Starting phenix.real_space_refine on Wed Apr 30 19:07:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jvh_36674/04_2025/8jvh_36674_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jvh_36674/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jvh_36674/04_2025/8jvh_36674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jvh_36674/04_2025/8jvh_36674.map" model { file = "/net/cci-nas-00/data/ceres_data/8jvh_36674/04_2025/8jvh_36674_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jvh_36674/04_2025/8jvh_36674_neut.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.98, per 1000 atoms: 0.62 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.17 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: 3.16 Time building geometry restraints manager: 3.14 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: 3.030 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.910 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.002 TRP A 186 HIS 0.011 0.002 HIS A 892 PHE 0.030 0.002 PHE A 294 TYR 0.027 0.002 TYR A 940 ARG 0.007 0.001 ARG A1176 Details of bonding type rmsd hydrogen bonds : bond 0.18261 ( 421) hydrogen bonds : angle 6.02301 ( 1227) covalent geometry : bond 0.00524 ( 9876) covalent geometry : angle 0.78461 (13305) *********************** 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 : 2.430 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: 0.3863 time to fit residues: 101.4589 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 : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4297 r_free = 0.4297 target = 0.185696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.131481 restraints weight = 12888.498| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.93 r_work: 0.3555 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9876 Z= 0.142 Angle : 0.618 9.804 13305 Z= 0.324 Chirality : 0.043 0.167 1529 Planarity : 0.004 0.042 1654 Dihedral : 5.207 23.775 1301 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.56 % Allowed : 7.73 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.22), residues: 1191 helix: -1.32 (0.18), residues: 716 sheet: -2.93 (0.57), residues: 61 loop : -3.02 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.009 0.002 HIS A 676 PHE 0.015 0.001 PHE A 294 TYR 0.020 0.002 TYR A1266 ARG 0.005 0.001 ARG A1283 Details of bonding type rmsd hydrogen bonds : bond 0.05926 ( 421) hydrogen bonds : angle 4.48102 ( 1227) covalent geometry : bond 0.00309 ( 9876) covalent geometry : angle 0.61846 (13305) *********************** 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 136 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 153 SER cc_start: 0.8540 (t) cc_final: 0.7936 (p) REVERT: A 160 GLU cc_start: 0.7510 (pp20) cc_final: 0.7027 (pp20) REVERT: A 231 MET cc_start: 0.7973 (mtp) cc_final: 0.7658 (mtm) REVERT: A 251 LYS cc_start: 0.8420 (ttmm) cc_final: 0.7887 (mptt) REVERT: A 348 GLU cc_start: 0.7259 (pp20) cc_final: 0.6979 (pp20) REVERT: A 382 ASN cc_start: 0.6728 (m110) cc_final: 0.6171 (p0) REVERT: A 431 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6841 (t0) REVERT: A 776 ARG cc_start: 0.7003 (ptp90) cc_final: 0.6278 (mmm-85) REVERT: A 845 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8100 (mm-30) REVERT: A 897 VAL cc_start: 0.6861 (t) cc_final: 0.6633 (m) REVERT: A 1134 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.7120 (ttm-80) REVERT: A 1256 GLN cc_start: 0.7409 (tp-100) cc_final: 0.6561 (mm110) outliers start: 17 outliers final: 11 residues processed: 131 average time/residue: 0.2500 time to fit residues: 45.4010 Evaluate side-chains 109 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 431 ASP 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 1284 VAL 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 40 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 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 365 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 = 0.4262 r_free = 0.4262 target = 0.182531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.126886 restraints weight = 13187.530| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.98 r_work: 0.3491 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9876 Z= 0.124 Angle : 0.550 9.306 13305 Z= 0.289 Chirality : 0.042 0.157 1529 Planarity : 0.004 0.042 1654 Dihedral : 4.758 22.735 1301 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.75 % Allowed : 8.92 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.23), residues: 1191 helix: -0.72 (0.19), residues: 719 sheet: -2.80 (0.58), residues: 71 loop : -2.74 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.006 0.001 HIS A1400 PHE 0.012 0.001 PHE A 78 TYR 0.016 0.001 TYR A 290 ARG 0.004 0.000 ARG A1283 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 421) hydrogen bonds : angle 4.05520 ( 1227) covalent geometry : bond 0.00260 ( 9876) covalent geometry : angle 0.55028 (13305) *********************** 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 127 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7548 (pp20) cc_final: 0.7203 (pp20) REVERT: A 185 ILE cc_start: 0.8096 (tp) cc_final: 0.7816 (mp) REVERT: A 251 LYS cc_start: 0.8539 (ttmm) cc_final: 0.7993 (mptt) REVERT: A 382 ASN cc_start: 0.6830 (m110) cc_final: 0.6309 (p0) REVERT: A 582 LYS cc_start: 0.6345 (mttm) cc_final: 0.5950 (mtmm) REVERT: A 776 ARG cc_start: 0.7028 (ptp90) cc_final: 0.6471 (mmm160) REVERT: A 897 VAL cc_start: 0.6915 (t) cc_final: 0.6638 (m) REVERT: A 1249 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8636 (t0) REVERT: A 1256 GLN cc_start: 0.7472 (tp-100) cc_final: 0.6573 (mm110) outliers start: 19 outliers final: 10 residues processed: 120 average time/residue: 0.2678 time to fit residues: 44.9755 Evaluate side-chains 105 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1249 ASN 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 88 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 12 optimal weight: 0.0020 chunk 31 optimal weight: 0.0980 chunk 1 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.184228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128683 restraints weight = 13012.049| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.98 r_work: 0.3513 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9876 Z= 0.101 Angle : 0.506 8.768 13305 Z= 0.264 Chirality : 0.041 0.194 1529 Planarity : 0.003 0.041 1654 Dihedral : 4.401 20.510 1301 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.56 % Allowed : 10.03 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.24), residues: 1191 helix: -0.20 (0.19), residues: 723 sheet: -2.56 (0.59), residues: 73 loop : -2.58 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.005 0.001 HIS A1400 PHE 0.010 0.001 PHE A 633 TYR 0.015 0.001 TYR A 290 ARG 0.005 0.000 ARG A1134 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 421) hydrogen bonds : angle 3.77121 ( 1227) covalent geometry : bond 0.00199 ( 9876) covalent geometry : angle 0.50569 (13305) *********************** 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: 17 poor density : 108 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7555 (pp20) cc_final: 0.7287 (pp20) REVERT: A 185 ILE cc_start: 0.7940 (tp) cc_final: 0.7738 (mt) REVERT: A 251 LYS cc_start: 0.8521 (ttmm) cc_final: 0.7979 (mptt) REVERT: A 382 ASN cc_start: 0.6859 (m110) cc_final: 0.6355 (p0) REVERT: A 409 TYR cc_start: 0.5380 (m-10) cc_final: 0.4926 (m-10) REVERT: A 431 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6991 (t0) REVERT: A 776 ARG cc_start: 0.6826 (ptp90) cc_final: 0.6155 (mmm-85) REVERT: A 897 VAL cc_start: 0.6832 (t) cc_final: 0.6587 (m) REVERT: A 1249 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8497 (t0) REVERT: A 1256 GLN cc_start: 0.7484 (tp-100) cc_final: 0.6611 (mm110) outliers start: 17 outliers final: 12 residues processed: 120 average time/residue: 0.2372 time to fit residues: 39.9460 Evaluate side-chains 108 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.182166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125901 restraints weight = 12978.812| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.93 r_work: 0.3478 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9876 Z= 0.107 Angle : 0.499 8.734 13305 Z= 0.265 Chirality : 0.042 0.204 1529 Planarity : 0.003 0.042 1654 Dihedral : 4.317 20.049 1301 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.02 % Allowed : 10.12 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1191 helix: 0.10 (0.20), residues: 723 sheet: -2.42 (0.58), residues: 73 loop : -2.47 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 PHE 0.010 0.001 PHE A 257 TYR 0.022 0.001 TYR A1266 ARG 0.005 0.000 ARG A1134 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 421) hydrogen bonds : angle 3.69813 ( 1227) covalent geometry : bond 0.00225 ( 9876) covalent geometry : angle 0.49931 (13305) *********************** 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 121 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7671 (pp20) cc_final: 0.7433 (pp20) REVERT: A 185 ILE cc_start: 0.8016 (tp) cc_final: 0.7801 (mp) REVERT: A 239 MET cc_start: 0.8142 (tpp) cc_final: 0.7598 (mpp) REVERT: A 251 LYS cc_start: 0.8492 (ttmm) cc_final: 0.7918 (mptt) REVERT: A 382 ASN cc_start: 0.6857 (m110) cc_final: 0.6357 (p0) REVERT: A 437 ILE cc_start: 0.7292 (mm) cc_final: 0.6899 (mm) REVERT: A 776 ARG cc_start: 0.6863 (ptp90) cc_final: 0.6322 (mmm160) REVERT: A 897 VAL cc_start: 0.6955 (t) cc_final: 0.6668 (m) REVERT: A 1249 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8512 (t0) REVERT: A 1256 GLN cc_start: 0.7529 (tp-100) cc_final: 0.6911 (tp40) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 0.2724 time to fit residues: 43.9895 Evaluate side-chains 108 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL 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 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 988 GLU 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 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 77 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.181844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125009 restraints weight = 13050.269| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.94 r_work: 0.3470 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9876 Z= 0.105 Angle : 0.500 8.475 13305 Z= 0.262 Chirality : 0.041 0.174 1529 Planarity : 0.003 0.042 1654 Dihedral : 4.233 19.742 1301 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1191 helix: 0.25 (0.20), residues: 724 sheet: -2.34 (0.58), residues: 73 loop : -2.40 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 PHE 0.009 0.001 PHE A1170 TYR 0.019 0.001 TYR A1266 ARG 0.005 0.000 ARG A1134 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 421) hydrogen bonds : angle 3.64753 ( 1227) covalent geometry : bond 0.00223 ( 9876) covalent geometry : angle 0.50000 (13305) *********************** 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 119 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ILE cc_start: 0.8008 (tp) cc_final: 0.7801 (mp) REVERT: A 251 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7892 (mptt) REVERT: A 382 ASN cc_start: 0.6870 (m110) cc_final: 0.6380 (p0) REVERT: A 431 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.7102 (t0) REVERT: A 776 ARG cc_start: 0.6962 (ptp90) cc_final: 0.6420 (mmm160) REVERT: A 897 VAL cc_start: 0.6979 (t) cc_final: 0.6680 (m) REVERT: A 1249 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8494 (t0) REVERT: A 1256 GLN cc_start: 0.7560 (tp-100) cc_final: 0.6947 (tp40) outliers start: 19 outliers final: 13 residues processed: 114 average time/residue: 0.2659 time to fit residues: 42.8493 Evaluate side-chains 108 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 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 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 53 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 44 optimal weight: 0.0670 chunk 36 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 116 optimal weight: 8.9990 chunk 85 optimal weight: 0.0670 chunk 109 optimal weight: 7.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4267 r_free = 0.4267 target = 0.183330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.128910 restraints weight = 13077.514| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.03 r_work: 0.3491 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9876 Z= 0.096 Angle : 0.476 8.523 13305 Z= 0.249 Chirality : 0.041 0.227 1529 Planarity : 0.003 0.041 1654 Dihedral : 4.045 18.420 1301 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.38 % Allowed : 11.59 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.24), residues: 1191 helix: 0.50 (0.20), residues: 726 sheet: -2.13 (0.57), residues: 79 loop : -2.34 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1047 HIS 0.003 0.001 HIS A1400 PHE 0.008 0.001 PHE A 78 TYR 0.019 0.001 TYR A1266 ARG 0.006 0.000 ARG A1134 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 421) hydrogen bonds : angle 3.51645 ( 1227) covalent geometry : bond 0.00189 ( 9876) covalent geometry : angle 0.47579 (13305) *********************** 