Starting phenix.real_space_refine on Sat Aug 23 04:51:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jvh_36674/08_2025/8jvh_36674_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jvh_36674/08_2025/8jvh_36674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jvh_36674/08_2025/8jvh_36674_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jvh_36674/08_2025/8jvh_36674_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jvh_36674/08_2025/8jvh_36674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jvh_36674/08_2025/8jvh_36674.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.077 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 40 5.16 5 C 6289 2.51 5 N 1599 2.21 5 O 1771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9699 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9699 Classifications: {'peptide': 1205} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 1178} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.15, per 1000 atoms: 0.22 Number of scatterers: 9699 At special positions: 0 Unit cell: (72.6, 119.9, 144.1, 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 40 16.00 O 1771 8.00 N 1599 7.00 C 6289 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: 0.55 Conformation dependent library (CDL) restraints added in 344.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 62.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.645A pdb=" N GLU A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.694A pdb=" N ARG A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.622A pdb=" N LYS A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS A 48 " --> pdb=" O PRO A 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 48' Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.668A pdb=" N ALA A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.823A pdb=" N SER A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 137 removed outlier: 4.102A pdb=" N SER A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A 114 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.915A pdb=" N ASN A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 150 through 159 removed outlier: 4.017A pdb=" N ASP A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 170 removed outlier: 3.894A pdb=" N PHE A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.790A pdb=" N THR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.887A pdb=" N THR A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 240 removed outlier: 3.975A pdb=" N LYS A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.858A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 303 removed outlier: 3.682A pdb=" N THR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 299 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.681A pdb=" N SER A 318 " --> pdb=" O ASN A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 319 through 334 removed outlier: 3.797A pdb=" N LEU A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 351 removed outlier: 3.565A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.552A pdb=" N ILE A 448 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.842A pdb=" N ILE A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 removed outlier: 3.894A pdb=" N LEU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.697A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 539 " --> pdb=" O VAL A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 548 removed outlier: 3.775A pdb=" N LEU A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 removed outlier: 4.558A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.688A pdb=" N GLU A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 694 removed outlier: 3.547A pdb=" N LEU A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 783 removed outlier: 3.837A pdb=" N ILE A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 783 " --> pdb=" O TYR A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 803 removed outlier: 3.761A pdb=" N VAL A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 791 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.837A pdb=" N LEU A 808 " --> pdb=" O PRO A 804 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 815 " --> pdb=" O ALA A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 873 removed outlier: 3.746A pdb=" N ASN A 826 " --> pdb=" O ASN A 822 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE A 834 " --> pdb=" O TYR A 830 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN A 853 " --> pdb=" O ASN A 849 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 881 removed