Starting phenix.real_space_refine on Sun Oct 25 00:05:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r77_24294/10_2026/7r77_24294.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r77_24294/10_2026/7r77_24294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r77_24294/10_2026/7r77_24294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r77_24294/10_2026/7r77_24294.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7r77_24294/10_2026/7r77_24294.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r77_24294/10_2026/7r77_24294.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r77_24294/10_2026/7r77_24294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r77_24294/10_2026/7r77_24294.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 24 5.49 5 S 70 5.16 5 C 9338 2.51 5 N 2709 2.21 5 O 2834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14980 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 14464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1830, 14464 Classifications: {'peptide': 1830} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 88, 'TRANS': 1741} Chain breaks: 11 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' ZN': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3883 SG CYS A 817 65.967 70.429 59.010 1.00 26.78 S ATOM 3898 SG CYS A 819 63.523 67.857 59.085 1.00 30.19 S ATOM 4052 SG CYS A 840 64.629 70.291 62.140 1.00 27.50 S ATOM 4073 SG CYS A 843 67.026 67.639 61.788 1.00 30.66 S ATOM 6739 SG CYS A1200 35.062 39.965 34.272 1.00 59.77 S ATOM 7299 SG CYS A1271 35.622 36.983 35.898 1.00 70.35 S ATOM 7325 SG CYS A1274 37.968 39.423 35.974 1.00 53.10 S ATOM 3988 SG CYS A 832 74.246 81.825 60.784 1.00 28.82 S ATOM 4012 SG CYS A 835 76.389 80.860 57.365 1.00 29.36 S ATOM 5839 SG CYS A1065 78.003 80.945 60.453 1.00 30.34 S ATOM 12714 SG CYS A2081 88.599 80.915 82.593 1.00 75.53 S ATOM 12901 SG CYS A2107 85.651 82.602 81.187 1.00 56.57 S ATOM 12844 SG CYS A2099 85.323 67.384 84.585 1.00 44.10 S ATOM 13017 SG CYS A2123 89.315 67.024 82.960 1.00 54.15 S Time building chain proxies: 3.11, per 1000 atoms: 0.21 Number of scatterers: 14980 At special positions: 0 Unit cell: (120.232, 110.656, 124.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 70 16.00 P 24 15.00 O 2834 8.00 N 2709 7.00 C 9338 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: 1.31 Conformation dependent library (CDL) restraints added in 663.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2401 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 817 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 819 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 840 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 843 " pdb=" ZN A2402 " pdb="ZN ZN A2402 " - pdb=" ND1 HIS A1348 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1271 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1200 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1274 " pdb=" ZN A2403 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 832 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 835 " pdb="ZN ZN A2403 " - pdb=" ND1 HIS A 849 " pdb="ZN ZN A2403 " - pdb=" SG CYS A1065 " pdb=" ZN A2404 " pdb="ZN ZN A2404 " - pdb=" SG CYS A2081 " pdb="ZN ZN A2404 " - pdb=" ND1 HIS A2083 " pdb="ZN ZN A2404 " - pdb=" SG CYS A2107 " pdb=" ZN A2405 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2123 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2099 " Number of angles added : 12 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 41.7% alpha, 16.2% beta 9 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 320 through 332 removed outlier: 3.526A pdb=" N ILE A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.885A pdb=" N VAL A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 375 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.977A pdb=" N ARG A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 498 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 535 through 546 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 563 through 580 removed outlier: 3.587A pdb=" N THR A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.944A pdb=" N ARG A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 701 through 708 Processing helix chain 'A' and resid 712 through 716 removed outlier: 4.130A pdb=" N GLU A 715 " --> pdb=" O PRO A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 733 Processing helix chain 'A' and resid 735 through 750 Processing helix chain 'A' and resid 759 through 780 removed outlier: 3.912A pdb=" N GLU A 763 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 814 Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.664A pdb=" N GLY A 821 " --> pdb=" O GLN A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 872 removed outlier: 3.636A pdb=" N LEU A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 896 Processing helix chain 'A' and resid 902 through 918 Processing helix chain 'A' and resid 969 through 975 removed outlier: 3.556A pdb=" N ALA A 973 " --> pdb=" O SER A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1025 Processing helix chain 'A' and resid 1044 through 1051 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1189 through 1195 Processing helix chain 'A' and resid 1198 through 1202 removed outlier: 4.471A pdb=" N SER A1201 " --> pdb=" O GLU A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1240 removed outlier: 7.126A pdb=" N ASN A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A1238 " --> pdb=" O HIS A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1248 Processing helix chain 'A' and resid 1306 through 1319 Processing helix chain 'A' and resid 1342 through 1354 removed outlier: 3.693A pdb=" N LEU A1346 " --> pdb=" O ASN A1342 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A1354 " --> pdb=" O ALA A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1422 removed outlier: 3.532A pdb=" N ARG A1411 " --> pdb=" O LYS A1407 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A1412 " --> pdb=" O GLU A1408 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP A1415 " --> pdb=" O ARG