Starting phenix.real_space_refine on Tue May 20 11:41:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8izl_35864/05_2025/8izl_35864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8izl_35864/05_2025/8izl_35864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8izl_35864/05_2025/8izl_35864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8izl_35864/05_2025/8izl_35864.map" model { file = "/net/cci-nas-00/data/ceres_data/8izl_35864/05_2025/8izl_35864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8izl_35864/05_2025/8izl_35864.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1459 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 108 5.16 5 C 11882 2.51 5 N 3168 2.21 5 O 3452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18612 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 459 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "E" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 440 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 517 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 680 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "A" Number of atoms: 16514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2067, 16514 Classifications: {'peptide': 2067} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 102, 'TRANS': 1964} Chain breaks: 13 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11235 SG CYS A1187 61.628 34.367 84.778 1.00 61.98 S ATOM 11260 SG CYS A1190 63.351 36.726 87.965 1.00 63.63 S ATOM 10893 SG CYS A1142 75.148 38.838 70.096 1.00 49.70 S ATOM 12598 SG CYS A1379 74.361 36.441 72.802 1.00 69.42 S ATOM 12604 SG CYS A1380 72.136 39.519 72.185 1.00 66.62 S Time building chain proxies: 10.97, per 1000 atoms: 0.59 Number of scatterers: 18612 At special positions: 0 Unit cell: (103.88, 171.19, 143.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 108 16.00 O 3452 8.00 N 3168 7.00 C 11882 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: 4.47 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A1374 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A1372 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1187 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1190 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1142 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1379 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1380 " Number of angles added : 1 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4472 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 12 sheets defined 63.6% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'D' and resid 218 through 243 removed outlier: 3.727A pdb=" N MET D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 271 removed outlier: 4.166A pdb=" N MET D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 267 Processing helix chain 'E' and resid 268 through 273 removed outlier: 3.817A pdb=" N THR E 272 " --> pdb=" O GLY E 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 244 removed outlier: 3.537A pdb=" N GLN B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 275 removed outlier: 3.531A pdb=" N THR B 258 " --> pdb=" O ASN B 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 243 removed outlier: 3.621A pdb=" N MET C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 272 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.705A pdb=" N LEU A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.650A pdb=" N LEU A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 42 " --> pdb=" O PRO A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 37 through 42' Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.968A pdb=" N LEU A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 175 through 199 Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 265 through 285 removed outlier: 4.365A pdb=" N ARG A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.715A pdb=" N ILE A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.652A pdb=" N ILE A 312 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.946A pdb=" N GLN A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 361 through 362 No H-bonds generated for 'chain 'A' and resid 361 through 362' Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.946A