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: 15 poor density : 100 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 ASN cc_start: 0.6876 (m110) cc_final: 0.6401 (p0) REVERT: A 431 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7075 (t0) REVERT: A 437 ILE cc_start: 0.7310 (mm) cc_final: 0.7025 (mm) REVERT: A 776 ARG cc_start: 0.6927 (ptp90) cc_final: 0.6389 (mmm160) REVERT: A 897 VAL cc_start: 0.6892 (t) cc_final: 0.6621 (m) REVERT: A 1088 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: A 1249 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8451 (t0) REVERT: A 1256 GLN cc_start: 0.7570 (tp-100) cc_final: 0.6996 (tp40) REVERT: A 1274 GLU cc_start: 0.8881 (pt0) cc_final: 0.8263 (mt-10) outliers start: 15 outliers final: 9 residues processed: 109 average time/residue: 0.2517 time to fit residues: 40.1310 Evaluate side-chains 105 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 188 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 1088 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 0.0040 chunk 78 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.178629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120653 restraints weight = 13157.489| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.94 r_work: 0.3461 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4239 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= 0.101 Angle : 0.485 8.470 13305 Z= 0.254 Chirality : 0.041 0.200 1529 Planarity : 0.003 0.042 1654 Dihedral : 4.012 18.362 1301 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1191 helix: 0.62 (0.20), residues: 726 sheet: -2.21 (0.57), residues: 78 loop : -2.28 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 186 HIS 0.003 0.001 HIS A1400 PHE 0.009 0.001 PHE A 257 TYR 0.017 0.001 TYR A1266 ARG 0.003 0.000 ARG A1283 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 421) hydrogen bonds : angle 3.53476 ( 1227) covalent geometry : bond 0.00212 ( 9876) covalent geometry : angle 0.48520 (13305) *********************** 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 116 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8128 (mtm) REVERT: A 382 ASN cc_start: 0.6884 (m110) cc_final: 0.6402 (p0) REVERT: A 409 TYR cc_start: 0.5266 (m-10) cc_final: 0.4783 (m-10) REVERT: A 431 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7196 (t0) REVERT: A 437 ILE cc_start: 0.7406 (mm) cc_final: 0.7195 (mm) REVERT: A 776 ARG cc_start: 0.6984 (ptp90) cc_final: 0.6428 (mmm160) REVERT: A 897 VAL cc_start: 0.7037 (t) cc_final: 0.6743 (m) REVERT: A 1249 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8436 (t0) REVERT: A 1256 GLN cc_start: 0.7612 (tp-100) cc_final: 0.7066 (tp40) REVERT: A 1274 GLU cc_start: 0.8884 (pt0) cc_final: 0.8290 (mt-10) outliers start: 17 outliers final: 11 residues processed: 111 average time/residue: 0.2139 time to fit residues: 34.4952 Evaluate side-chains 107 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 431 ASP 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 1025 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 118 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 0.0570 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.178659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120726 restraints weight = 13022.774| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.91 r_work: 0.3453 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4375 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 : 0.479 8.346 13305 Z= 0.251 Chirality : 0.041 0.197 1529 Planarity : 0.003 0.042 1654 Dihedral : 3.966 18.026 1301 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.47 % Allowed : 11.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1191 helix: 0.76 (0.20), residues: 720 sheet: -2.14 (0.58), residues: 78 loop : -2.24 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 186 HIS 0.003 0.001 HIS A1400 PHE 0.008 0.001 PHE A 78 TYR 0.017 0.001 TYR A1266 ARG 0.003 0.000 ARG A1283 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 421) hydrogen bonds : angle 3.51235 ( 1227) covalent geometry : bond 0.00206 ( 9876) covalent geometry : angle 0.47944 (13305) *********************** 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 116 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8112 (mtm) REVERT: A 239 MET cc_start: 0.8062 (tpp) cc_final: 0.7558 (tpp) REVERT: A 251 LYS cc_start: 