A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1480 removed outlier: 3.763A pdb=" N SER A1473 " --> pdb=" O LYS A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1519 removed outlier: 3.878A pdb=" N ASN A1513 " --> pdb=" O LYS A1509 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A1517 " --> pdb=" O ASN A1513 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1553 through 1556 Processing helix chain 'A' and resid 1557 through 1569 removed outlier: 3.681A pdb=" N TRP A1561 " --> pdb=" O SER A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1601 removed outlier: 4.425A pdb=" N ILE A1601 " --> pdb=" O SER A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1713 through 1715 No H-bonds generated for 'chain 'A' and resid 1713 through 1715' Processing helix chain 'A' and resid 1734 through 1741 Processing helix chain 'A' and resid 1757 through 1769 removed outlier: 3.500A pdb=" N ILE A1761 " --> pdb=" O ASP A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1790 Processing helix chain 'A' and resid 1793 through 1803 removed outlier: 3.813A pdb=" N PHE A1801 " --> pdb=" O LYS A1797 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A1803 " --> pdb=" O HIS A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1806 through 1824 removed outlier: 3.796A pdb=" N HIS A1810 " --> pdb=" O SER A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1864 removed outlier: 3.781A pdb=" N VAL A1853 " --> pdb=" O SER A1849 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A1854 " --> pdb=" O GLU A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1876 through 1888 Processing helix chain 'A' and resid 1895 through 1906 removed outlier: 3.566A pdb=" N ALA A1899 " --> pdb=" O THR A1895 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1961 removed outlier: 3.588A pdb=" N ASP A1926 " --> pdb=" O GLN A1922 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A1960 " --> pdb=" O TRP A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1971 through 1981 removed outlier: 3.638A pdb=" N GLU A1975 " --> pdb=" O GLN A1971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2003 removed outlier: 3.776A pdb=" N ALA A1993 " --> pdb=" O ASP A1989 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2068 removed outlier: 3.847A pdb=" N GLY A2068 " --> pdb=" O LYS A2064 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2078 removed outlier: 3.641A pdb=" N VAL A2075 " --> pdb=" O ASP A2071 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A2078 " --> pdb=" O ILE A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2105 through 2114 removed outlier: 3.652A pdb=" N LYS A2110 " --> pdb=" O LYS A2106 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA A2111 " --> pdb=" O CYS A2107 " (cutoff:3.500A) Processing helix chain 'A' and resid 2128 through 2130 No H-bonds generated for 'chain 'A' and resid 2128 through 2130' Processing helix chain 'A' and resid 2135 through 2139 removed outlier: 3.910A pdb=" N GLY A2139 " --> pdb=" O VAL A2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2135 through 2139' Processing helix chain 'A' and resid 2150 through 2163 Processing helix chain 'A' and resid 2176 through 2189 removed outlier: 4.180A pdb=" N GLY A2180 " --> pdb=" O GLU A2176 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A2181 " --> pdb=" O ASP A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2201 through 2211 removed outlier: 3.978A pdb=" N ASN A2205 " --> pdb=" O LYS A2201 " (cutoff:3.500A) Processing helix chain 'A' and resid 2251 through 2267 removed outlier: 3.871A pdb=" N VAL A2266 " --> pdb=" O ALA A2262 " (cutoff:3.500A) Processing helix chain 'A' and resid 2285 through 2303 removed outlier: 3.515A pdb=" N LYS A2299 " --> pdb=" O ARG A2295 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A2300 " --> pdb=" O THR A2296 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A2302 " --> pdb=" O LEU A2298 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP A2303 " --> pdb=" O LYS A2299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 406 removed outlier: 8.326A pdb=" N PHE A 406 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER A 385 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A 347 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 383 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 349 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 385 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR A 351 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 434 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU A 481 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 436 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 416 through 417 Processing sheet with id=AA3, first strand: chain 'A' and resid 663 through 665 Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 783 removed outlier: 7.622A pdb=" N ILE A 783 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N LEU A1207 " --> pdb=" O ILE A 783 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A 792 " --> pdb=" O PHE A1182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 782 through 783 removed outlier: 7.622A pdb=" N ILE A 783 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N LEU A1207 " --> pdb=" O ILE A 783 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A1339 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A1208 " --> pdb=" O PHE A1337 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A1337 " --> pdb=" O SER A1208 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG A1210 " --> pdb=" O GLY A1335 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY A1335 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 830 through 831 Processing sheet with id=AA7, first strand: chain 'A' and resid 1154 through 1157 removed outlier: 6.928A pdb=" N VAL A 936 " --> pdb=" O ARG A 925 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 927 " --> pdb=" O THR A 934 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR A 934 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP A 933 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 980 