pdb=" N ARG A 366 " --> pdb=" O CYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.777A pdb=" N LYS A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.670A pdb=" N ILE A 419 " --> pdb=" O HIS A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 444 through 451 Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.547A pdb=" N SER A 456 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 4.371A pdb=" N ASP A 471 " --> pdb=" O PRO A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 493 through 504 removed outlier: 3.517A pdb=" N ILE A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLN A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.762A pdb=" N TYR A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 585 Processing helix chain 'A' and resid 586 through 590 removed outlier: 3.760A pdb=" N MET A 590 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 678 through 694 Proline residue: A 684 - end of helix Processing helix chain 'A' and resid 700 through 707 removed outlier: 4.176A pdb=" N LEU A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 768 removed outlier: 3.553A pdb=" N TRP A 753 " --> pdb=" O CYS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 820 removed outlier: 4.187A pdb=" N LEU A 808 " --> pdb=" O LYS A 804 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 809 " --> pdb=" O ALA A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 857 removed outlier: 3.911A pdb=" N ASN A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 887 removed outlier: 3.516A pdb=" N SER A 873 " --> pdb=" O CYS A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 912 Processing helix chain 'A' and resid 920 through 928 Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.604A pdb=" N ILE A 933 " --> pdb=" O HIS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 961 through 977 removed outlier: 3.659A pdb=" N SER A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 989 removed outlier: 3.628A pdb=" N LEU A 984 " --> pdb=" O ASP A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1003 removed outlier: 3.635A pdb=" N ALA A1001 " --> pdb=" O TRP A 997 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A1003 " --> pdb=" O THR A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1031 removed outlier: 3.510A pdb=" N PHE A1018 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1057 Processing helix chain 'A' and resid 1062 through 1072 Processing helix chain 'A' and resid 1073 through 1084 Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1102 through 1111 Processing helix chain 'A' and resid 1111 through 1122 removed outlier: 3.898A pdb=" N GLU A1122 " --> pdb=" O SER A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1137 removed outlier: 3.771A pdb=" N LEU A1134 " --> pdb=" O GLN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1155 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1171 through 1176 removed outlier: 3.524A pdb=" N VAL A1176 " --> pdb=" O PRO A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1260 Processing helix chain 'A' and resid 1262 through 1275 Processing helix chain 'A' and resid 1280 through 1288 Processing helix chain 'A' and resid 1317 through 1321 removed outlier: 3.546A pdb=" N PHE A1320 " --> pdb=" O PHE A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1358 Processing helix chain 'A' and resid 1415 through 1432 Processing helix chain 'A' and resid 1438 through 1459 removed outlier: 3.662A pdb=" N ILE A1443 " --> pdb=" O LEU A1439 " (cutoff:3.500A) Proline residue: A1444 - end of helix Processing helix chain 'A' and resid 1481 through 1486 Processing helix chain 'A' and resid 1489 through 1512 removed outlier: 4.851A pdb=" N TYR A1507 " --> pdb=" O LEU A1503 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLN A1508 " --> pdb=" O GLU A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1531 Processing helix chain 'A' and resid 1536 through 1545 Processing helix chain 'A' and resid 1545 through 1555 Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1570 through 1593 Processing helix chain 'A' and resid 1610 through 1627 Processing helix chain 'A' and resid 1640 through 1643 Processing helix chain 'A' and resid 1644 through 1657 removed outlier: 3.838A pdb=" N