0.8319 (ttmm) cc_final: 0.7799 (mptt) REVERT: A 382 ASN cc_start: 0.6886 (m110) cc_final: 0.6391 (p0) REVERT: A 409 TYR cc_start: 0.5636 (m-10) cc_final: 0.5214 (m-10) REVERT: A 431 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7021 (t0) REVERT: A 437 ILE cc_start: 0.7394 (mm) cc_final: 0.7117 (mm) REVERT: A 776 ARG cc_start: 0.6944 (ptp90) cc_final: 0.6416 (mmm160) REVERT: A 897 VAL cc_start: 0.7072 (t) cc_final: 0.6775 (m) REVERT: A 1249 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8416 (t0) REVERT: A 1256 GLN cc_start: 0.7622 (tp-100) cc_final: 0.6904 (mm110) REVERT: A 1274 GLU cc_start: 0.8812 (pt0) cc_final: 0.8250 (mt-10) REVERT: A 1348 LYS cc_start: 0.8506 (tptt) cc_final: 0.8262 (ttpt) outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 0.2239 time to fit residues: 35.7531 Evaluate side-chains 114 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 431 ASP 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 1025 ILE 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 62 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 105 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 774 ASN 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 = 0.175430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117404 restraints weight = 13131.532| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.97 r_work: 0.3391 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9876 Z= 0.144 Angle : 0.547 8.290 13305 Z= 0.288 Chirality : 0.043 0.208 1529 Planarity : 0.003 0.041 1654 Dihedral : 4.245 19.346 1301 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.56 % Allowed : 11.41 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.24), residues: 1191 helix: 0.49 (0.19), residues: 737 sheet: -2.18 (0.57), residues: 78 loop : -2.27 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 186 HIS 0.004 0.001 HIS A1400 PHE 0.016 0.001 PHE A 842 TYR 0.018 0.002 TYR A1266 ARG 0.003 0.000 ARG A1134 Details of bonding type rmsd hydrogen bonds : bond 0.05556 ( 421) hydrogen bonds : angle 3.77188 ( 1227) covalent geometry : bond 0.00338 ( 9876) covalent geometry : angle 0.54687 (13305) ********************** 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 115 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8094 (mtm) REVERT: A 251 LYS cc_start: 0.8403 (ttmm) cc_final: 0.7808 (mptt) REVERT: A 332 MET cc_start: 0.7759 (mmt) cc_final: 0.7036 (mmt) REVERT: A 382 ASN cc_start: 0.6875 (m110) cc_final: 0.6354 (p0) REVERT: A 437 ILE cc_start: 0.7545 (mm) cc_final: 0.7240 (mm) REVERT: A 776 ARG cc_start: 0.7237 (ptp90) cc_final: 0.6590 (mmm160) REVERT: A 1249 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8445 (t0) REVERT: A 1256 GLN cc_start: 0.7584 (tp-100) cc_final: 0.6876 (mm110) REVERT: A 1274 GLU cc_start: 0.8834 (pt0) cc_final: 0.8273 (mt-10) REVERT: A 1287 PHE cc_start: 0.7078 (m-80) cc_final: 0.6749 (m-10) REVERT: A 1292 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7735 (pp20) outliers start: 17 outliers final: 11 residues processed: 110 average time/residue: 0.2444 time to fit residues: 38.0549 Evaluate side-chains 106 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain A residue 231 MET 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 1025 ILE 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 100 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.178766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122729 restraints weight = 13097.517| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.13 r_work: 0.3408 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9876 Z= 0.109 Angle : 0.502 8.222 13305 Z= 0.264 Chirality : 0.042 0.199 1529 Planarity : 0.003 0.041 1654 Dihedral : 4.158 19.322 1301 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.38 % Allowed : 11.87 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1191 helix: 0.60 (0.20), residues: 738 sheet: -2.11 (0.58), residues: 78 loop : -2.22 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 PHE 0.009 0.001 PHE A 257 TYR 0.017 0.001 TYR A1266 ARG 0.003 0.000 ARG A1134 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 421) hydrogen bonds : angle 3.63946 ( 1227) covalent geometry : bond 0.00234 ( 9876) covalent geometry : angle 0.50160 (13305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5787.27 seconds wall clock time: 102 minutes 45.45 seconds (6165.45 seconds total)