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER A1002 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER A1144 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS A1004 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP A1142 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A1006 " --> pdb=" O LYS A1140 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS A1140 " --> pdb=" O ILE A1006 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A1008 " --> pdb=" O LYS A1138 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS A1138 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A1010 " --> pdb=" O GLN A1136 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN A1136 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A1123 " --> pdb=" O PHE A1106 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG A1103 " --> pdb=" O ASP A1092 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A1092 " --> pdb=" O ARG A1103 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER A1037 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLU A1015 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL A1039 " --> pdb=" O LYS A1013 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A1013 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE A1041 " --> pdb=" O THR A1011 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR A1011 " --> pdb=" O ILE A1041 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1364 through 1371 Processing sheet with id=AA9, first strand: chain 'A' and resid 1364 through 1371 Processing sheet with id=AB1, first strand: chain 'A' and resid 1494 through 1495 removed outlier: 5.907A pdb=" N ILE A1494 " --> pdb=" O ARG A1718 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ARG A1720 " --> pdb=" O ILE A1494 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR A1499 " --> pdb=" O ILE A1548 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N MET A1550 " --> pdb=" O THR A1499 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A1501 " --> pdb=" O MET A1550 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1494 through 1495 removed outlier: 5.907A pdb=" N ILE A1494 " --> pdb=" O ARG A1718 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ARG A1720 " --> pdb=" O ILE A1494 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ARG A1718 " --> pdb=" O SER A1743 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N TYR A1745 " --> pdb=" O ARG A1718 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG A1720 " --> pdb=" O TYR A1745 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N TRP A1747 " --> pdb=" O ARG A1720 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL A1722 " --> pdb=" O TRP A1747 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU A1749 " --> pdb=" O VAL A1722 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA A1724 " --> pdb=" O LEU A1749 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ARG A1826 " --> pdb=" O GLY A1458 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A1460 " --> pdb=" O ARG A1826 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1837 through 1844 removed outlier: 3.546A pdb=" N LEU A2173 " --> pdb=" O LEU A2223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2094 through 2096 616 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2464 1.30 - 1.43: 4053 1.43 - 1.56: 8665 1.56 - 1.69: 49 1.69 - 1.83: 100 Bond restraints: 15331 Sorted by residual: bond pdb=" O4' 5CM B 30 " pdb=" C1' 5CM B 30 " ideal model delta sigma weight residual 1.400 1.633 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C2' 5CM B 30 " pdb=" C1' 5CM B 30 " ideal model delta sigma weight residual 1.530 1.314 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C4' 5CM B 30 " pdb=" O4' 5CM B 30 " ideal model delta sigma weight residual 1.432 1.275 0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" C2 5CM B 30 " pdb=" N3 5CM B 30 " ideal model delta sigma weight residual 1.348 1.475 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C5 5CM B 30 " pdb=" C6 5CM B 30 " ideal model delta sigma weight residual 1.353 1.478 -0.125 2.00e-02 2.50e+03 3.88e+01 ... (remaining 15326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 20475 2.80 - 5.59: 344 5.59 - 8.39: 30 8.39 - 11.19: 4 11.19 - 13.98: 2 Bond angle restraints: 20855 Sorted by residual: angle pdb=" N PRO A 847 " pdb=" CA PRO A 847 " pdb=" C PRO A 847 " ideal model delta sigma weight residual 112.47 99.64 12.83 2.06e+00 2.36e-01 3.88e+01 angle pdb=" C PRO A 847 " pdb=" N GLU A 848 " pdb=" CA GLU A 848 " ideal model delta sigma weight residual 123.23 114.00 9.23 1.57e+00 4.06e-01 3.45e+01 angle pdb=" N ASP A1533 " pdb=" CA ASP A1533 " pdb=" C ASP A1533 " ideal model delta sigma weight residual 114.62 108.43 6.19 1.14e+00 7.69e-01 2.94e+01 angle pdb=" C VAL A2102 " pdb=" N ALA A2103 " pdb=" CA ALA A2103 " ideal model delta sigma weight residual 121.90 115.61 6.29 1.26e+00 6.30e-01 2.49e+01 angle pdb=" CA TRP A1574 " pdb=" CB TRP A1574 " pdb=" CG TRP A1574 " ideal model delta sigma weight residual 113.60 122.13 -8.53 1.90e+00 2.77e-01 2.02e+01 ... (remaining 20850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 7977 17.56 - 35.12: 953 35.12 - 52.68: 255 52.68 - 70.24: 85 70.24 - 87.81: 19 Dihedral angle restraints: 9289 sinusoidal: 3973 harmonic: 5316 Sorted by residual: dihedral pdb=" CA THR A2087 " pdb=" C THR A2087 " pdb=" N ASN A2088 " pdb=" CA ASN A2088 " ideal model delta harmonic sigma weight residual 180.00 155.44 24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA TRP A 626 " pdb=" C TRP A 626 " pdb=" N THR A 627 " pdb=" CA THR A 627 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA GLN A2124 " pdb=" C GLN A2124 " pdb=" N ALA A2125 " pdb=" CA ALA A2125 " ideal model delta harmonic sigma weight residual -180.00 -156.79 -23.21 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 9286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1805 0.056 - 0.112: 439 0.112 - 0.168: 72 0.168 - 0.225: 9 0.225 - 0.281: 4 Chirality restraints: 2329 Sorted by residual: chirality pdb=" CA PRO A 847 " pdb=" N PRO A 847 " pdb=" C PRO A 847 " pdb=" CB PRO A 847 " both_signs ideal model delta sigma weight residual False 2.72 3.00 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA SER A2015 " pdb=" N SER A2015 " pdb=" C SER A2015 " pdb=" CB SER A2015 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' 5CM B 30 " pdb=" C4' 5CM B 30 " pdb=" O3' 5CM B 30 " pdb=" C2' 5CM B 30 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 2326 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 846 " 0.099 5.00e-02 4.00e+02 1.52e-01 3.69e+01 pdb=" N PRO A 847 " -0.263 5.00e-02 4.00e+02 pdb=" CA PRO A 847 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO A 847 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A2011 " -0.083 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO A2012 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO A2012 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO A2012 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A2088 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO A2089 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A2089 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2089 " -0.046 5.00e-02 4.00e+02 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 321 2.65 - 3.21: 14171 3.21 - 3.78: 22534 3.78 - 4.34: 30894 4.34 - 4.90: 50643 Nonbonded interactions: 118563 Sorted by model distance: nonbonded pdb=" N2 DG B 25 " pdb=" O2 DC D 12 " model vdw 2.090 2.496 nonbonded pdb=" OD2 ASP A 562 " pdb=" NE2 GLN A 822 " model vdw 2.095 3.120 nonbonded pdb=" OG SER A1019 " pdb=" OG1 THR A1033 " model vdw 2.131 3.040 nonbonded pdb=" OG1 THR A 613 " pdb=" OE2 GLU A 644 " model vdw 2.137 3.040 nonbonded pdb=" OG SER A1893 " pdb=" N LYS A1894 " model vdw 2.151 3.120 ... (remaining 118558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.340 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.930 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 0.013 0.417 15348 Z= 0.576 Angle : 1.024 24.932 20867 Z= 0.577 Chirality : 0.051 0.281 2329 Planarity : 0.007 0.152 2610 Dihedral : 17.363 87.806 5819 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.40 % Allowed : 11.66 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.17), residues: 1806 helix: -1.35 (0.17), residues: 693 sheet: -1.51 (0.27), residues: 296 loop : -2.97 (0.18), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 548 TYR 0.040 0.003 TYR A2149 PHE 0.026 0.003 PHE A1337 TRP 0.016 0.003 TRP A1222 HIS 0.012 0.002 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.01140 / 0.55 (15331) covalent geometry : angle 0.96070 / 0.57 (20855) hydrogen bonds : bond 0.17974 / 11.74 ( 630) hydrogen bonds : angle 6.85142 / 4.81 ( 1809) metal coordination : bond 0.16888 / 9.06 ( 17) metal coordination : angle 14.83266 / 8.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.584 Fit side-chains REVERT: A 442 ASP cc_start: 0.7638 (t0) cc_final: 0.7246 (t0) REVERT: A 1250 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 1378 PRO cc_start: 0.6588 (Cg_endo) cc_final: 0.6310 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8248 (p) cc_final: 0.8040 (m) REVERT: A 1563 ARG cc_start: 0.7537 (tpt170) cc_final: 0.7255 (tpp-160) REVERT: A 1567 LEU cc_start: 0.7989 (mt) cc_final: 0.7704 (mt) outliers start: 22 outliers final: 10 residues processed: 163 average time/residue: 0.7006 time to fit residues: 124.1452 Evaluate side-chains 108 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 2220 VAL Chi-restraints excluded: chain A residue 2221 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 HIS A 565 ASN A 629 ASN ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 ASN A 780 ASN A 802 ASN A 833 GLN A 857 GLN A 977 HIS A1234 HIS ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1379 GLN A1397 GLN A1409 GLN A1810 HIS A1827 GLN A1940 GLN A2009 ASN A2101 HIS A2115 GLN A2131 ASN A2211 GLN ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.124170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101284 restraints weight = 25971.729| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.21 r_work: 0.3231 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 15348 Z= 0.246 Angle : 0.755 12.271 20867 Z= 0.386 Chirality : 0.046 0.222 2329 Planarity : 0.006 0.082 2610 Dihedral : 13.705 68.572 2274 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.57 % Allowed : 16.89 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.18), residues: 1806 helix: -0.09 (0.19), residues: 699 sheet: -0.63 (0.29), residues: 290 loop : -2.60 (0.19), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2268 TYR 0.028 0.002 TYR A2149 PHE 0.021 0.002 PHE A1518 TRP 0.014 0.002 TRP A2304 HIS 0.012 0.001 HIS A2193 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (15331) covalent geometry : angle 0.73905 / 0.38 (20855) hydrogen bonds : bond 0.06789 / 4.34 ( 630) hydrogen bonds : angle 5.26922 / 3.69 ( 1809) metal coordination : bond 0.02123 / 1.21 ( 17) metal coordination : angle 6.47028 / 3.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 112 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7743 (t0) cc_final: 0.7145 (t0) REVERT: A 717 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8252 (tt) REVERT: A 795 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6552 (tp) REVERT: A 1098 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: A 1250 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 1373 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.6392 (p-80) REVERT: A 1378 PRO cc_start: 0.6276 (Cg_endo) cc_final: 0.5984 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8472 (p) cc_final: 0.8017 (m) REVERT: A 1563 ARG cc_start: 0.7746 (tpt170) cc_final: 0.7456 (tpp-160) REVERT: A 1567 LEU cc_start: 0.8014 (mt) cc_final: 0.7696 (mt) REVERT: A 1716 MET cc_start: 0.8396 (ptp) cc_final: 0.8003 (ptt) REVERT: A 1732 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6600 (tmmm) REVERT: A 2170 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8404 (tp) REVERT: A 2304 TRP cc_start: 0.6923 (OUTLIER) cc_final: 0.6204 (t60) outliers start: 56 outliers final: 25 residues processed: 161 average time/residue: 0.5161 time to fit residues: 93.0820 