaluate side-chains 80 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1221 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 50 optimal weight: 0.0870 chunk 3 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 823 ASN A 909 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.179895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130116 restraints weight = 9203.368| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.11 r_work: 0.3354 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7814 Z= 0.115 Angle : 0.538 9.845 10603 Z= 0.278 Chirality : 0.041 0.134 1231 Planarity : 0.004 0.073 1310 Dihedral : 5.498 54.313 1035 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.88 % Allowed : 15.23 % Favored : 81.89 % Cbeta Deviations : 0.11 % 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: -0.93 (0.28), residues: 941 helix: 0.23 (0.21), residues: 652 sheet: -0.44 (0.86), residues: 36 loop : -2.81 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.011 0.001 TYR A 728 PHE 0.012 0.001 PHE A 948 TRP 0.009 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7814) covalent geometry : angle 0.53778 (10603) hydrogen bonds : bond 0.05222 ( 380) hydrogen bonds : angle 3.36228 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7521 (mp) REVERT: A 840 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: A 1166 MET cc_start: 0.4550 (OUTLIER) cc_final: 0.3702 (mmt) REVERT: A 1245 MET cc_start: 0.8043 (mtm) cc_final: 0.7625 (mtp) outliers start: 24 outliers final: 11 residues processed: 86 average time/residue: 0.5215 time to fit residues: 47.4539 Evaluate side-chains 82 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1239 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 823 ASN A 909 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.177501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127553 restraints weight = 9233.720| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.18 r_work: 0.3310 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7814 Z= 0.131 Angle : 0.563 9.921 10603 Z= 0.288 Chirality : 0.041 0.134 1231 Planarity : 0.004 0.071 1310 Dihedral : 5.495 55.603 1035 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.76 % Allowed : 16.79 % Favored : 80.46 % Cbeta Deviations : 0.11 % 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: -0.72 (0.28), residues: 941 helix: 0.38 (0.21), residues: 652 sheet: -0.31 (0.87), residues: 36 loop : -2.70 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1090 TYR 0.014 0.001 TYR A 92 PHE 0.027 0.001 PHE A 324 TRP 0.009 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7814) covalent geometry : angle 0.56259 (10603) hydrogen bonds : bond 0.05842 ( 380) hydrogen bonds : angle 3.38107 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 840 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: A 975 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: A 1166 MET cc_start: 0.4530 (OUTLIER) cc_final: 0.3905 (tpt) outliers start: 23 outliers final: 11 residues processed: 82 average time/residue: 0.4856 time to fit residues: 42.0867 Evaluate side-chains 81 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1239 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN A 823 ASN A 909 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.176828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126992 restraints weight = 9153.505| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.12 r_work: 0.3318 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7814 Z= 0.133 Angle : 0.561 10.142 10603 Z= 0.289 Chirality : 0.041 0.135 1231 Planarity : 0.004 0.072 1310 Dihedral : 5.540 56.759 1035 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.76 % Allowed : 17.51 % Favored : 79.74 % Cbeta Deviations : 0.11 % 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: -0.58 (0.28), residues: 941 helix: 0.49 (0.21), residues: 652 sheet: -0.13 (0.87), residues: 36 loop : -2.67 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1090 TYR 0.014 0.001 TYR A 92 PHE 0.014 0.001 PHE A 352 TRP 0.009 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7814) covalent geometry : angle 0.56067 (10603) hydrogen bonds : bond 0.05837 ( 380) hydrogen bonds : angle 3.38676 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8176 (ppp) REVERT: A 245 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7554 (mp) REVERT: A 840 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7211 (m-80) REVERT: A 975 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: A 1166 MET cc_start: 0.4555 (OUTLIER) cc_final: 0.3930 (tpt) outliers start: 23 outliers final: 13 residues processed: 83 average time/residue: 0.5029 time to fit residues: 44.1672 Evaluate side-chains 81 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1123 GLU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1239 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 41 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.176442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126654 restraints weight = 9177.570| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.10 r_work: 0.3315 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7814 Z= 0.133 Angle : 0.561 10.259 10603 Z= 0.288 Chirality : 0.041 0.135 1231 Planarity : 0.004 0.071 1310 Dihedral : 5.567 57.408 1035 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.76 % Allowed : 17.99 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.28), residues: 941 helix: 0.57 (0.21), residues: 652 sheet: -0.04 (0.88), residues: 36 loop : -2.66 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 37 TYR 0.014 0.001 TYR A 92 PHE 0.025 0.001 PHE A 324 TRP 0.010 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7814) covalent geometry : angle 0.56112 (10603) hydrogen bonds : bond 0.05837 ( 380) hydrogen bonds : angle 3.36960 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8164 (ppp) REVERT: A 245 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7539 (mp) REVERT: A 840 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: A 975 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: A 1166 MET cc_start: 0.4569 (OUTLIER) cc_final: 0.3990 (tpt) outliers start: 23 outliers final: 14 residues processed: 79 average time/residue: 0.4286 time to fit residues: 36.1172 Evaluate