Starting phenix.real_space_refine on Sun Oct 25 03:22:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r78_24295/10_2026/7r78_24295.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r78_24295/10_2026/7r78_24295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r78_24295/10_2026/7r78_24295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r78_24295/10_2026/7r78_24295.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7r78_24295/10_2026/7r78_24295.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r78_24295/10_2026/7r78_24295.cif" model { file = "/net/cci-nas-00/data/ceres_data/7r78_24295/10_2026/7r78_24295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r78_24295/10_2026/7r78_24295.cif" } resolution = 3.5 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= 0.005 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 20 5.49 5 Mg 1 5.21 5 S 72 5.16 5 C 9483 2.51 5 N 2756 2.21 5 O 2901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s 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: 15238 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 14810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1880, 14810 Classifications: {'peptide': 1880} Link IDs: {'PTRANS': 89, 'TRANS': 1790} Chain breaks: 6 Chain: "D" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 63 Unusual residues: {' MG': 1, ' ZN': 5, 'ANP': 1} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3945 SG CYS A 817 71.375 72.832 60.619 1.00 44.98 S ATOM 3960 SG CYS A 819 70.233 69.601 61.157 1.00 45.98 S ATOM 4114 SG CYS A 840 68.351 73.358 62.510 1.00 45.74 S ATOM 4050 SG CYS A 832 78.993 84.373 65.074 1.00 43.82 S ATOM 4074 SG CYS A 835 81.452 83.071 61.227 1.00 42.36 S ATOM 5901 SG CYS A1065 82.602 83.158 64.911 1.00 39.33 S ATOM 6801 SG CYS A1200 44.677 46.916 34.498 1.00 61.37 S ATOM 7361 SG CYS A1271 44.581 43.896 35.833 1.00 61.48 S ATOM 7387 SG CYS A1274 46.898 46.677 37.104 1.00 56.78 S ATOM 12993 SG CYS A2081 86.979 77.986 97.399 1.00 96.97 S ATOM 13123 SG CYS A2099 85.214 66.624 92.667 1.00 68.23 S ATOM 13255 SG CYS A2117 87.178 69.100 90.557 1.00 76.49 S ATOM 13296 SG CYS A2123 88.898 65.946 90.578 1.00 69.74 S Time building chain proxies: 3.17, per 1000 atoms: 0.21 Number of scatterers: 15238 At special positions: 0 Unit cell: (128.744, 111.72, 123.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 72 16.00 P 20 15.00 Mg 1 11.99 O 2901 8.00 N 2756 7.00 C 9483 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: 1.60 Conformation dependent library (CDL) restraints added in 456.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2402 " pdb="ZN ZN A2402 " - pdb=" SG CYS A 819 " pdb="ZN ZN A2402 " - pdb=" SG CYS A 840 " pdb="ZN ZN A2402 " - pdb=" SG CYS A 817 " pdb=" ZN A2403 " pdb="ZN ZN A2403 " - pdb=" ND1 HIS A 849 " pdb="ZN ZN A2403 " - pdb=" SG CYS A1065 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 832 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 835 " pdb=" ZN A2404 " pdb="ZN ZN A2404 " - pdb=" SG CYS A1200 " pdb="ZN ZN A2404 " - pdb=" SG CYS A1271 " pdb="ZN ZN A2404 " - pdb=" SG CYS A1274 " pdb=" ZN A2405 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2081 " pdb=" ZN A2406 " pdb="ZN ZN A2406 " - pdb=" SG CYS A2123 " pdb="ZN ZN A2406 " - pdb=" SG CYS A2117 " pdb="ZN ZN A2406 " - pdb=" SG CYS A2099 " Number of angles added : 3 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3558 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 14 sheets defined 39.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 320 through 332 removed outlier: 3.857A pdb=" N ILE A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.172A pdb=" N VAL A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 374 Processing helix chain 'A' and resid 391 through 400 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.789A pdb=" N GLY A 413 " --> pdb=" O THR A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.752A pdb=" N GLN A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 498 removed outlier: 3.645A pdb=" N VAL A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 498 " --> pdb=" O TYR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 546 removed outlier: 3.868A pdb=" N LYS A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 563 through 574 removed outlier: 3.607A pdb=" N HIS A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 572 " --> pdb=" O ARG A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 4.039A 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 669 through 673 Processing helix chain 'A' and resid 701 through 708 Processing helix chain 'A' and resid 722 through 733 removed outlier: 3.698A pdb=" N ASN A 732 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 750 Processing helix chain 'A' and resid 759 through 781 removed outlier: 3.682A pdb=" N GLU A 763 " --> pdb=" O ASN A 759 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 778 " --> pdb=" O ASP A 774 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 860 through 872 removed outlier: 3.822A pdb=" N GLY A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 902 through 914 removed outlier: 3.596A pdb=" N ALA A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 975 Processing helix chain 'A' and resid 1019 through 1025 Processing helix chain 'A' and resid 1044 through 1050 Processing helix chain 'A' and resid 1188 through 1195 removed outlier: 3.686A pdb=" N SER A1192 " --> pdb=" O ALA A1188 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A1193 " --> pdb=" O SER A1189 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A1194 " --> pdb=" O ALA A1190 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1188 through 1195' Processing helix chain 'A' and resid 1237 through 1243 removed outlier: 3.709A pdb=" N LEU A1243 " --> pdb=" O THR A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1248 Processing helix chain 'A' and resid 1306 through 1317 Processing helix chain 'A' and resid 1342 through 1353 removed outlier: 3.781A pdb=" N ARG A1353 " --> pdb=" O ARG A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1422 