outlier: 4.115A pdb=" N PHE A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 903 removed outlier: 4.001A pdb=" N ILE A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 897 " --> pdb=" O ILE A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 927 removed outlier: 5.210A pdb=" N VAL A 909 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 920 " --> pdb=" O MET A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 945 removed outlier: 3.768A pdb=" N ALA A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 934 " --> pdb=" O PRO A 930 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 963 removed outlier: 4.068A pdb=" N ILE A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 removed outlier: 3.715A pdb=" N PHE A 990 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 986 through 991' Processing helix chain 'A' and resid 992 through 997 removed outlier: 3.783A pdb=" N VAL A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1014 Processing helix chain 'A' and resid 1016 through 1036 removed outlier: 4.364A pdb=" N ARG A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A1029 " --> pdb=" O ILE A1025 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1054 removed outlier: 4.006A pdb=" N LYS A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1081 removed outlier: 3.799A pdb=" N PHE A1068 " --> pdb=" O MET A1064 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 removed outlier: 3.998A pdb=" N ALA A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A1091 " --> pdb=" O SER A1087 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A1094 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1175 Processing helix chain 'A' and resid 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1264 through 1270 removed outlier: 3.532A pdb=" N LYS A1270 " --> pdb=" O TYR A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1288 removed outlier: 3.846A pdb=" N VAL A1281 " --> pdb=" O THR A1277 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1297 removed outlier: 3.928A pdb=" N LEU A1297 " --> pdb=" O ILE A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1303 removed outlier: 4.001A pdb=" N THR A1303 " --> pdb=" O LYS A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1310 Processing helix chain 'A' and resid 1313 through 1327 removed outlier: 3.823A pdb=" N GLN A1318 " --> pdb=" O GLY A1314 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A1319 " --> pdb=" O GLY A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1358 Processing helix chain 'A' and resid 1371 through 1378 removed outlier: 4.403A pdb=" N ARG A1377 " --> pdb=" O ALA A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1417 Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.016A pdb=" N ILE A 618 " --> pdb=" O TYR A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.082A pdb=" N GLY A 458 " --> pdb=" O ILE A 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 635 through 636 removed outlier: 4.613A pdb=" N SER A 636 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 669 " --> pdb=" O SER A 636 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1149 through 1151 removed outlier: 6.319A pdb=" N GLU A1231 " --> pdb=" O LYS A1129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1158 through 1161 removed outlier: 6.618A pdb=" N ALA A1158 " --> pdb=" O VAL A1382 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE A1384 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A1160 " --> pdb=" O PHE A1384 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A1385 " --> pdb=" O PHE A1393 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A1393 " --> pdb=" O ASN A1385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1251 through 1254 421 hydrogen bonds defined for protein. 1227 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: 1.33 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3013 1.34 - 1.46: 1987 1.46 - 1.58: 4809 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 9876 Sorted by residual: bond pdb=" CB ASP A 441 " pdb=" CG ASP A 441 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 2.00e+00 bond pdb=" CG LEU A1080 " pdb=" CD2 LEU A1080 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" CA LEU A 362 " pdb=" C LEU A 362 " ideal model delta sigma weight residual 1.523 1.543 -0.021 1.49e-02 4.50e+03 1.92e+00 bond pdb=" C ILE A 328 " pdb=" N SER A 329 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.31e-02 5.83e+03 1.89e+00 bond pdb=" CB ASN A1106 " pdb=" CG ASN A1106 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.74e+00 ... (remaining 