LEU A1652 " --> pdb=" O LEU A1648 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A1653 " --> pdb=" O THR A1649 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A1656 " --> pdb=" O LEU A1652 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1675 removed outlier: 4.246A pdb=" N ILE A1669 " --> pdb=" O GLU A1665 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A1673 " --> pdb=" O ILE A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1689 through 1699 Processing helix chain 'A' and resid 1699 through 1711 Processing helix chain 'A' and resid 1775 through 1781 Processing helix chain 'A' and resid 1789 through 1801 removed outlier: 4.246A pdb=" N SER A1795 " --> pdb=" O TYR A1791 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A1796 " --> pdb=" O LYS A1792 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR A1799 " --> pdb=" O SER A1795 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1828 removed outlier: 3.872A pdb=" N PHE A1827 " --> pdb=" O LEU A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1840 through 1844 removed outlier: 3.606A pdb=" N GLU A1843 " --> pdb=" O ASN A1840 " (cutoff:3.500A) Processing helix chain 'A' and resid 1854 through 1859 removed outlier: 4.186A pdb=" N GLU A1859 " --> pdb=" O THR A1855 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1868 removed outlier: 3.610A pdb=" N ALA A1868 " --> pdb=" O ARG A1864 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1892 removed outlier: 3.581A pdb=" N THR A1891 " --> pdb=" O ASN A1887 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1907 Processing helix chain 'A' and resid 1930 through 1943 Processing helix chain 'A' and resid 1958 through 1972 removed outlier: 3.976A pdb=" N PHE A1972 " --> pdb=" O VAL A1968 " (cutoff:3.500A) Processing helix chain 'A' and resid 2005 through 2020 removed outlier: 3.641A pdb=" N ALA A2009 " --> pdb=" O SER A2005 " (cutoff:3.500A) Processing helix chain 'A' and resid 2025 through 2054 removed outlier: 3.741A pdb=" N GLU A2038 " --> pdb=" O ARG A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2069 removed outlier: 3.683A pdb=" N ASN A2063 " --> pdb=" O TYR A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2074 through 2079 Processing helix chain 'A' and resid 2086 through 2102 removed outlier: 3.599A pdb=" N THR A2099 " --> pdb=" O ALA A2095 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2113 Processing helix chain 'A' and resid 2128 through 2150 Processing helix chain 'A' and resid 2155 through 2168 removed outlier: 3.633A pdb=" N LEU A2168 " --> pdb=" O GLN A2164 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2176 removed outlier: 3.807A pdb=" N ASP A2175 " --> pdb=" O ARG A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2186 Processing helix chain 'A' and resid 2194 through 2206 Processing helix chain 'A' and resid 2207 through 2210 Processing helix chain 'A' and resid 2214 through 2232 Processing sheet with id=AA1, first strand: chain 'C' and resid 274 through 277 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.065A pdb=" N ALA A 87 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR A 234 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA4, first strand: chain 'A' and resid 549 through 552 Processing sheet with id=AA5, first strand: chain 'A' and resid 780 through 790 Processing sheet with id=AA6, first strand: chain 'A' and resid 710 through 712 Processing sheet with id=AA7, first strand: chain 'A' and resid 835 through 838 removed outlier: 3.575A pdb=" N PHE A 836 " --> pdb=" O PHE A 843 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1180 through 1182 Processing sheet with id=AA9, first strand: chain 'A' and resid 1206 through 1207 removed outlier: 3.664A pdb=" N ILE A1206 " --> pdb=" O SER A1365 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1598 through 1601 removed outlier: 6.300A pdb=" N ILE A1598 " --> pdb=" O THR A1679 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR A1681 " --> pdb=" O ILE A1598 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A1600 " --> pdb=" O TYR A1681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1741 through 1745 removed outlier: 3.829A pdb=" N PHE A1741 " --> pdb=" O ARG A1980 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A1976 " --> pdb=" O LEU A1745 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR A1975 " --> pdb=" O THR A1996 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR A1996 " --> pdb=" O THR A1975 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A1991 " --> pdb=" O ALA A1954 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY A1948 " --> pdb=" O LEU A1997 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N CYS A1911 " --> pdb=" O LYS A1945 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLY A1947 " --> pdb=" O CYS A1911 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU A1913 " --> pdb=" O GLY A1947 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A1949 " --> pdb=" O LEU A1913 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HIS A1915 " --> pdb=" O LEU A1949 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE A1951 " --> pdb=" O HIS A1915 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A1809 " --> pdb=" O LEU A1913 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N HIS A1915 " --> pdb=" O ALA A1809 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A1811 " --> pdb=" O HIS A1915 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2170 through 2171 removed outlier: 3.655A pdb=" N ILE A2211 " --> pdb=" O PHE A2171 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 3036 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: 7.75 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3045 1.29 - 1.42: 4598 1.42 - 1.56: 11144 1.56 - 1.69: 2 1.69 - 1.82: 177 Bond restraints: 18966 Sorted by residual: bond pdb=" C ALA A1932 " pdb=" N GLN A1933 " ideal model delta sigma weight residual 1.334 1.233 0.102 1.33e-02 5.65e+03 5.83e+01 bond pdb=" C PRO A1845 " pdb=" O PRO A1845 " ideal model delta sigma weight residual 1.240 1.158 0.082 1.12e-02 7.97e+03 5.40e+01 bond pdb=" C GLU A 200 " pdb=" N LEU A 201 " ideal model delta sigma weight residual 1.331 1.417 -0.086 1.40e-02 5.10e+03 3.81e+01 bond pdb=" C GLN A1933 " pdb=" N VAL A1934 " ideal model delta sigma weight residual 1.335 1.402 -0.066 1.21e-02 6.83e+03 3.02e+01 bond pdb=" C PRO A 38 " pdb=" N ASP A 39 " ideal model delta sigma weight residual 1.334 1.257 0.078 1.46e-02 4.69e+03 2.84e+01 ... (remaining 18961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 24980 2.36 - 4.72: 652 4.72 - 7.07: 80 7.07 - 9.43: 12 9.43 - 11.79: 4 Bond angle restraints: 25728 Sorted by residual: angle pdb=" N LEU B 235 " pdb=" CA LEU B 235 " pdb=" C LEU B 235 " ideal model delta sigma weight residual 111.28 101.42 9.86 1.09e+00 8.42e-01 8.19e+01 angle pdb=" N LEU A 361 " pdb=" CA LEU A 361 " pdb=" C LEU A 361 " ideal model delta sigma weight residual 112.72 103.43 9.29 1.14e+00 7.69e-01 6.65e+01 angle pdb=" C VAL A1388 " pdb=" N VAL A1389 " pdb=" CA VAL A1389 " ideal model delta sigma weight residual 122.43 114.76 7.67 1.26e+00 6.30e-01 3.71e+01 angle pdb=" N ILE A 455 " pdb=" CA ILE A 455 " pdb=" C ILE A 455 " ideal model delta sigma weight residual 111.09 103.63 7.46 1.25e+00 6.40e-01 3.56e+01 angle pdb=" N VAL A1636 " pdb=" CA VAL A1636 " pdb=" C VAL A1636 " ideal model delta sigma weight residual 113.20 107.55 5.65 9.60e-01 1.09e+00 3.47e+01 ... (remaining 25723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10153 17.96 - 35.92: 1087 35.92 - 53.88: 276 53.88 - 71.84: 37 71.84 - 89.79: 15 Dihedral angle restraints: 11568 sinusoidal: 4689 harmonic: 6879 Sorted by residual: dihedral pdb=" CA LEU A 849 " pdb=" C LEU A 849 " pdb=" N THR A 850 " pdb=" CA THR A 850 " ideal model delta harmonic sigma weight residual 180.00 -156.31 -23.69 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LEU A 698 " pdb=" C LEU A 698 " pdb=" N PHE A 699 " pdb=" CA PHE A 699 " ideal model delta harmonic sigma weight residual 180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C ARG A1077 " pdb=" N ARG A1077 " pdb=" CA ARG A1077 " pdb=" CB ARG A1077 " ideal model delta harmonic sigma weight residual -122.60 -113.33 -9.27 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 11565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2404 0.055 - 0.110: 479 0.110 - 0.165: 103 0.165 - 0.220: 26 0.220 - 0.275: 7 Chirality restraints: 3019 Sorted by residual: chirality pdb=" CA