Processing helix chain 'A' and resid 1468 through 1481 Processing helix chain 'A' and resid 1504 through 1508 removed outlier: 4.069A pdb=" N SER A1508 " --> pdb=" O GLY A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1519 Processing helix chain 'A' and resid 1530 through 1536 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1553 through 1557 Processing helix chain 'A' and resid 1558 through 1569 removed outlier: 3.632A pdb=" N SER A1562 " --> pdb=" O ASP A1558 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1603 removed outlier: 3.798A pdb=" N ARG A1587 " --> pdb=" O PHE A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1610 through 1622 removed outlier: 3.597A pdb=" N GLU A1615 " --> pdb=" O MET A1611 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A1616 " --> pdb=" O ARG A1612 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A1617 " --> pdb=" O ALA A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1730 Processing helix chain 'A' and resid 1731 through 1739 removed outlier: 4.039A pdb=" N ALA A1737 " --> pdb=" O LYS A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1757 through 1769 removed outlier: 3.701A pdb=" N ILE A1761 " --> pdb=" O ASP A1757 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A1764 " --> pdb=" O ALA A1760 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A1767 " --> pdb=" O SER A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1797 Processing helix chain 'A' and resid 1806 through 1824 removed outlier: 3.862A pdb=" N HIS A1810 " --> pdb=" O SER A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1864 Processing helix chain 'A' and resid 1881 through 1886 Processing helix chain 'A' and resid 1895 through 1906 removed outlier: 3.512A pdb=" N ARG A1903 " --> pdb=" O ALA A1899 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS A1905 " --> pdb=" O LEU A1901 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS A1906 " --> pdb=" O LYS A1902 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1960 Processing helix chain 'A' and resid 1971 through 1982 removed outlier: 3.765A pdb=" N ALA A1978 " --> pdb=" O ALA A1974 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A1982 " --> pdb=" O ALA A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1986 Processing helix chain 'A' and resid 1989 through 2002 removed outlier: 3.781A pdb=" N ALA A1993 " --> pdb=" O ASP A1989 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2068 removed outlier: 3.872A pdb=" N HIS A2040 " --> pdb=" O ARG A2036 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A2058 " --> pdb=" O ARG A2054 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A2068 " --> pdb=" O LYS A2064 " (cutoff:3.500A) Processing helix chain 'A' and resid 2068 through 2076 Processing helix chain 'A' and resid 2104 through 2114 removed outlier: 3.846A pdb=" N SER A2114 " --> pdb=" O LYS A2110 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2163 removed outlier: 3.603A pdb=" N VAL A2157 " --> pdb=" O LEU A2153 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A2158 " --> pdb=" O GLU A2154 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A2159 " --> pdb=" O HIS A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2177 No H-bonds generated for 'chain 'A' and resid 2175 through 2177' Processing helix chain 'A' and resid 2178 through 2187 removed outlier: 3.550A pdb=" N SER A2187 " --> pdb=" O SER A2183 " (cutoff:3.500A) Processing helix chain 'A' and resid 2201 through 2212 removed outlier: 3.692A pdb=" N ASN A2205 " --> pdb=" O LYS A2201 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2231 removed outlier: 3.510A pdb=" N ALA A2231 " --> pdb=" O ALA A2228 " (cutoff:3.500A) Processing helix chain 'A' and resid 2251 through 2265 Processing helix chain 'A' and resid 2286 through 2301 Processing sheet with id=AA1, first strand: chain 'A' and resid 404 through 406 removed outlier: 9.841A pdb=" N ILE A 404 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A 383 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N PHE A 406 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER A 385 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 347 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 383 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL A 349 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER A 385 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR A 351 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG A 348 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE A 435 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 350 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU A 434 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLU A 481 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 520 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 503 " --> pdb=" O PHE A 524 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 664 through 665 removed outlier: 3.789A pdb=" N TRP A 692 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 791 through 792 removed outlier: 3.829A pdb=" N HIS A 791 " --> pdb=" O PHE A1182 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A1182 " --> pdb=" O HIS A 791 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A1339 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A1208 " --> pdb=" O PHE A1337 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A1337 " --> pdb=" O SER A1208 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A1210 " --> pdb=" O GLY A1335 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A1335 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A1326 " --> pdb=" O ILE A1230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 838 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 876 through 878 Processing sheet with id=AA6, first strand: chain 'A' and resid 923 through 927 removed outlier: 4.457A pdb=" N VAL A 936 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1003 through 1018 removed outlier: 7.516A pdb=" N THR A1011 " --> pdb=" O ILE A1041 