Evaluate side-chains 124 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1098 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1574 TRP Chi-restraints excluded: chain A residue 1732 LYS Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 2031 VAL Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [1, 17, 175, 159, 20, 45, 126, 179, 67, 178, 11] chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 0.0070 chunk 175 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 HIS ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.126455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102936 restraints weight = 26073.286| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.18 r_work: 0.3269 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15348 Z= 0.152 Angle : 0.660 11.070 20867 Z= 0.335 Chirality : 0.043 0.219 2329 Planarity : 0.005 0.075 2610 Dihedral : 13.261 66.775 2266 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.95 % Allowed : 18.48 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1806 helix: 0.57 (0.19), residues: 701 sheet: -0.42 (0.30), residues: 288 loop : -2.32 (0.19), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 940 TYR 0.029 0.002 TYR A2269 PHE 0.014 0.002 PHE A 864 TRP 0.013 0.001 TRP A1809 HIS 0.007 0.001 HIS A1217 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (15331) covalent geometry : angle 0.64797 / 0.33 (20855) hydrogen bonds : bond 0.05590 / 3.49 ( 630) hydrogen bonds : angle 4.77957 / 3.34 ( 1809) metal coordination : bond 0.01612 / 0.88 ( 17) metal coordination : angle 5.24194 / 2.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 114 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 324 MET cc_start: 0.8998 (mtt) cc_final: 0.8757 (mtt) REVERT: A 442 ASP cc_start: 0.7594 (t0) cc_final: 0.7111 (t0) REVERT: A 717 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8200 (tt) REVERT: A 778 VAL cc_start: 0.8557 (p) cc_final: 0.8189 (m) REVERT: A 1003 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7442 (mpt) REVERT: A 1098 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: A 1250 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8112 (mp) REVERT: A 1373 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.6501 (p-80) REVERT: A 1378 PRO cc_start: 0.6196 (Cg_endo) cc_final: 0.5919 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8424 (p) cc_final: 0.7851 (m) REVERT: A 2170 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8308 (tp) REVERT: A 2304 TRP cc_start: 0.6797 (OUTLIER) cc_final: 0.6179 (t60) outliers start: 62 outliers final: 25 residues processed: 167 average time/residue: 0.4676 time to fit residues: 88.3294 Evaluate side-chains 123 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1098 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1574 TRP Chi-restraints excluded: chain A residue 1587 ARG Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 2031 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [143, 33, 9, 98, 70, 34, 76, 85, 150, 170, 107] chunk 143 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.126833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103661 restraints weight = 26068.084| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.23 r_work: 0.3275 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15348 Z= 0.147 Angle : 0.635 10.015 20867 Z= 0.321 Chirality : 0.043 0.238 2329 Planarity : 0.005 0.071 2610 Dihedral : 13.069 65.458 2262 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.89 % Allowed : 20.59 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.19), residues: 1806 helix: 0.89 (0.19), residues: 703 sheet: -0.35 (0.31), residues: 289 loop : -2.17 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2268 TYR 0.021 0.002 TYR A2269 PHE 0.015 0.002 PHE A 864 TRP 0.013 0.001 TRP A2304 HIS 0.007 0.001 HIS A1217 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (15331) covalent geometry : angle 0.62551 / 0.32 (20855) hydrogen bonds : bond 0.05285 / 3.28 ( 630) hydrogen bonds : angle 4.59770 / 3.22 ( 1809) metal coordination : bond 0.01127 / 0.62 ( 17) metal coordination : angle 4.69997 / 2.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 114 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 324 MET cc_start: 0.9016 (mtt) cc_final: 0.8741 (mtt) REVERT: A 442 ASP cc_start: 0.7575 (t0) cc_final: 0.7016 (t0) REVERT: A 641 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8787 (t0) REVERT: A 717 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8156 (tt) REVERT: A 778 VAL cc_start: 0.8572 (p) cc_final: 0.8209 (m) REVERT: A 1232 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7922 (mt) REVERT: A 1250 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8144 (mp) REVERT: A 1373 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.6435 (p-80) REVERT: A 1378 PRO cc_start: 0.6126 (Cg_endo) cc_final: 0.5863 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8408 (p) cc_final: 0.7971 (m) REVERT: A 1586 ASP cc_start: 0.7550 (p0) cc_final: 0.7003 (m-30) REVERT: A 1775 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: A 1782 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7740 (t) REVERT: A 2170 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 2178 LEU cc_start: 0.8769 (mm) cc_final: 0.8518 (mt) REVERT: A 2269 TYR cc_start: 0.6030 (t80) cc_final: 0.5696 (t80) REVERT: A 2304 TRP cc_start: 0.6753 (OUTLIER) cc_final: 0.5812 (t60) outliers start: 61 outliers final: 29 residues processed: 170 average time/residue: 0.4369 time to fit residues: 84.9803 Evaluate side-chains 133 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1522 MET Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1574 TRP Chi-restraints excluded: chain A residue 1587 ARG Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 2098 CYS Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [134, 90, 12, 127, 160, 92, 47, 43, 45, 72, 156] chunk 134 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 160 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 0.0970 chunk 72 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN A 669 