side-chains 81 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1239 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 73 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 76 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 70 optimal weight: 0.0670 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 823 ASN A 909 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.181824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.133311 restraints weight = 9132.183| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.11 r_work: 0.3392 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7814 Z= 0.106 Angle : 0.526 9.943 10603 Z= 0.269 Chirality : 0.039 0.136 1231 Planarity : 0.004 0.071 1310 Dihedral : 5.457 57.679 1035 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.88 % Allowed : 17.87 % Favored : 79.26 % 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: -0.17 (0.28), residues: 941 helix: 0.81 (0.21), residues: 652 sheet: 0.08 (0.90), residues: 36 loop : -2.57 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 37 TYR 0.011 0.001 TYR A 728 PHE 0.009 0.001 PHE A 336 TRP 0.011 0.001 TRP A 733 HIS 0.002 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 7814) covalent geometry : angle 0.52581 (10603) hydrogen bonds : bond 0.04435 ( 380) hydrogen bonds : angle 3.15001 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8175 (ppp) REVERT: A 193 GLN cc_start: 0.7034 (pp30) cc_final: 0.6832 (pp30) REVERT: A 245 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7527 (mp) REVERT: A 840 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: A 1091 LEU cc_start: 0.8031 (mp) cc_final: 0.7807 (mm) REVERT: A 1166 MET cc_start: 0.4572 (OUTLIER) cc_final: 0.4072 (tpt) outliers start: 24 outliers final: 10 residues processed: 87 average time/residue: 0.4531 time to fit residues: 41.9343 Evaluate side-chains 84 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1239 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.0030 chunk 84 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.175592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125055 restraints weight = 9207.953| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.08 r_work: 0.3286 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7814 Z= 0.164 Angle : 0.598 10.532 10603 Z= 0.304 Chirality : 0.042 0.135 1231 Planarity : 0.004 0.070 1310 Dihedral : 5.608 59.120 1035 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.28 % Allowed : 18.59 % Favored : 79.14 % 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: -0.36 (0.28), residues: 941 helix: 0.62 (0.21), residues: 658 sheet: 0.06 (0.90), residues: 36 loop : -2.60 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.016 0.001 TYR A 92 PHE 0.026 0.002 PHE A 324 TRP 0.008 0.001 TRP A1035 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7814) covalent geometry : angle 0.59843 (10603) hydrogen bonds : bond 0.06377 ( 380) hydrogen bonds : angle 3.39862 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7018 (pp30) cc_final: 0.6799 (pt0) REVERT: A 245 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7496 (mp) REVERT: A 298 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7672 (tt) REVERT: A 840 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: A 1166 MET cc_start: 0.4706 (OUTLIER) cc_final: 0.4180 (tpt) outliers start: 19 outliers final: 8 residues processed: 84 average time/residue: 0.5631 time to fit residues: 49.8468 Evaluate side-chains 77 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 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 909 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.177087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127409 restraints weight = 9158.558| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.09 r_work: 0.3315 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7814 Z= 0.130 Angle : 0.573 10.617 10603 Z= 0.291 Chirality : 0.041 0.137 1231 Planarity : 0.004 0.071 1310 Dihedral : 5.648 59.438 1035 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.56 % Allowed : 19.78 % Favored : 78.66 % 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: -0.28 (0.28), residues: 941 helix: 0.68 (0.21), residues: 658 sheet: 0.11 (0.91), residues: 36 loop : -2.59 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1090 TYR 0.012 0.001 TYR A 92 PHE 0.013 0.001 PHE A 336 TRP 0.010 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7814) covalent geometry : angle 0.57308 (10603) hydrogen bonds : bond 0.05738 ( 380) hydrogen bonds : angle 3.33032 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8378 (ppp) cc_final: 0.8172 (ppp) REVERT: A 193 GLN cc_start: 0.6988 (pp30) cc_final: 0.6760 (pt0) REVERT: A 245 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7434 (mp) REVERT: A 298 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7628 (tt) REVERT: A 840 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: A 1166 MET cc_start: 0.4657 (OUTLIER) cc_final: 0.4162 (tpt) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.4859 time to fit residues: 42.4424 Evaluate side-chains 83 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 0.0670 chunk 51 optimal weight: 3.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.172278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119860 restraints weight = 9162.007| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.56 r_work: 0.3183 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7814 Z= 0.143 Angle : 0.599 11.064 10603 Z= 0.303 Chirality : 0.041 0.136 1231 Planarity : 0.004 0.070 1310 Dihedral : 5.718 59.712 1035 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.04 % Allowed : 19.42 % Favored : 78.54 % 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: -0.34 (0.28), residues: 941 helix: 0.64 (0.21), residues: 659 sheet: -0.65 (0.86), residues: 43 loop : -2.51 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1090 TYR 0.015 0.001 TYR A 92 PHE 0.024 0.001 PHE A 324 TRP 0.008 0.001 TRP A1035 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7814) covalent geometry : angle 0.59869 (10603) hydrogen bonds : bond 0.06140 ( 380) hydrogen bonds : angle 3.37598 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.72 seconds wall clock time: 41 minutes 48.08 seconds (2508.08 seconds total)