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILE A1041 " --> pdb=" O THR A1011 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS A1013 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL A1039 " --> pdb=" O LYS A1013 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU A1015 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER A1037 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A1072 " --> pdb=" O LEU A1062 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR A1104 " --> pdb=" O ARG A1124 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ARG A1124 " --> pdb=" O TYR A1104 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE A1106 " --> pdb=" O ILE A1122 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A1122 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER A1144 " --> pdb=" O ILE A1122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1264 through 1265 removed outlier: 3.537A pdb=" N ASP A1265 " --> pdb=" O ILE A1363 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A1363 " --> pdb=" O ASP A1265 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1451 " --> pdb=" O SER A1364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A1429 " --> pdb=" O VAL A1454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1368 through 1370 removed outlier: 3.854A pdb=" N TRP A1444 " --> pdb=" O LEU A1439 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1525 through 1528 removed outlier: 5.744A pdb=" N THR A1499 " --> pdb=" O ILE A1548 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N MET A1550 " --> pdb=" O THR A1499 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A1501 " --> pdb=" O MET A1550 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A1500 " --> pdb=" O ILE A1723 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP A1725 " --> pdb=" O LEU A1500 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A1502 " --> pdb=" O ASP A1725 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG A1720 " --> pdb=" O SER A1743 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A1745 " --> pdb=" O ARG A1720 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1749 " --> pdb=" O ALA A1724 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A1750 " --> pdb=" O ILE A1461 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A1460 " --> pdb=" O ARG A1826 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1842 through 1844 removed outlier: 6.443A pdb=" N HIS A1842 " --> pdb=" O LEU A2281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 2095 through 2096 Processing sheet with id=AB4, first strand: chain 'A' and resid 2169 through 2170 removed outlier: 3.649A pdb=" N LEU A2170 " --> pdb=" O HIS A2240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2172 through 2173 removed outlier: 6.790A pdb=" N VAL A2194 " --> pdb=" O LEU A2222 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LYS A2224 " --> pdb=" O VAL A2194 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4791 1.33 - 1.45: 2353 1.45 - 1.57: 8294 1.57 - 1.69: 38 1.69 - 1.81: 104 Bond restraints: 15580 Sorted by residual: bond pdb=" N3B ANP A2407 " pdb=" PG ANP A2407 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" P 5CM D 30 " pdb=" O5' 5CM D 30 " ideal model delta sigma weight residual 1.714 1.610 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C LEU A 681 " pdb=" N ALA A 682 " ideal model delta sigma weight residual 1.329 1.236 0.093 1.86e-02 2.89e+03 2.51e+01 bond pdb=" O3A ANP A2407 " pdb=" PB ANP A2407 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C LEU A 976 " pdb=" N HIS A 977 " ideal model delta sigma weight residual 1.327 1.280 0.046 1.71e-02 3.42e+03 7.33e+00 ... (remaining 15575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 20465 2.05 - 4.09: 625 4.09 - 6.14: 62 6.14 - 8.19: 19 8.19 - 10.23: 3 Bond angle restraints: 21174 Sorted by residual: angle pdb=" N PRO A 861 " pdb=" CA PRO A 861 " pdb=" C PRO A 861 " ideal model delta sigma weight residual 113.65 105.93 7.72 1.35e+00 5.49e-01 3.27e+01 angle pdb=" O4' DC D 32 " pdb=" C4' DC D 32 " pdb=" C3' DC D 32 " ideal model delta sigma weight residual 106.00 102.67 3.33 6.00e-01 2.78e+00 3.08e+01 angle pdb=" O4' DC E 6 " pdb=" C4' DC E 6 " pdb=" C3' DC E 6 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT E 9 " pdb=" C4 DT E 9 " pdb=" O4 DT E 9 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT D 34 " pdb=" C4 DT D 34 " pdb=" O4 DT D 34 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 ... (remaining 21169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.87: 9002 30.87 - 61.74: 410 61.74 - 92.62: 32 92.62 - 123.49: 0 123.49 - 154.36: 1 Dihedral angle restraints: 9445 sinusoidal: 3986 harmonic: 5459 Sorted by residual: dihedral pdb=" CA ASP A 501 " pdb=" C ASP A 501 " pdb=" N ALA A 502 " pdb=" CA ALA A 502 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA SER A 444 " pdb=" C SER A 444 " pdb=" N ASN A 445 " pdb=" CA ASN A 445 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA THR A 932 " pdb=" C THR A 932 " pdb=" N TRP A 933 " pdb=" CA TRP A 933 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1866 0.057 - 0.115: 433 0.115 - 0.172: 51 0.172 - 0.230: 2 0.230 - 0.287: 4 Chirality restraints: 2356 Sorted by residual: chirality pdb=" C3' ANP A2407 " pdb=" C2' ANP A2407 " pdb=" C4' ANP A2407 " pdb=" O3' ANP A2407 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA VAL A 859 " pdb=" N VAL A 859 " pdb=" C VAL A 859 " pdb=" CB VAL A 859 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA LEU A 881 " pdb=" N LEU A 881 " pdb=" C LEU A 881 " pdb=" CB LEU A 881 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2353 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A2186 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.81e+00 pdb=" C LEU A2186 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A2186 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A2187 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 858 " 0.013 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C ARG A 858 " -0.048 2.00e-02 2.50e+03 pdb=" O