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.128955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.105859 restraints weight = 26152.243| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.24 r_work: 0.3310 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15348 Z= 0.116 Angle : 0.602 9.810 20867 Z= 0.303 Chirality : 0.041 0.223 2329 Planarity : 0.005 0.067 2610 Dihedral : 12.792 63.966 2262 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.89 % Allowed : 21.16 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1806 helix: 1.23 (0.19), residues: 705 sheet: -0.12 (0.32), residues: 286 loop : -2.09 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2268 TYR 0.017 0.001 TYR A2149 PHE 0.014 0.001 PHE A 864 TRP 0.012 0.001 TRP A2304 HIS 0.006 0.001 HIS A1217 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15331) covalent geometry : angle 0.59443 / 0.30 (20855) hydrogen bonds : bond 0.04759 / 2.89 ( 630) hydrogen bonds : angle 4.35922 / 3.04 ( 1809) metal coordination : bond 0.01072 / 0.58 ( 17) metal coordination : angle 3.97534 / 2.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 119 time to evaluate : 0.614 Fit side-chains REVERT: A 324 MET cc_start: 0.8932 (mtt) cc_final: 0.8700 (mtt) REVERT: A 442 ASP cc_start: 0.7408 (t0) cc_final: 0.6906 (t0) REVERT: A 717 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8078 (tt) REVERT: A 778 VAL cc_start: 0.8550 (p) cc_final: 0.8200 (m) REVERT: A 1003 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7349 (mpt) REVERT: A 1232 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8041 (mt) REVERT: A 1373 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.6532 (p-80) REVERT: A 1378 PRO cc_start: 0.6173 (Cg_endo) cc_final: 0.5886 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8447 (p) cc_final: 0.8102 (m) REVERT: A 1775 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: A 1782 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7723 (t) REVERT: A 2170 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8169 (tp) REVERT: A 2178 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8543 (mt) REVERT: A 2269 TYR cc_start: 0.5862 (t80) cc_final: 0.5517 (t80) REVERT: A 2304 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.5589 (t60) outliers start: 61 outliers final: 25 residues processed: 168 average time/residue: 0.4553 time to fit residues: 87.0553 Evaluate side-chains 130 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1574 TRP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [146, 64, 169, 152, 85, 118, 116, 133, 172, 36, 143] chunk 146 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 673 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.128206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.105139 restraints weight = 25664.225| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.11 r_work: 0.3296 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15348 Z= 0.146 Angle : 0.626 9.820 20867 Z= 0.312 Chirality : 0.042 0.270 2329 Planarity : 0.005 0.065 2610 Dihedral : 12.773 64.313 2258 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.46 % Allowed : 21.61 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1806 helix: 1.34 (0.19), residues: 706 sheet: -0.18 (0.31), residues: 296 loop : -2.08 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2268 TYR 0.022 0.001 TYR A2149 PHE 0.021 0.002 PHE A2172 TRP 0.013 0.001 TRP A2304 HIS 0.006 0.001 HIS A1217 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (15331) covalent geometry : angle 0.61860 / 0.31 (20855) hydrogen bonds : bond 0.04907 / 3.00 ( 630) hydrogen bonds : angle 4.32378 / 3.02 ( 1809) metal coordination : bond 0.00883 / 0.49 ( 17) metal coordination : angle 4.15235 / 2.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 101 time to evaluate : 0.581 Fit side-chains REVERT: A 324 MET cc_start: 0.9045 (mtt) cc_final: 0.8784 (mtt) REVERT: A 442 ASP cc_start: 0.7384 (t0) cc_final: 0.6850 (t0) REVERT: A 641 ASP cc_start: 0.9229 (OUTLIER) cc_final: 0.8942 (t70) REVERT: A 717 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8197 (tt) REVERT: A 778 VAL cc_start: 0.8566 (p) cc_final: 0.8203 (m) REVERT: A 1003 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7558 (mpt) REVERT: A 1098 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: A 1232 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 1250 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8046 (mp) REVERT: A 1373 HIS cc_start: 0.8096 (OUTLIER) cc_final: 0.6584 (p-80) REVERT: A 1378 PRO cc_start: 0.6345 (Cg_endo) cc_final: 0.6024 (Cg_exo) REVERT: A 1775 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: A 1782 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7766 (t) REVERT: A 2178 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8628 (mt) REVERT: A 2304 TRP cc_start: 0.6845 (OUTLIER) cc_final: 0.5698 (t60) outliers start: 70 outliers final: 37 residues processed: 160 average time/residue: 0.4189 time to fit residues: 76.7146 Evaluate side-chains 144 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1098 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1574 TRP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1714 LEU Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2098 CYS Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [108, 155, 46, 87, 172, 86, 61, 29, 54, 123, 162] chunk 108 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 54 optimal weight: 0.0030 chunk 123 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 overall best weight: 2.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 977 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.126444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.103146 restraints weight = 25760.228| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.20 r_work: 0.3267 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15348 Z= 0.191 Angle : 0.662 10.166 20867 Z= 0.330 Chirality : 0.043 0.247 2329 Planarity : 0.005 0.063 2610 Dihedral : 12.909 65.021 2258 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.27 % Allowed : 22.31 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1806 helix: 1.29 (0.19), residues: 705 sheet: -0.17 (0.32), residues: 280 loop : -2.08 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2268 TYR 0.021 0.002 TYR A2149 PHE 0.016 0.002 PHE A 864 TRP 0.013 0.001 TRP A2304 HIS 0.005 0.001 HIS A1217 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (15331) covalent geometry : angle 0.65298 / 0.33 (20855) hydrogen bonds : bond 0.05223 / 3.24 ( 630) hydrogen bonds : angle 4.39637 / 3.07 ( 1809) metal coordination : bond 0.00979 / 0.59 ( 17) metal coordination : angle 4.48831 / 2.