LEU B 235 " pdb=" N LEU B 235 " pdb=" C LEU B 235 " pdb=" CB LEU B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA MET A1035 " pdb=" N MET A1035 " pdb=" C MET A1035 " pdb=" CB MET A1035 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL E 259 " pdb=" N VAL E 259 " pdb=" C VAL E 259 " pdb=" CB VAL E 259 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 3016 not shown) Planarity restraints: 3239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 358 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C THR A 358 " 0.079 2.00e-02 2.50e+03 pdb=" O THR A 358 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA A 359 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1790 " 0.025 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP A1790 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A1790 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A1790 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1790 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1790 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1790 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1790 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1790 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1790 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 246 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C GLY C 246 " 0.055 2.00e-02 2.50e+03 pdb=" O GLY C 246 " -0.021 2.00e-02 2.50e+03 pdb=" N SER C 247 " -0.018 2.00e-02 2.50e+03 ... (remaining 3236 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3039 2.76 - 3.29: 19130 3.29 - 3.83: 32201 3.83 - 4.36: 38251 4.36 - 4.90: 64753 Nonbonded interactions: 157374 Sorted by model distance: nonbonded pdb=" O LEU A1272 " pdb=" OG1 THR A1275 " model vdw 2.222 3.040 nonbonded pdb=" O GLY A1816 " pdb=" OH TYR A1835 " model vdw 2.224 3.040 nonbonded pdb=" OG SER A 952 " pdb=" OD1 ASP A1171 " model vdw 2.254 3.040 nonbonded pdb=" NE2 HIS A 13 " pdb=" O THR A 862 " model vdw 2.260 3.120 nonbonded pdb=" OE1 GLN A 118 " pdb=" OG SER A 167 " model vdw 2.271 3.040 ... (remaining 157369 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 218 through 277) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 47.820 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 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 : 0.008 0.547 18973 Z= 0.397 Angle : 0.834 11.790 25729 Z= 0.548 Chirality : 0.050 0.275 3019 Planarity : 0.005 0.063 3239 Dihedral : 15.748 89.794 7096 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.19 % Allowed : 24.99 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2309 helix: 1.04 (0.14), residues: 1298 sheet: -0.88 (0.43), residues: 144 loop : -0.41 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A1790 HIS 0.005 0.001 HIS B 234 PHE 0.014 0.001 PHE A2201 TYR 0.015 0.001 TYR A1409 ARG 0.007 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.14346 ( 1052) hydrogen bonds : angle 6.15369 ( 3036) metal coordination : bond 0.29465 ( 7) metal coordination : angle 6.36879 ( 1) covalent geometry : bond 0.00540 (18966) covalent geometry : angle 0.83327 (25728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 558 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 219 ASN cc_start: 0.8420 (m-40) cc_final: 0.7894 (m-40) REVERT: D 260 LYS cc_start: 0.8606 (tptp) cc_final: 0.8396 (tptp) REVERT: E 234 HIS cc_start: 0.7797 (m170) cc_final: 0.7501 (m-70) REVERT: E 235 LEU cc_start: 0.8284 (mt) cc_final: 0.8072 (mt) REVERT: E 236 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7053 (tp30) REVERT: E 252 ILE cc_start: 0.8266 (tp) cc_final: 0.7995 (tp) REVERT: B 238 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8470 (mmtt) REVERT: B 251 GLN cc_start: 0.8805 (tt0) cc_final: 0.8497 (tt0) REVERT: B 254 ASN cc_start: 0.8278 (t0) cc_final: 0.8070 (t0) REVERT: B 273 VAL cc_start: 0.8556 (t) cc_final: 0.8342 (t) REVERT: C 233 GLN cc_start: 0.8133 (mt0) cc_final: 0.7801 (mt0) REVERT: C 235 LEU cc_start: 0.8277 (mt) cc_final: 0.8009 (mt) REVERT: C 238 LYS cc_start: 0.8871 (mttt) cc_final: 0.8588 (mttt) REVERT: C 249 VAL cc_start: 0.7836 (t) cc_final: 0.7532 (m) REVERT: C 250 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8247 (m) REVERT: A 50 LYS cc_start: 0.8285 (tmtt) cc_final: 0.8056 (tttp) REVERT: A 436 MET cc_start: 0.7323 (mtp) cc_final: 0.6944 (mtm) REVERT: A 499 GLN cc_start: 0.7360 (tp40) cc_final: 0.7137 (mm-40) REVERT: A 505 ASN cc_start: 0.8316 (t0) cc_final: 0.7881 (t0) REVERT: A 601 LYS cc_start: 0.8147 (ptmt) cc_final: 0.7873 (pttp) REVERT: A 780 ASN cc_start: 0.7764 (t0) cc_final: 0.7523 (t0) REVERT: A 994 LYS cc_start: 0.8372 (mptt) cc_final: 0.8091 (mtmm) REVERT: A 1048 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6780 (tt0) REVERT: A 1259 PHE cc_start: 0.6963 (m-80) cc_final: 0.6737 (m-80) REVERT: A 1419 MET cc_start: 0.7344 (mtp) cc_final: 0.7129 (mtt) REVERT: A 1580 MET cc_start: 0.8419 (mmm) cc_final: 0.8218 (tpp) REVERT: A 1623 LEU cc_start: 0.8655 (mm) cc_final: 0.8414 (mt) REVERT: A 1642 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7782 (tm-30) REVERT: A 1648 LEU cc_start: 0.8563 (tp) cc_final: 0.8279 (tm) REVERT: A 1666 LYS cc_start: 0.8023 (mttm) cc_final: 0.7804 (mppt) REVERT: A 1667 THR cc_start: 0.8628 (p) cc_final: 0.8198 (p) REVERT: A 1671 ARG cc_start: 0.8163 (ttp80) cc_final: 0.6948 (ttm110) REVERT: A 1675 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7127 (pp20) REVERT: A 1693 LEU cc_start: 0.7320 (tp) cc_final: 0.6960 (tm) REVERT: A 1696 ILE cc_start: 0.8821 (mt) cc_final: 0.8520 (mm) REVERT: A 1835 TYR cc_start: 0.7324 (t80) cc_final: 0.7098 (t80) REVERT: A 1945 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7874 (tptt) REVERT: A 1946 PRO cc_start: 0.8626 (Cg_exo) cc_final: 0.7475 (Cg_endo) REVERT: A 2044 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7567 (tm-30) REVERT: A 2049 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8174 (ttpp) REVERT: A 2052 SER cc_start: 0.8616 (m) cc_final: 0.8070 (p) REVERT: A 2098 ILE cc_start: 0.8602 (mt) cc_final: 0.8211 (mm) REVERT: A 2110 LYS cc_start: 0.8430 (tttt) cc_final: 0.8010 (tptt) REVERT: A 2192 LEU cc_start: 0.8200 (mt) cc_final: 0.7923 (mt) REVERT: A 2193 LYS cc_start: 0.7878 (tppt) cc_final: 0.7449 (mptt) REVERT: A 2204 LEU cc_start: 0.8448 (mt) cc_final: 0.8232 (tm) REVERT: A 2229 ILE cc_start: 0.7883 (mt) cc_final: 0.7645 (mp) outliers start: 25 outliers final: 6 residues processed: 575 average time/residue: 1.2034 time to fit residues: 786.8017 Evaluate side-chains 490 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 482 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain A residue 1048 GLU Chi-restraints excluded: chain A residue 1625 ILE Chi-restraints excluded: chain A residue 1652 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 0.0270 chunk 70 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 210 optimal weight: 0.0060 overall best weight: 0.4854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN A 304 GLN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 676 ASN A 769 ASN ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 HIS A 887 ASN ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN A1778 HIS A1847 GLN A2011 ASN ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.129061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114368 restraints weight = 37529.124| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.94 r_work: 0.3665 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18973 Z= 0.148 Angle : 0.672 9.252 25729 Z= 0.336 Chirality : 0.043 0.179 3019 Planarity : 0.005 0.054 3239 Dihedral : 4.580 47.570 2547 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.77 % Allowed : 26.66 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2309 helix: 1.40 (0.14), residues: 1328 sheet: -1.05 (0.42), residues: 154 loop : -0.22 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1790 HIS 0.007 0.001 HIS B 234 PHE 0.022 0.002 PHE A 394 TYR 0.032 0.002 TYR A 540 ARG 0.007 0.001 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 1052) hydrogen bonds : angle 4.80094 ( 3036) metal coordination : bond 0.01796 ( 7) metal coordination : angle 5.18874 ( 1) covalent geometry : bond 0.00331 (18966) covalent geometry : angle 0.67081 (25728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 490 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 219 ASN cc_start: 0.8034 (m-40) cc_final: 0.7577 (m-40) REVERT: D 260 LYS cc_start: 0.9021 (tptp) cc_final: 