ARG A 858 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 859 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 635 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C GLN A 635 " -0.047 2.00e-02 2.50e+03 pdb=" O GLN A 635 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 636 " 0.015 2.00e-02 2.50e+03 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 169 2.57 - 3.15: 13277 3.15 - 3.74: 22350 3.74 - 4.32: 30108 4.32 - 4.90: 50683 Nonbonded interactions: 116587 Sorted by model distance: nonbonded pdb=" O2B ANP A2407 " pdb="MG MG A2408 " model vdw 1.988 2.170 nonbonded pdb=" CD2 HIS A2101 " pdb="ZN ZN A2406 " model vdw 2.159 2.450 nonbonded pdb=" O THR A 519 " pdb=" NH1 ARG A 520 " model vdw 2.188 3.120 nonbonded pdb=" ND2 ASN A 897 " pdb=" OE2 GLU A1046 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU A1420 " pdb=" NH2 ARG A1721 " model vdw 2.207 3.120 ... (remaining 116582 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 group one per residue 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.150 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.009 0.649 15594 Z= 0.406 Angle : 0.862 17.770 21177 Z= 0.484 Chirality : 0.049 0.287 2356 Planarity : 0.005 0.067 2682 Dihedral : 16.767 154.361 5887 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 0.56 % Allowed : 12.32 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.16), residues: 1866 helix: -1.81 (0.17), residues: 661 sheet: -2.87 (0.29), residues: 207 loop : -3.54 (0.16), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 875 TYR 0.019 0.002 TYR A 395 PHE 0.030 0.002 PHE A1401 TRP 0.016 0.002 TRP A 692 HIS 0.011 0.002 HIS A2240 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.35 (15580) covalent geometry : angle 0.84629 / 0.48 (21174) hydrogen bonds : bond 0.16487 / 11.67 ( 528) hydrogen bonds : angle 7.33282 / 4.98 ( 1503) metal coordination : bond 0.18301 / 9.27 ( 14) metal coordination : angle 13.73556 / 10.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7750 (ptmt) REVERT: A 726 LEU cc_start: 0.8500 (mm) cc_final: 0.8220 (mm) REVERT: A 940 ARG cc_start: 0.7995 (ptm160) cc_final: 0.7442 (ttm-80) REVERT: A 1600 LYS cc_start: 0.7823 (tppt) cc_final: 0.7612 (tppp) REVERT: A 1798 PHE cc_start: 0.7505 (m-80) cc_final: 0.7134 (m-80) REVERT: A 2187 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8095 (p) outliers start: 9 outliers final: 6 residues processed: 189 average time/residue: 0.1479 time to fit residues: 39.2623 Evaluate side-chains 142 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2187 SER Chi-restraints excluded: chain A residue 2265 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN A 473 HIS ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 GLN A1202 HIS A1242 ASN ** A1269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 GLN A1342 ASN A1348 HIS A1409 GLN A1818 GLN A1822 ASN A1859 HIS ** A1922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2038 GLN A2101 HIS A2161 HIS A2211 GLN ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2271 GLN A2272 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111651 restraints weight = 28226.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114982 restraints weight = 15746.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115581 restraints weight = 9851.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115734 restraints weight = 8679.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115916 restraints weight = 8477.825| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15594 Z= 0.145 Angle : 0.680 8.455 21177 Z= 0.348 Chirality : 0.043 0.192 2356 Planarity : 0.006 0.059 2682 Dihedral : 12.325 160.982 2258 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.74 % Allowed : 13.63 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.18), residues: 1866 helix: -0.32 (0.19), residues: 674 sheet: -2.07 (0.30), residues: 234 loop : -2.98 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 520 TYR 0.020 0.001 TYR A 926 PHE 0.021 0.002 PHE A 864 TRP 0.018 0.002 TRP A1415 HIS 0.008 0.001 HIS A2240 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (15580) covalent geometry : angle 0.67973 / 0.35 (21174) hydrogen bonds : bond 0.05182 / 3.52 ( 528) hydrogen bonds : angle 5.17634 / 3.56 ( 1503) metal coordination : bond 0.01562 / 0.72 ( 14) metal coordination : angle 2.08494 / 1.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: A 490 LYS cc_start: 0.8052 (mmtp) cc_final: 0.7650 (ptmt) REVERT: A 644 GLU cc_start: 0.6883 (mp0) cc_final: 0.6455 (mp0) REVERT: A 726 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8023 (mm) REVERT: A 797 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8304 (ttpp) REVERT: A 809 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8708 (tt) REVERT: A 938 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 940 ARG cc_start: 0.7923 (ptm160) cc_final: 0.7353 (ttm-80) REVERT: A 1338 ARG cc_start: 0.7861 (mtt-85) cc_final: 0.7640 (mtm180) REVERT: A 1493 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7797 (pp) REVERT: A 1598 GLN cc_start: 0.8578 (tp40) cc_final: 0.8056 (tm-30) REVERT: A 1600 LYS cc_start: 0.7801 (tppt) cc_final: 0.7505 (tppp) REVERT: A 1829 ILE cc_start: 0.9004 (mm) cc_final: 0.8721 (mt) REVERT: A 2187 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.7878 (p) outliers start: 44 outliers final: 21 residues processed: 202 average time/residue: 0.1182 time to fit residues: 35.8634 Evaluate side-chains 167 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2093 MET Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2187 SER Chi-restraints excluded: chain A residue 2243 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: [49, 180, 182, 32, 79, 131, 156, 104, 13, 44, 70] chunk 49 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 HIS A1261 HIS A1269 HIS A1327 GLN ** A1922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2161 HIS ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.132478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112161 restraints weight = 28362.