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 97 time to evaluate : 0.434 Fit side-chains REVERT: A 324 MET cc_start: 0.9113 (mtt) cc_final: 0.8878 (mtt) REVERT: A 442 ASP cc_start: 0.7463 (t0) cc_final: 0.6935 (t0) REVERT: A 641 ASP cc_start: 0.9274 (OUTLIER) cc_final: 0.8928 (t0) REVERT: A 717 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8245 (tt) REVERT: A 778 VAL cc_start: 0.8577 (p) cc_final: 0.8208 (m) REVERT: A 1003 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7522 (mpt) REVERT: A 1098 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: A 1232 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8156 (mt) REVERT: A 1250 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 1373 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.6596 (p-80) REVERT: A 1378 PRO cc_start: 0.6314 (Cg_endo) cc_final: 0.5987 (Cg_exo) REVERT: A 1782 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7810 (t) REVERT: A 2304 TRP cc_start: 0.6935 (OUTLIER) cc_final: 0.5740 (t60) outliers start: 67 outliers final: 39 residues processed: 155 average time/residue: 0.3916 time to fit residues: 69.9626 Evaluate side-chains 139 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 91 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1098 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1574 TRP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1877 VAL Chi-restraints excluded: chain A residue 2098 CYS Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [151, 0, 145, 72, 180, 112, 61, 90, 109, 10, 27] chunk 151 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 112 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 chunk 90 optimal weight: 0.0030 chunk 109 optimal weight: 4.9990 chunk 10 optimal weight: 0.0570 chunk 27 optimal weight: 3.9990 overall best weight: 1.2270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1715 HIS A1818 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.105681 restraints weight = 26062.374| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.23 r_work: 0.3301 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15348 Z= 0.126 Angle : 0.630 10.856 20867 Z= 0.311 Chirality : 0.042 0.298 2329 Planarity : 0.005 0.059 2610 Dihedral : 12.746 64.063 2258 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.82 % Allowed : 22.63 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1806 helix: 1.49 (0.20), residues: 699 sheet: -0.13 (0.33), residues: 275 loop : -1.99 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1718 TYR 0.018 0.001 TYR A2149 PHE 0.016 0.001 PHE A1717 TRP 0.012 0.001 TRP A2304 HIS 0.006 0.001 HIS A1217 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15331) covalent geometry : angle 0.62332 / 0.31 (20855) hydrogen bonds : bond 0.04764 / 2.89 ( 630) hydrogen bonds : angle 4.27094 / 2.99 ( 1809) metal coordination : bond 0.01030 / 0.55 ( 17) metal coordination : angle 3.90097 / 2.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 99 time to evaluate : 0.591 Fit side-chains REVERT: A 324 MET cc_start: 0.8984 (mtt) cc_final: 0.8703 (mtt) REVERT: A 442 ASP cc_start: 0.7371 (t0) cc_final: 0.6931 (t0) REVERT: A 641 ASP cc_start: 0.9134 (OUTLIER) cc_final: 0.8803 (t70) REVERT: A 717 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8132 (tt) REVERT: A 778 VAL cc_start: 0.8561 (p) cc_final: 0.8216 (m) REVERT: A 1003 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7316 (mpt) REVERT: A 1098 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: A 1373 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.6564 (p-80) REVERT: A 1378 PRO cc_start: 0.6267 (Cg_endo) cc_final: 0.5938 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8443 (p) cc_final: 0.8028 (m) REVERT: A 1496 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8069 (mp) REVERT: A 1582 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7609 (ttm170) REVERT: A 1775 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: A 1782 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7830 (t) REVERT: A 2268 ARG cc_start: 0.7482 (mmm-85) cc_final: 0.7198 (mtp-110) REVERT: A 2304 TRP cc_start: 0.6675 (OUTLIER) cc_final: 0.5517 (t60) outliers start: 60 outliers final: 33 residues processed: 150 average time/residue: 0.4620 time to fit residues: 78.8591 Evaluate side-chains 135 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1098 GLU Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1574 TRP Chi-restraints excluded: chain A residue 1582 ARG Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1877 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [1, 28, 171, 53, 63, 139, 79, 147, 19, 78, 134] chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.128109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104830 restraints weight = 25955.816| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.19 r_work: 0.3295 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15348 Z= 0.139 Angle : 0.638 10.443 20867 Z= 0.315 Chirality : 0.042 0.291 2329 Planarity : 0.005 0.083 2610 Dihedral : 12.690 64.207 2256 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.57 % Allowed : 23.26 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1806 helix: 1.56 (0.20), residues: 698 sheet: -0.06 (0.33), residues: 281 loop : -1.99 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2268 TYR 0.017 0.001 TYR A2149 PHE 0.015 0.001 PHE A 864 TRP 0.013 0.001 TRP A2304 HIS 0.005 0.001 HIS A1217 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15331) covalent geometry : angle 0.63085 / 0.31 (20855) hydrogen bonds : bond 0.04808 / 2.93 ( 630) hydrogen bonds : angle 4.24758 / 2.97 ( 1809) metal coordination : bond 0.00991 / 0.54 ( 17) metal coordination : angle 4.02229 / 2.