9871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 12969 2.02 - 4.03: 288 4.03 - 6.05: 41 6.05 - 8.07: 4 8.07 - 10.09: 3 Bond angle restraints: 13305 Sorted by residual: angle pdb=" C SER A1105 " pdb=" N ASN A1106 " pdb=" CA ASN A1106 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" C ASN A 440 " pdb=" N ASP A 441 " pdb=" CA ASP A 441 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 angle pdb=" C ALA A 821 " pdb=" N ASN A 822 " pdb=" CA ASN A 822 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 9.99e+00 angle pdb=" CA ASN A1106 " pdb=" CB ASN A1106 " pdb=" CG ASN A1106 " ideal model delta sigma weight residual 112.60 115.68 -3.08 1.00e+00 1.00e+00 9.50e+00 angle pdb=" C PRO A 361 " pdb=" N LEU A 362 " pdb=" CA LEU A 362 " ideal model delta sigma weight residual 123.91 128.78 -4.87 1.66e+00 3.63e-01 8.62e+00 ... (remaining 13300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 5645 15.07 - 30.15: 274 30.15 - 45.22: 51 45.22 - 60.30: 1 60.30 - 75.37: 3 Dihedral angle restraints: 5974 sinusoidal: 2431 harmonic: 3543 Sorted by residual: dihedral pdb=" CA VAL A 905 " pdb=" C VAL A 905 " pdb=" N ASN A 906 " pdb=" CA ASN A 906 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA CYS A1151 " pdb=" C CYS A1151 " pdb=" N ASP A1152 " pdb=" CA ASP A1152 " ideal model delta harmonic sigma weight residual -180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LYS A1016 " pdb=" C LYS A1016 " pdb=" N ASN A1017 " pdb=" CA ASN A1017 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 5971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 987 0.039 - 0.079: 401 0.079 - 0.118: 116 0.118 - 0.157: 22 0.157 - 0.196: 3 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CB ILE A 437 " pdb=" CA ILE A 437 " pdb=" CG1 ILE A 437 " pdb=" CG2 ILE A 437 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA ASN A1106 " pdb=" N ASN A1106 " pdb=" C ASN A1106 " pdb=" CB ASN A1106 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA ASP A 441 " pdb=" N ASP A 441 " pdb=" C ASP A 441 " pdb=" CB ASP A 441 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1526 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 437 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C ILE A 437 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE A 437 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 438 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1257 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A1258 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1258 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1258 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 440 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ASN A 440 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN A 440 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 441 " -0.011 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 610 2.74 - 3.28: 10110 3.28 - 3.82: 13912 3.82 - 4.36: 17111 4.36 - 4.90: 29368 Nonbonded interactions: 71111 Sorted by model distance: nonbonded pdb=" O ILE A 286 " pdb=" OG SER A 289 " model vdw 2.195 3.040 nonbonded pdb=" O ILE A1375 " pdb=" OG SER A1378 " model vdw 2.244 3.040 nonbonded pdb=" OD2 ASP A 144 " pdb=" OH TYR A 430 " model vdw 2.253 3.040 nonbonded pdb=" O PRO A 338 " pdb=" OG1 THR A 341 " model vdw 2.255 3.040 nonbonded pdb=" ND2 ASN A 774 " pdb=" OE1 GLU A1095 " model vdw 2.264 3.120 ... (remaining 71106 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.490 Find NCS groups from input model: 0.050 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 : 0.005 0.052 9876 Z= 0.231 Angle : 0.785 10.087 13305 Z= 0.442 Chirality : 0.046 0.196 1529 Planarity : 0.004 0.050 1654 Dihedral : 9.557 75.370 3686 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % 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 aren not related in a simple way. whole: -4.48 (0.19), residues: 1191 helix: -2.45 (0.16), residues: 713 sheet: -3.43 (0.53), residues: 56 loop : -3.61 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1176 TYR 0.027 0.002 TYR A 940 PHE 0.030 0.002 PHE A 294 TRP 0.015 0.002 TRP A 186 HIS 0.011 0.002 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 9876) covalent geometry : angle 0.78461 (13305) hydrogen bonds : bond 0.18261 ( 421) hydrogen bonds : angle 6.02301 ( 1227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 THR cc_start: 0.8516 (p) cc_final: 0.8294 (m) REVERT: A 153 SER cc_start: 0.8701 (t) cc_final: 0.8091 (p) REVERT: A 160 GLU cc_start: 0.7203 (pp20) cc_final: 0.6774 (pp20) REVERT: A 251 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7973 (mptt) REVERT: A 776 ARG cc_start: 0.6492 (ptp90) cc_final: 0.6186 (mmm-85) REVERT: A 924 MET cc_start: 0.8738 (ptt) cc_final: 0.8474 (ptt) REVERT: A 955 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8216 (ttpt) REVERT: A 1092 LEU cc_start: 0.8725 (tp) cc_final: 0.8468 (tp) outliers start: 2 outliers final: 0 residues processed: 197 average time/residue: 0.1121 time to fit residues: 29.1842 Evaluate side-chains 99 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 894 ASN A 992 ASN A1256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.188618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.135353 restraints weight = 12841.816| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.93 r_work: 0.3608 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9876 Z= 0.134 Angle : 0.602 9.757 13305 Z= 0.315 Chirality : 0.043 0.173 1529 Planarity : 0.004 0.043 1654 Dihedral : 5.098 23.353 1301 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.38 % Allowed : 7.54 % Favored : 91.08 % 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 aren not related in a simple way. whole: -3.01 (0.22), residues: 1191 helix: -1.24 (0.18), residues: 716 sheet: -3.32 (0.52), residues: 71 loop : -2.96 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1283 TYR 0.019 0.001 TYR A1266 PHE 0.013 0.001 PHE A 633 TRP 0.010 0.001 TRP A1047 HIS 0.008 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9876) covalent geometry : angle 0.60204 (13305) hydrogen bonds : bond 0.05506 ( 421) hydrogen bonds : angle 4.38757 ( 1227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 153 SER cc_start: 0.8590 (t) cc_final: 0.7995 (p) REVERT: A 160 GLU cc_start: 0.7429 (pp20) cc_final: 0.6941 (pp20) REVERT: A 231 MET cc_start: 0.7956 (mtp) cc_final: 0.7632 (mtm) REVERT: A 251 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7802 (mptt) REVERT: A 348 GLU cc_start: 0.7183 (pp20) cc_final: 0.6916 (pp20) REVERT: A 382 ASN cc_start: 0.6720 (m110) cc_final: 0.6154 (p0) REVERT: A 776 ARG cc_start: 0.6802 (ptp90) cc_final: 0.6109 (mmm-85) REVERT: A 1134 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.7071 (ttm-80) outliers start: 15 outliers final: 10 residues processed: 131 average time/residue: 0.0844 time to fit residues: 15.4288 Evaluate side-chains 101 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.182076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126241 restraints weight = 12950.345| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.93 r_work: 0.3483 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9876 Z= 0.129 Angle : 0.562 9.363 13305 Z= 0.295 Chirality : 0.043 0.155 1529 Planarity : 0.004 0.041 1654 Dihedral : 4.794 22.611 1301 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.93 % Allowed : 8.56 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.23), residues: 1191 helix: -0.71 (0.19), residues: 719 sheet: -2.84 (0.58), residues: 71 loop : -2.71 (0.26), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1283 TYR 0.019 0.002 TYR A1242 PHE 0.013 0.001 PHE A1261 TRP 0.010 0.002 TRP A1047 HIS 0.006 0.001 HIS A1400 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9876) covalent geometry : angle 0.56248 (13305) hydrogen bonds : bond 0.05428 ( 421) hydrogen bonds : angle 4.05183 ( 1227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7527 (pp20) cc_final: 0.7189 (pp20) REVERT: A 185 ILE cc_start: 0.8151 (tp) cc_final: 0.7851 (mp) REVERT: A 231 MET cc_start: 0.8187 (mtp) cc_final: 0.7907 (mtm) REVERT: A 251 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8009 (mptt) REVERT: A 382 ASN cc_start: 0.6844 (m110) cc_final: 0.6316 (p0) REVERT: A 431 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6936 (t0) REVERT: A 582 LYS cc_start: 0.6565 (mttm) cc_final: 0.6113 (mtmm) REVERT: A 776 ARG cc_start: 0.7038 (ptp90) cc_final: 0.6482 (mmm160) REVERT: A 1249 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8623 (t0) REVERT: A 1256 GLN cc_start: 0.7562 (tp40) cc_final: 0.7047 (tp40) outliers start: 21 outliers final: 13 residues processed: 121 average time/residue: 0.0893 time to fit residues: 15.2396 Evaluate side-chains 103 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.0570 chunk 19 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.182305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125925 restraints weight = 13120.716| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.98 r_work: 0.3478 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9876 Z= 0.109 Angle : 0.515 8.648 13305 Z= 0.271 Chirality : 0.041 0.153 1529 Planarity : 0.003 