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114567 restraints weight = 15551.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115555 restraints weight = 10661.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115770 restraints weight = 10022.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116031 restraints weight = 8922.243| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15594 Z= 0.145 Angle : 0.644 9.056 21177 Z= 0.328 Chirality : 0.043 0.207 2356 Planarity : 0.005 0.056 2682 Dihedral : 12.056 161.553 2251 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.86 % Allowed : 16.86 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.19), residues: 1866 helix: 0.19 (0.20), residues: 677 sheet: -1.90 (0.31), residues: 240 loop : -2.77 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 568 TYR 0.018 0.002 TYR A 926 PHE 0.022 0.001 PHE A1798 TRP 0.014 0.001 TRP A1415 HIS 0.008 0.001 HIS A2240 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (15580) covalent geometry : angle 0.64351 / 0.33 (21174) hydrogen bonds : bond 0.04822 / 3.29 ( 528) hydrogen bonds : angle 4.92175 / 3.41 ( 1503) metal coordination : bond 0.00466 / 0.20 ( 14) metal coordination : angle 2.03853 / 1.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8382 (mmp) cc_final: 0.8073 (mmp) REVERT: A 378 LEU cc_start: 0.8865 (pt) cc_final: 0.8643 (pt) REVERT: A 490 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7646 (ptmt) REVERT: A 726 LEU cc_start: 0.8408 (mm) cc_final: 0.8030 (mm) REVERT: A 771 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 940 ARG cc_start: 0.7933 (ptm160) cc_final: 0.7339 (ttm-80) REVERT: A 1493 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7893 (pp) REVERT: A 1735 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8723 (tt) REVERT: A 1829 ILE cc_start: 0.8982 (mm) cc_final: 0.8692 (mt) outliers start: 46 outliers final: 28 residues processed: 184 average time/residue: 0.1178 time to fit residues: 32.6427 Evaluate side-chains 165 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2243 PHE Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: [131, 16, 161, 6, 45, 112, 137, 162, 88, 124, 166] chunk 131 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 HIS A1261 HIS A1427 HIS A1922 GLN ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109307 restraints weight = 27928.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.111376 restraints weight = 15879.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113337 restraints weight = 11009.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113242 restraints weight = 8440.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113467 restraints weight = 8395.971| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15594 Z= 0.273 Angle : 0.738 10.965 21177 Z= 0.375 Chirality : 0.046 0.217 2356 Planarity : 0.006 0.060 2682 Dihedral : 12.131 158.821 2250 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.92 % Allowed : 18.05 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.19), residues: 1866 helix: 0.24 (0.20), residues: 670 sheet: -1.97 (0.30), residues: 252 loop : -2.76 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1338 TYR 0.021 0.002 TYR A 395 PHE 0.025 0.002 PHE A1089 TRP 0.017 0.002 TRP A 692 HIS 0.009 0.001 HIS A2240 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.27 (15580) covalent geometry : angle 0.73776 / 0.38 (21174) hydrogen bonds : bond 0.05236 / 3.58 ( 528) hydrogen bonds : angle 5.10802 / 3.53 ( 1503) metal coordination : bond 0.01191 / 0.55 ( 14) metal coordination : angle 2.45449 / 2.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 147 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: A 378 LEU cc_start: 0.8922 (pt) cc_final: 0.8709 (pt) REVERT: A 490 LYS cc_start: 0.8024 (mmtp) cc_final: 0.7618 (ptmt) REVERT: A 726 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8050 (mm) REVERT: A 771 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 930 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7109 (pp30) REVERT: A 940 ARG cc_start: 0.7900 (ptm160) cc_final: 0.7372 (ttm-80) REVERT: A 1204 MET cc_start: 0.7796 (mmt) cc_final: 0.7446 (mmt) REVERT: A 1401 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7695 (m-10) REVERT: A 1493 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7940 (pp) REVERT: A 1735 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8755 (tt) REVERT: A 1798 PHE cc_start: 0.7391 (m-80) cc_final: 0.6514 (m-80) REVERT: A 2011 PRO cc_start: 0.7833 (Cg_endo) cc_final: 0.7523 (Cg_exo) REVERT: A 2080 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5960 (tm-30) outliers start: 63 outliers final: 40 residues processed: 195 average time/residue: 0.1113 time to fit residues: 33.1788 Evaluate side-chains 181 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1500 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1904 CYS Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: [118, 111, 30, 37, 126, 157, 82, 20, 62, 102, 52] chunk 118 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1922 GLN ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.131946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112089 restraints weight = 28180.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114429 restraints weight = 15931.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114793 restraints weight = 10936.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115169 restraints weight = 10664.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115478 restraints weight = 9539.724| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15594 Z= 0.146 Angle : 0.652 12.988 21177 Z= 0.330 Chirality : 0.043 0.193 2356 Planarity : 0.005 0.059 2682 Dihedral : 11.976 163.088 2250 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.11 % Allowed : 19.79 % Favored : 77.10 % 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: -1.94 (0.19), residues: 1866 helix: 0.54 (0.20), residues: 672 sheet: -1.76 (0.32), residues: 240 loop : -2.63 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1249 TYR 0.021 0.001 TYR A 926 PHE 0.019 0.001 PHE A 864 TRP 0.037 0.002 TRP A1227 HIS 0.007 0.001 HIS A2240 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (15580) covalent geometry : angle 0.65221 / 0.33 (21174) hydrogen bonds : bond 0.04565 / 3.11 ( 528) hydrogen bonds : angle 4.70328 / 3.25 ( 1503) metal coordination : bond 0.00328 / 0.15 ( 14) metal coordination : angle 1.26501 / 1.