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 105 time to evaluate : 0.351 Fit side-chains REVERT: A 324 MET cc_start: 0.9069 (mtt) cc_final: 0.8790 (mtt) REVERT: A 442 ASP cc_start: 0.7358 (t0) cc_final: 0.6913 (t0) REVERT: A 641 ASP cc_start: 0.9227 (OUTLIER) cc_final: 0.8910 (t70) REVERT: A 717 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 778 VAL cc_start: 0.8557 (p) cc_final: 0.8213 (m) REVERT: A 1003 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7497 (mpt) REVERT: A 1098 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: A 1373 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.6638 (p-80) REVERT: A 1378 PRO cc_start: 0.6205 (Cg_endo) cc_final: 0.5874 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8490 (p) cc_final: 0.8084 (m) REVERT: A 1496 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 1582 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7657 (ttm170) REVERT: A 1717 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7425 (p90) REVERT: A 1782 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7864 (t) REVERT: A 2268 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7361 (mtp-110) REVERT: A 2269 TYR cc_start: 0.6355 (t80) cc_final: 0.6041 (t80) REVERT: A 2304 TRP cc_start: 0.6707 (OUTLIER) cc_final: 0.5623 (t60) outliers start: 56 outliers final: 38 residues processed: 152 average time/residue: 0.4763 time to fit residues: 81.7753 Evaluate side-chains 146 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1098 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1574 TRP Chi-restraints excluded: chain A residue 1582 ARG Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1717 PHE Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1877 VAL Chi-restraints excluded: chain A residue 2098 CYS Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [184, 76, 12, 14, 86, 31, 45, 50, 177, 53, 43] chunk 184 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1860 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.129697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106312 restraints weight = 25907.145| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.13 r_work: 0.3324 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15348 Z= 0.116 Angle : 0.631 11.756 20867 Z= 0.309 Chirality : 0.042 0.349 2329 Planarity : 0.005 0.056 2610 Dihedral : 12.547 62.864 2256 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.12 % Allowed : 24.16 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1806 helix: 1.66 (0.20), residues: 701 sheet: -0.02 (0.33), residues: 282 loop : -1.93 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1718 TYR 0.021 0.001 TYR A2149 PHE 0.013 0.001 PHE A 864 TRP 0.012 0.001 TRP A1809 HIS 0.005 0.001 HIS A1217 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (15331) covalent geometry : angle 0.62540 / 0.31 (20855) hydrogen bonds : bond 0.04506 / 2.69 ( 630) hydrogen bonds : angle 4.16689 / 2.92 ( 1809) metal coordination : bond 0.01104 / 0.60 ( 17) metal coordination : angle 3.55571 / 1.82 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 0.504 Fit side-chains REVERT: A 324 MET cc_start: 0.9001 (mtt) cc_final: 0.8753 (mtt) REVERT: A 330 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8773 (p) REVERT: A 442 ASP cc_start: 0.7110 (t0) cc_final: 0.6628 (t0) REVERT: A 641 ASP cc_start: 0.9204 (OUTLIER) cc_final: 0.8861 (t70) REVERT: A 717 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8143 (tt) REVERT: A 778 VAL cc_start: 0.8534 (p) cc_final: 0.8210 (m) REVERT: A 1003 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7541 (mpt) REVERT: A 1098 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: A 1373 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.6674 (p-80) REVERT: A 1378 PRO cc_start: 0.6135 (Cg_endo) cc_final: 0.5823 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8465 (p) cc_final: 0.8068 (m) REVERT: A 1496 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7849 (mp) REVERT: A 1775 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: A 1782 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7867 (t) REVERT: A 2268 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.7273 (mtp-110) REVERT: A 2269 TYR cc_start: 0.6119 (t80) cc_final: 0.5816 (t80) REVERT: A 2304 TRP cc_start: 0.6519 (OUTLIER) cc_final: 0.5593 (t60) outliers start: 49 outliers final: 32 residues processed: 157 average time/residue: 0.4758 time to fit residues: 84.3646 Evaluate side-chains 138 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1098 GLU Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1877 VAL Chi-restraints excluded: chain A residue 2098 CYS Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [124, 40, 147, 167, 1, 92, 160, 48, 43, 25, 115] chunk 124 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.129604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106549 restraints weight = 25682.021| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.11 r_work: 0.3310 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15348 Z= 0.132 Angle : 0.636 11.117 20867 Z= 0.314 Chirality : 0.042 0.352 2329 Planarity : 0.005 0.056 2610 Dihedral : 12.553 63.241 2256 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.12 % Allowed : 24.60 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1806 helix: 1.70 (0.20), residues: 701 sheet: -0.03 (0.33), residues: 278 loop : -1.93 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1718 TYR 0.022 0.001 TYR A2149 PHE 0.015 0.001 PHE A 864 TRP 0.013 0.001 TRP A2304 HIS 0.005 0.001 HIS A1217 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (15331) covalent geometry : angle 0.62994 / 0.31 (20855) hydrogen bonds : bond 0.04611 / 2.77 ( 630) hydrogen bonds : angle 4.16254 / 2.91 ( 1809) metal coordination : bond 0.00985 / 0.54 ( 17) metal coordination : angle 3.83331 / 1.93 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4170.40 seconds wall clock time: 71 minutes 58.00 seconds (4318.00 seconds total)