0.042 1654 Dihedral : 4.489 20.921 1301 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.02 % Allowed : 9.29 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.23), residues: 1191 helix: -0.26 (0.19), residues: 722 sheet: -2.58 (0.58), residues: 73 loop : -2.61 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1134 TYR 0.015 0.001 TYR A 290 PHE 0.010 0.001 PHE A1170 TRP 0.010 0.001 TRP A1047 HIS 0.005 0.001 HIS A1400 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9876) covalent geometry : angle 0.51526 (13305) hydrogen bonds : bond 0.04781 ( 421) hydrogen bonds : angle 3.79340 ( 1227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7607 (pp20) cc_final: 0.7341 (pp20) REVERT: A 185 ILE cc_start: 0.8003 (tp) cc_final: 0.7770 (mp) REVERT: A 231 MET cc_start: 0.8138 (mtp) cc_final: 0.7902 (mtm) REVERT: A 251 LYS cc_start: 0.8501 (ttmm) cc_final: 0.7926 (mptt) REVERT: A 382 ASN cc_start: 0.6880 (m110) cc_final: 0.6368 (p0) REVERT: A 431 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6909 (t0) REVERT: A 776 ARG cc_start: 0.6860 (ptp90) cc_final: 0.6344 (mmm160) REVERT: A 1249 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8509 (t0) REVERT: A 1256 GLN cc_start: 0.7573 (tp40) cc_final: 0.7056 (tp40) outliers start: 22 outliers final: 13 residues processed: 120 average time/residue: 0.0880 time to fit residues: 14.9491 Evaluate side-chains 105 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.178925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121526 restraints weight = 13149.643| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.95 r_work: 0.3425 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9876 Z= 0.122 Angle : 0.518 8.710 13305 Z= 0.275 Chirality : 0.042 0.180 1529 Planarity : 0.003 0.043 1654 Dihedral : 4.428 20.855 1301 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.30 % Allowed : 9.94 % Favored : 87.76 % 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 aren not related in a simple way. whole: -1.56 (0.24), residues: 1191 helix: -0.11 (0.19), residues: 736 sheet: -2.18 (0.61), residues: 74 loop : -2.52 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1134 TYR 0.016 0.001 TYR A1097 PHE 0.014 0.001 PHE A1170 TRP 0.008 0.001 TRP A 186 HIS 0.005 0.001 HIS A1400 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9876) covalent geometry : angle 0.51847 (13305) hydrogen bonds : bond 0.05161 ( 421) hydrogen bonds : angle 3.77570 ( 1227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7743 (pp20) cc_final: 0.7508 (pp20) REVERT: A 185 ILE cc_start: 0.8000 (tp) cc_final: 0.7763 (mp) REVERT: A 231 MET cc_start: 0.8296 (mtp) cc_final: 0.7983 (mtm) REVERT: A 239 MET cc_start: 0.8143 (tpp) cc_final: 0.7615 (mpp) REVERT: A 251 LYS cc_start: 0.8465 (ttmm) cc_final: 0.7936 (mptt) REVERT: A 382 ASN cc_start: 0.6816 (m110) cc_final: 0.6309 (p0) REVERT: A 488 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6376 (pmm) REVERT: A 776 ARG cc_start: 0.7024 (ptp90) cc_final: 0.6510 (mmm160) REVERT: A 1249 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8543 (t0) REVERT: A 1256 GLN cc_start: 0.7599 (tp40) cc_final: 0.7072 (tp40) outliers start: 25 outliers final: 15 residues processed: 111 average time/residue: 0.0994 time to fit residues: 15.3222 Evaluate side-chains 107 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.0470 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.180458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123090 restraints weight = 13238.589| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.98 r_work: 0.3447 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9876 Z= 0.102 Angle : 0.489 8.380 13305 Z= 0.258 Chirality : 0.041 0.150 1529 Planarity : 0.003 0.042 1654 Dihedral : 4.275 20.071 1301 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.75 % Allowed : 10.67 % Favored : 87.58 % 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 aren not related in a simple way. whole: -1.30 (0.24), residues: 1191 helix: 0.14 (0.19), residues: 731 sheet: -2.14 (0.59), residues: 79 loop : -2.46 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1134 TYR 0.014 0.001 TYR A 290 PHE 0.010 0.001 PHE A1393 TRP 0.008 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9876) covalent geometry : angle 0.48867 (13305) hydrogen bonds : bond 0.04647 ( 421) hydrogen bonds : angle 3.64561 ( 1227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.8127 (tpp) cc_final: 0.7543 (tpp) REVERT: A 251 LYS cc_start: 0.8348 (ttmm) cc_final: 0.7806 (mptt) REVERT: A 382 ASN cc_start: 0.6891 (m110) cc_final: 0.6389 (p0) REVERT: A 776 ARG cc_start: 0.6992 (ptp90) cc_final: 0.6467 (mmm160) REVERT: A 987 GLN cc_start: 0.8697 (tt0) cc_final: 0.8451 (tp40) REVERT: A 1249 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8469 (t0) REVERT: A 1256 GLN cc_start: 0.7554 (tp40) cc_final: 0.7049 (tp40) outliers start: 19 outliers final: 14 residues processed: 117 average time/residue: 0.0898 time to fit residues: 14.4956 Evaluate side-chains 105 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 0.0270 chunk 85 optimal weight: 0.0000 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.180099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123114 restraints weight = 13034.162| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.94 r_work: 0.3453 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9876 Z= 0.097 Angle : 0.486 8.535 13305 Z= 0.256 Chirality : 0.040 0.155 1529 Planarity : 0.003 0.042 1654 Dihedral : 4.118 19.197 1301 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.66 % Allowed : 11.13 % Favored : 87.21 % 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 aren not related in a simple way. whole: -0.97 (0.24), residues: 1191 helix: 0.41 (0.20), residues: 732 sheet: -2.03 (0.59), residues: 79 loop : -2.38 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1134 TYR 0.014 0.001 TYR A 290 PHE 0.009 0.001 PHE A1393 TRP 0.007 0.001 TRP A1047 HIS 0.003 0.001 HIS A1400 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 9876) covalent geometry : angle 0.48551 (13305) hydrogen bonds : bond 0.04309 ( 421) hydrogen bonds : angle 3.54996 ( 1227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 251 LYS cc_start: 0.8343 (ttmm) cc_final: 0.7821 (mptt) REVERT: A 382 ASN cc_start: 0.6881 (m110) cc_final: 0.6386 (p0) REVERT: A 776 ARG cc_start: 0.6951 (ptp90) cc_final: 0.6412 (mmm160) REVERT: A 1249 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8473 (t0) REVERT: A 1256 GLN cc_start: 0.7604 (tp40) cc_final: 0.7111 (tp40) outliers start: 18 outliers final: 11 residues processed: 110 average time/residue: 0.0798 time to fit residues: 12.5066 Evaluate side-chains 104 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 74 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 0.0970 chunk 105 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.179202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.121992 restraints weight = 13108.870| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.95 r_work: 0.3437 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9876 Z= 0.101 Angle : 0.484 8.351 13305 Z= 0.255 Chirality : 0.041 0.220 1529 Planarity : 0.003 0.043 1654 Dihedral : 4.067 18.757 1301 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.56 % Allowed : 11.59 % Favored : 86.84 % 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 aren not related in a simple way. whole: -0.83 (0.24), residues: 1191 helix: 0.52 (0.19), residues: 735 sheet: -2.03 (0.58), residues: 79 loop : -2.30 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1283 TYR 0.014 0.001 TYR A 290 PHE 0.009 0.001 PHE A1393 TRP 0.007 0.001 TRP A1047 HIS 0.003 0.001 HIS A1400 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9876) covalent geometry : angle 0.48393 (13305) hydrogen bonds : bond 0.04467 ( 421) hydrogen bonds : angle 3.52519 ( 1227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8448 (mtm) cc_final: 0.8149 (mtm) REVERT: A 239 MET cc_start: 0.8100 (tpp) cc_final: 0.7570 (mpp) REVERT: A 251 LYS cc_start: 0.8348 (ttmm) cc_final: 0.7799 (mptt) REVERT: A 382 ASN cc_start: 0.6899 (m110) cc_final: 0.6410 (p0) REVERT: A 437 ILE cc_start: 0.7503 (mm) cc_final: 0.7255 (mm) REVERT: A 776 ARG cc_start: 0.7004 (ptp90) cc_final: 0.6448 (mmm160) REVERT: A 1249 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8470 (t0) REVERT: A 1256 GLN cc_start: 0.7610 (tp40) cc_final: 0.7115 (tp40) REVERT: A 1274 GLU cc_start: 0.8866 (pt0) cc_final: 0.8280 (mt-10) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.0785 time to fit residues: 12.2146 Evaluate side-chains 109 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 114 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 60 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.179548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122336 restraints weight = 12982.178| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.93 r_work: 0.3457 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9876 Z= 0.099 Angle : 0.483 8.442 13305 Z= 0.253 Chirality : 0.041 0.208 1529 Planarity : 0.003 0.043 1654 Dihedral : 4.021 18.590 1301 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.56 % Allowed : 11.96 % Favored : 86.48 % 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 aren not related in a simple way. whole: -0.70 (0.24), residues: 1191 helix: 0.61 (0.19), residues: 735 sheet: -1.99 (0.58), residues: 79 loop : -2.22 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1283 TYR 0.015 0.001 TYR A 290 PHE 0.010 0.001 PHE A1393 TRP 0.007 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 9876) covalent geometry : angle 0.48269 (13305) hydrogen bonds : bond 0.04420 ( 421) hydrogen bonds : angle 3.50413 ( 1227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8449 (mtm) cc_final: 0.8107 (mtm) REVERT: A 239 MET cc_start: 0.8073 (tpp) cc_final: 0.7564 (tpp) REVERT: A 251 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7746 (mptt) REVERT: A 332 MET cc_start: 0.7809 (mmt) cc_final: 0.7025 (mmt) REVERT: A 382 ASN cc_start: 0.6896 (m110) cc_final: 0.6411 (p0) REVERT: A 409 TYR cc_start: 0.5268 (m-10) cc_final: 0.4743 (m-10) REVERT: A 437 ILE cc_start: 0.7501 (mm) cc_final: 0.7257 (mm) REVERT: A 776 ARG cc_start: 0.6992 (ptp90) cc_final: 0.6431 (mmm160) REVERT: A 1249 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8444 (t0) REVERT: A 1256 GLN cc_start: 0.7612 (tp40) cc_final: 0.7124 (tp40) REVERT: A 1274 GLU cc_start: 0.8858 (pt0) cc_final: 0.8269 (mt-10) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.0960 time to fit residues: 15.4095 Evaluate side-chains 113 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.0670 chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.179453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122133 restraints weight = 13022.201| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.95 r_work: 0.3439 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9876 Z= 0.100 Angle : 0.485 8.411 13305 Z= 0.254 Chirality : 0.041 0.204 1529 Planarity : 0.003 0.043 1654 Dihedral : 4.006 18.430 1301 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.75 % Allowed : 11.59 % Favored : 86.66 % 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 aren not related in a simple way. whole: -0.65 (0.24), residues: 1191 helix: 0.65 (0.19), residues: 735 sheet: -2.14 (0.57), residues: 78 loop : -2.17 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1283 TYR 0.015 0.001 TYR A 290 PHE 0.009 0.001 PHE A1393 TRP 0.007 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9876) covalent geometry : angle 0.48516 (13305) hydrogen bonds : bond 0.04426 ( 421) hydrogen bonds : angle 3.49628 ( 1227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.8455 (mtm) cc_final: 0.8118 (mtm) REVERT: A 239 MET cc_start: 0.8089 (tpp) cc_final: 0.7574 (tpp) REVERT: A 251 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7823 (mptt) REVERT: A 382 ASN cc_start: 0.6899 (m110) cc_final: 0.6411 (p0) REVERT: A 409 TYR cc_start: 0.5330 (m-10) cc_final: 0.4823 (m-10) REVERT: A 437 ILE cc_start: 0.7602 (mm) cc_final: 0.7364 (mm) REVERT: A 776 ARG cc_start: 0.7005 (ptp90) cc_final: 0.6444 (mmm160) REVERT: A 987 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8101 (tp40) REVERT: A 1249 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8472 (t0) REVERT: A 1256 GLN cc_start: 0.7615 (tp40) cc_final: 0.7118 (tp40) REVERT: A 1274 GLU cc_start: 0.8854 (pt0) cc_final: 0.8282 (mt-10) outliers start: 19 outliers final: 13 residues processed: 114 average time/residue: 0.0897 time to fit residues: 14.5090 Evaluate side-chains 109 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.176813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.118275 restraints weight = 13128.576| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.93 r_work: 0.3419 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9876 Z= 0.111 Angle : 0.496 8.345 13305 Z= 0.261 Chirality : 0.042 0.199 1529 Planarity : 0.003 0.043 1654 Dihedral : 4.043 18.649 1301 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.56 % Allowed : 11.78 % Favored : 86.66 % 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 aren not related in a simple way. whole: -0.69 (0.24), residues: 1191 helix: 0.60 (0.19), residues: 740 sheet: -2.14 (0.57), residues: 78 loop : -2.18 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1283 TYR 0.015 0.001 TYR A 290 PHE 0.010 0.001 PHE A1393 TRP 0.006 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9876) covalent geometry : angle 0.49573 (13305) hydrogen bonds : bond 0.04690 ( 421) hydrogen bonds : angle 3.53592 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2292.72 seconds wall clock time: 39 minutes 53.26 seconds (2393.26 seconds total)