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8437 (mmp) cc_final: 0.8167 (mmp) REVERT: A 490 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7578 (ptmt) REVERT: A 726 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8023 (mm) REVERT: A 771 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 809 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8726 (tt) REVERT: A 940 ARG cc_start: 0.7935 (ptm160) cc_final: 0.7342 (ttm-80) REVERT: A 1204 MET cc_start: 0.7648 (mmt) cc_final: 0.7342 (mmt) REVERT: A 1401 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7684 (m-10) REVERT: A 1493 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7918 (pp) REVERT: A 1735 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 1798 PHE cc_start: 0.7463 (m-80) cc_final: 0.6679 (m-80) REVERT: A 2011 PRO cc_start: 0.7858 (Cg_endo) cc_final: 0.7575 (Cg_exo) outliers start: 50 outliers final: 32 residues processed: 187 average time/residue: 0.1110 time to fit residues: 31.5023 Evaluate side-chains 174 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1922 GLN Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2083 HIS Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: [134, 47, 159, 67, 102, 154, 146, 171, 96, 94, 77] chunk 134 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 chunk 154 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1827 GLN ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110555 restraints weight = 28161.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113204 restraints weight = 15898.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114605 restraints weight = 10696.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114647 restraints weight = 9504.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.114767 restraints weight = 8866.442| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15594 Z= 0.172 Angle : 0.649 10.737 21177 Z= 0.330 Chirality : 0.043 0.212 2356 Planarity : 0.005 0.059 2682 Dihedral : 11.939 163.056 2250 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 3.73 % Allowed : 20.04 % Favored : 76.23 % 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: -1.87 (0.19), residues: 1866 helix: 0.62 (0.20), residues: 672 sheet: -1.73 (0.32), residues: 240 loop : -2.60 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1224 TYR 0.023 0.002 TYR A 522 PHE 0.019 0.002 PHE A1089 TRP 0.050 0.002 TRP A1227 HIS 0.007 0.001 HIS A2240 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (15580) covalent geometry : angle 0.64908 / 0.33 (21174) hydrogen bonds : bond 0.04577 / 3.12 ( 528) hydrogen bonds : angle 4.69612 / 3.25 ( 1503) metal coordination : bond 0.00534 / 0.25 ( 14) metal coordination : angle 1.37601 / 1.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 142 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 LYS cc_start: 0.8009 (mmtp) cc_final: 0.7563 (ptmt) REVERT: A 726 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8003 (mm) REVERT: A 771 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 809 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8672 (tt) REVERT: A 874 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6780 (tpt) REVERT: A 940 ARG cc_start: 0.7927 (ptm160) cc_final: 0.7329 (ttm-80) REVERT: A 1338 ARG cc_start: 0.7443 (mtm180) cc_final: 0.6760 (mtm180) REVERT: A 1401 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: A 1493 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7849 (pp) REVERT: A 1536 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: A 1735 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8692 (tt) REVERT: A 1798 PHE cc_start: 0.7488 (m-80) cc_final: 0.6659 (m-80) REVERT: A 2011 PRO cc_start: 0.7816 (Cg_endo) cc_final: 0.7520 (Cg_exo) outliers start: 60 outliers final: 37 residues processed: 187 average time/residue: 0.1024 time to fit residues: 29.4370 Evaluate side-chains 182 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1550 MET Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2083 HIS Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2102 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: [144, 33, 120, 4, 35, 1, 49, 184, 136, 155, 125] chunk 144 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 HIS A1827 GLN ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2158 ASN ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.133494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112717 restraints weight = 28095.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114608 restraints weight = 16660.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115837 restraints weight = 12677.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116115 restraints weight = 9798.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116423 restraints weight = 9904.964| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15594 Z= 0.142 Angle : 0.630 10.178 21177 Z= 0.318 Chirality : 0.043 0.244 2356 Planarity : 0.005 0.058 2682 Dihedral : 11.853 164.695 2250 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.36 % Allowed : 20.78 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.67 (0.19), residues: 1866 helix: 0.80 (0.21), residues: 673 sheet: -1.65 (0.33), residues: 234 loop : -2.49 (0.18), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1338 TYR 0.021 0.002 TYR A 926 PHE 0.018 0.001 PHE A1089 TRP 0.052 0.002 TRP A1227 HIS 0.009 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (15580) covalent geometry : angle 0.62972 / 0.32 (21174) hydrogen bonds : bond 0.04311 / 2.93 ( 528) hydrogen bonds : angle 4.54794 / 3.14 ( 1503) metal coordination : bond 0.00319 / 0.15 ( 14) metal coordination : angle 1.12548 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8496 (mmp) cc_final: 0.8252 (mmp) REVERT: A 490 LYS cc_start: 0.7957 (mmtp) cc_final: 0.7534 (ptmt) REVERT: A 771 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7233 (tm-30) REVERT: A 809 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8744 (tt) REVERT: A 874 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6737 (tpt) REVERT: A 940 ARG cc_start: 0.8013 (ptm160) cc_final: 0.7372 (ttm-80) REVERT: A 1338 ARG cc_start: 0.7336 (mtm180) cc_final: 0.6818 (mtm180) REVERT: A 1401 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7680 (m-10) REVERT: A 1493 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7731 (pp) REVERT: A 1536 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: A 1735 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8728 (tt) REVERT: A 1798 PHE cc_start: 0.7496 (m-80) cc_final: 0.6676 (m-80) REVERT: A 2011 PRO cc_start: 0.7786 (Cg_endo) cc_final: 0.7534 (Cg_exo) REVERT: A 2027 LYS cc_start: 0.6792 (mmmt) cc_final: 0.6285 (mmtm) outliers start: 54 outliers final: 31 residues processed: 191 average time/residue: 0.1077 time to fit residues: 31.8335 Evaluate side-chains 175 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1550 MET Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2083 HIS Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2102 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: [86, 162, 66, 7, 132, 129, 32, 113, 131, 101, 155] chunk 86 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 132 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 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 = 0.3770 r_free = 0.3770 target = 0.132325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112080 restraints weight = 27990.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114442 restraints weight = 15379.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114821 restraints weight = 10615.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115310 restraints weight = 10505.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115577 restraints weight = 9329.945| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15594 Z= 0.151 Angle : 0.636 9.446 21177 Z= 0.321 Chirality : 0.043 0.179 2356 Planarity : 0.005 0.057 2682 Dihedral : 11.804 164.960 2250 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.17 % Allowed : 21.34 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.19), residues: 1866 helix: 0.86 (0.21), residues: 674 sheet: -1.64 (0.32), residues: 243 loop : -2.44 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1100 TYR 0.019 0.002 TYR A 926 PHE 0.019 0.001 PHE A1089 TRP 0.059 0.002 TRP A1227 HIS 0.007 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (15580) covalent geometry : angle 0.63565 / 0.32 (21174) hydrogen bonds : bond 0.04263 / 2.90 ( 528) hydrogen bonds : angle 4.49406 / 3.11 ( 1503) metal coordination : bond 0.00380 / 0.18 ( 14) metal coordination : angle 1.13193 / 0.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8524 (mmp) cc_final: 0.8256 (mmp) REVERT: A 490 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7531 (ptmt) REVERT: A 726 LEU cc_start: 0.8303 (mm) cc_final: 0.8014 (mm) REVERT: A 771 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7205 (tm-30) REVERT: A 809 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8707 (tt) REVERT: A 874 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6739 (tpt) REVERT: A 940 ARG cc_start: 0.8011 (ptm160) cc_final: 0.7355 (ttm-80) REVERT: A 1401 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: A 1493 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7768 (pp) REVERT: A 1536 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: A 1735 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8718 (tt) REVERT: A 1798 PHE cc_start: 0.7490 (m-80) cc_final: 0.6660 (m-80) REVERT: A 2011 PRO cc_start: 0.7762 (Cg_endo) cc_final: 0.7516 (Cg_exo) outliers start: 51 outliers final: 36 residues processed: 177 average time/residue: 0.1055 time to fit residues: 29.0154 Evaluate side-chains 174 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1550 MET Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2083 HIS Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2102 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: [110, 136, 158, 47, 55, 25, 64, 9, 154, 70, 143] chunk 110 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 HIS ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.111653 restraints weight = 28129.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113791 restraints weight = 16641.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115236 restraints weight = 11776.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115421 restraints weight = 10148.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115607 restraints weight = 9569.914| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15594 Z= 0.166 Angle : 0.646 10.180 21177 Z= 0.327 Chirality : 0.043 0.183 2356 Planarity : 0.005 0.057 2682 Dihedral : 11.784 164.906 2250 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.17 % Allowed : 21.59 % Favored : 75.23 % 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: -1.54 (0.19), residues: 1866 helix: 0.94 (0.21), residues: 670 sheet: -1.64 (0.32), residues: 243 loop : -2.41 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1932 TYR 0.020 0.002 TYR A 926 PHE 0.020 0.002 PHE A1089 TRP 0.035 0.002 TRP A1227 HIS 0.007 0.001 HIS A2240 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (15580) covalent geometry : angle 0.64541 / 0.33 (21174) hydrogen bonds : bond 0.04295 / 2.92 ( 528) hydrogen bonds : angle 4.49820 / 3.11 ( 1503) metal coordination : bond 0.00529 / 0.24 ( 14) metal coordination : angle 1.30554 / 1.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8521 (mmp) cc_final: 0.8208 (mmp) REVERT: A 490 LYS cc_start: 0.7961 (mmtp) cc_final: 0.7537 (ptmt) REVERT: A 726 LEU cc_start: 0.8354 (mm) cc_final: 0.8051 (mm) REVERT: A 771 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7203 (tm-30) REVERT: A 809 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8741 (tt) REVERT: A 874 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6742 (tpt) REVERT: A 940 ARG cc_start: 0.8003 (ptm160) cc_final: 0.7360 (ttm-80) REVERT: A 1401 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7682 (m-10) REVERT: A 1493 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7844 (pp) REVERT: A 1536 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: A 1735 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8750 (tt) REVERT: A 1798 PHE cc_start: 0.7517 (m-80) cc_final: 0.6682 (m-80) REVERT: A 2011 PRO cc_start: 0.7755 (Cg_endo) cc_final: 0.7512 (Cg_exo) outliers start: 51 outliers final: 42 residues processed: 176 average time/residue: 0.1145 time to fit residues: 31.3492 Evaluate side-chains 183 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1550 MET Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2083 HIS Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2102 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: [82, 76, 187, 52, 31, 144, 188, 80, 124, 45, 159] chunk 82 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 188 optimal weight: 40.0000 chunk 80 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1922 GLN ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.131247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111084 restraints weight = 28200.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113024 restraints weight = 16015.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114725 restraints weight = 11591.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114925 restraints weight = 10261.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114990 restraints weight = 8992.625| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15594 Z= 0.196 Angle : 0.671 10.027 21177 Z= 0.340 Chirality : 0.044 0.185 2356 Planarity : 0.005 0.057 2682 Dihedral : 11.797 164.412 2250 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.17 % Allowed : 21.78 % Favored : 75.05 % 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: -1.58 (0.19), residues: 1866 helix: 0.85 (0.20), residues: 679 sheet: -1.68 (0.32), residues: 244 loop : -2.41 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1932 TYR 0.020 0.002 TYR A 522 PHE 0.021 0.002 PHE A1089 TRP 0.024 0.002 TRP A1227 HIS 0.008 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (15580) covalent geometry : angle 0.67030 / 0.34 (21174) hydrogen bonds : bond 0.04442 / 3.02 ( 528) hydrogen bonds : angle 4.56365 / 3.15 ( 1503) metal coordination : bond 0.00679 / 0.32 ( 14) metal coordination : angle 1.58645 / 1.49 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 141 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8576 (mmp) cc_final: 0.8308 (mmp) REVERT: A 490 LYS cc_start: 0.7966 (mmtp) cc_final: 0.7544 (ptmt) REVERT: A 726 LEU cc_start: 0.8416 (mm) cc_final: 0.8117 (mm) REVERT: A 771 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7283 (tm-30) REVERT: A 809 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8763 (tt) REVERT: A 874 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6801 (tpt) REVERT: A 930 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.6974 (pp30) REVERT: A 940 ARG cc_start: 0.7919 (ptm160) cc_final: 0.7318 (ttm-80) REVERT: A 1401 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7699 (m-10) REVERT: A 1493 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7936 (pp) REVERT: A 1536 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: A 1735 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8770 (tt) REVERT: A 1798 PHE cc_start: 0.7434 (m-80) cc_final: 0.6666 (m-80) REVERT: A 2011 PRO cc_start: 0.7774 (Cg_endo) cc_final: 0.7535 (Cg_exo) outliers start: 51 outliers final: 44 residues processed: 180 average time/residue: 0.1117 time to fit residues: 30.9889 Evaluate side-chains 190 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1550 MET Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1922 GLN Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2083 HIS Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2102 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: [107, 89, 144, 63, 141, 91, 92, 69, 5, 104, 26] chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 0.0970 chunk 63 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 104 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 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 = 0.3755 r_free = 0.3755 target = 0.131311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111183 restraints weight = 27925.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113353 restraints weight = 15781.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115011 restraints weight = 11236.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.115085 restraints weight = 9944.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115253 restraints weight = 8987.860| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.427 15594 Z= 0.314 Angle : 0.845 65.898 21177 Z= 0.471 Chirality : 0.043 0.186 2356 Planarity : 0.006 0.185 2682 Dihedral : 11.801 164.500 2250 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 3.36 % Allowed : 21.66 % Favored : 74.98 % 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: -1.58 (0.19), residues: 1866 helix: 0.85 (0.20), residues: 679 sheet: -1.68 (0.32), residues: 244 loop : -2.41 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1932 TYR 0.019 0.002 TYR A 926 PHE 0.021 0.002 PHE A1089 TRP 0.020 0.001 TRP A1227 HIS 0.007 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.31 (15580) covalent geometry : angle 0.84490 / 0.47 (21174) hydrogen bonds : bond 0.04397 / 2.99 ( 528) hydrogen bonds : angle 4.55945 / 3.15 ( 1503) metal coordination : bond 0.00621 / 0.28 ( 14) metal coordination : angle 1.57834 / 1.49 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2072.77 seconds wall clock time: 36 minutes 49.33 seconds (2209.33 seconds total)