0.8679 (tptp) REVERT: E 234 HIS cc_start: 0.7549 (m170) cc_final: 0.7315 (m-70) REVERT: E 252 ILE cc_start: 0.8408 (tp) cc_final: 0.8135 (tp) REVERT: E 258 THR cc_start: 0.8349 (m) cc_final: 0.8142 (p) REVERT: B 259 VAL cc_start: 0.8675 (t) cc_final: 0.8471 (p) REVERT: C 233 GLN cc_start: 0.7925 (mt0) cc_final: 0.7581 (mt0) REVERT: C 235 LEU cc_start: 0.8517 (mt) cc_final: 0.8259 (mt) REVERT: C 238 LYS cc_start: 0.8713 (mttt) cc_final: 0.8466 (mttt) REVERT: C 280 ASN cc_start: 0.8269 (t0) cc_final: 0.7738 (t0) REVERT: A 65 GLN cc_start: 0.8385 (tp40) cc_final: 0.8182 (tp40) REVERT: A 105 GLN cc_start: 0.8193 (pm20) cc_final: 0.7909 (pm20) REVERT: A 228 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7114 (tm-30) REVERT: A 326 ASP cc_start: 0.7849 (t0) cc_final: 0.7494 (t0) REVERT: A 366 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.8005 (mmt90) REVERT: A 386 MET cc_start: 0.8110 (mtt) cc_final: 0.7413 (mtt) REVERT: A 414 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8071 (ttp-110) REVERT: A 435 GLU cc_start: 0.7624 (pp20) cc_final: 0.7388 (pp20) REVERT: A 457 MET cc_start: 0.8816 (mtm) cc_final: 0.8413 (mtm) REVERT: A 499 GLN cc_start: 0.7836 (tp40) cc_final: 0.7227 (mm-40) REVERT: A 503 ASP cc_start: 0.8162 (m-30) cc_final: 0.7672 (m-30) REVERT: A 505 ASN cc_start: 0.8478 (t0) cc_final: 0.8105 (t0) REVERT: A 545 GLU cc_start: 0.8060 (mp0) cc_final: 0.7694 (mp0) REVERT: A 601 LYS cc_start: 0.7946 (ptmt) cc_final: 0.7548 (pttp) REVERT: A 715 ASP cc_start: 0.7884 (t0) cc_final: 0.7679 (t0) REVERT: A 780 ASN cc_start: 0.7887 (t0) cc_final: 0.7668 (t0) REVERT: A 856 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8431 (p) REVERT: A 858 LYS cc_start: 0.8812 (ptpt) cc_final: 0.8473 (ptpp) REVERT: A 916 LYS cc_start: 0.8606 (tmtt) cc_final: 0.8365 (tmtt) REVERT: A 994 LYS cc_start: 0.8683 (mptt) cc_final: 0.8131 (mtmm) REVERT: A 1020 LYS cc_start: 0.8408 (mttt) cc_final: 0.7936 (mttt) REVERT: A 1042 GLU cc_start: 0.8329 (mp0) cc_final: 0.8087 (mm-30) REVERT: A 1054 TYR cc_start: 0.7465 (t80) cc_final: 0.7210 (t80) REVERT: A 1058 ARG cc_start: 0.7923 (mmt90) cc_final: 0.7614 (mmt180) REVERT: A 1072 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8079 (mm-40) REVERT: A 1122 GLU cc_start: 0.7618 (pp20) cc_final: 0.7308 (pp20) REVERT: A 1174 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: A 1235 MET cc_start: 0.7747 (tpt) cc_final: 0.7498 (tpp) REVERT: A 1264 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 1419 MET cc_start: 0.7697 (mtp) cc_final: 0.7269 (mtt) REVERT: A 1421 LYS cc_start: 0.7759 (tppt) cc_final: 0.7350 (tptp) REVERT: A 1441 GLU cc_start: 0.7848 (tp30) cc_final: 0.7544 (tp30) REVERT: A 1550 ARG cc_start: 0.8122 (tpp-160) cc_final: 0.7910 (tpp-160) REVERT: A 1611 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7834 (ptt90) REVERT: A 1620 LEU cc_start: 0.8240 (mp) cc_final: 0.7725 (pp) REVERT: A 1648 LEU cc_start: 0.8564 (tp) cc_final: 0.8349 (tm) REVERT: A 1667 THR cc_start: 0.8616 (p) cc_final: 0.8413 (p) REVERT: A 1671 ARG cc_start: 0.8583 (ttp80) cc_final: 0.7599 (ttm110) REVERT: A 1675 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7300 (pp20) REVERT: A 1693 LEU cc_start: 0.7544 (tp) cc_final: 0.7246 (tm) REVERT: A 1694 ASN cc_start: 0.7824 (p0) cc_final: 0.7293 (p0) REVERT: A 1696 ILE cc_start: 0.9031 (mt) cc_final: 0.8669 (mm) REVERT: A 1697 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7790 (mtm110) REVERT: A 1800 ILE cc_start: 0.8889 (pt) cc_final: 0.8151 (pp) REVERT: A 1945 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8039 (mtpp) REVERT: A 1971 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 1979 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7786 (tp) REVERT: A 2023 LEU cc_start: 0.7562 (tm) cc_final: 0.7288 (tt) REVERT: A 2044 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8284 (tp-100) REVERT: A 2049 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8496 (ttpp) REVERT: A 2052 SER cc_start: 0.8666 (m) cc_final: 0.8033 (p) REVERT: A 2088 ASN cc_start: 0.8902 (t0) cc_final: 0.8634 (t0) REVERT: A 2090 LEU cc_start: 0.8921 (tp) cc_final: 0.8674 (tm) REVERT: A 2110 LYS cc_start: 0.8545 (tttt) cc_final: 0.8162 (tptt) REVERT: A 2180 MET cc_start: 0.8374 (mpp) cc_final: 0.8119 (mpp) REVERT: A 2184 LYS cc_start: 0.9017 (mppt) cc_final: 0.8679 (mppt) REVERT: A 2193 LYS cc_start: 0.7644 (tppt) cc_final: 0.7355 (mptt) REVERT: A 2204 LEU cc_start: 0.8475 (mt) cc_final: 0.8255 (tm) REVERT: A 2229 ILE cc_start: 0.8305 (mt) cc_final: 0.7990 (mp) outliers start: 79 outliers final: 27 residues processed: 534 average time/residue: 1.1918 time to fit residues: 724.3583 Evaluate side-chains 483 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 451 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 1174 GLU Chi-restraints excluded: chain A residue 1262 THR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1611 ARG Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1790 TRP Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1978 ILE Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2074 SER Chi-restraints excluded: chain A residue 2132 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 180 optimal weight: 0.0040 chunk 187 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 451 ASN A 510 GLN A 817 ASN A 823 HIS A 914 GLN A 956 ASN A1135 ASN A1562 ASN ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2039 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.129036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.114265 restraints weight = 37194.022| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.93 r_work: 0.3662 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18973 Z= 0.138 Angle : 0.661 12.631 25729 Z= 0.326 Chirality : 0.042 0.236 3019 Planarity : 0.004 0.055 3239 Dihedral : 4.268 55.374 2535 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.62 % Allowed : 27.09 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2309 helix: 1.53 (0.14), residues: 1340 sheet: -0.71 (0.44), residues: 144 loop : -0.17 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1790 HIS 0.010 0.001 HIS B 234 PHE 0.031 0.001 PHE A 394 TYR 0.027 0.001 TYR A1094 ARG 0.008 0.001 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 1052) hydrogen bonds : angle 4.54429 ( 3036) metal coordination : bond 0.01588 ( 7) metal coordination : angle 6.09152 ( 1) covalent geometry : bond 0.00307 (18966) covalent geometry : angle 0.65989 (25728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 471 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 251 GLN cc_start: 0.8473 (tp-100) cc_final: 0.8083 (tp40) REVERT: D 260 LYS cc_start: 0.9018 (tptp) cc_final: 0.8696 (tptp) REVERT: D 269 MET cc_start: 0.8523 (ppp) cc_final: 0.8280 (ppp) REVERT: E 258 THR cc_start: 0.8308 (m) cc_final: 0.8098 (p) REVERT: B 238 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8499 (mmtt) REVERT: C 235 LEU cc_start: 0.8518 (mt) cc_final: 0.8268 (mt) REVERT: C 238 LYS cc_start: 0.8750 (mttt) cc_final: 0.8522 (mttt) REVERT: C 280 ASN cc_start: 0.8406 (t0) cc_final: 0.7861 (t0) REVERT: A 65 GLN cc_start: 0.8370 (tp40) cc_final: 0.8075 (tp40) REVERT: A 97 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8359 (mt) REVERT: A 184 MET cc_start: 0.8262 (mmm) cc_final: 0.8044 (tpp) REVERT: A 326 ASP cc_start: 0.7844 (t0) cc_final: 0.7492 (t0) REVERT: A 386 MET cc_start: 0.8065 (mtt) cc_final: 0.7376 (mtt) REVERT: A 414 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8037 (ttp-110) REVERT: A 435 GLU cc_start: 0.7731 (pp20) cc_final: 0.7410 (pp20) REVERT: A 451 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8042 (t160) REVERT: A 499 GLN cc_start: 0.7905 (tp40) cc_final: 0.7094 (tm-30) REVERT: A 503 ASP cc_start: 0.8155 (m-30) cc_final: 0.7531 (m-30) REVERT: A 505 ASN cc_start: 0.8523 (t0) cc_final: 0.8149 (t0) REVERT: A 514 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8195 (mmm-85) REVERT: A 540 TYR cc_start: 0.8590 (p90) cc_final: 0.8292 (p90) REVERT: A 545 GLU cc_start: 0.7940 (mp0) cc_final: 0.7561 (mp0) REVERT: A 588 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8473 (mttp) REVERT: A 601 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7481 (pttp) REVERT: A 672 LYS cc_start: 0.8537 (mppt) cc_final: 0.8044 (ptmm) REVERT: A 715 ASP cc_start: 0.7894 (t0) cc_final: 0.7646 (t0) REVERT: A 856 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8484 (p) REVERT: A 858 LYS cc_start: 0.8798 (ptpt) cc_final: 0.8463 (ptpp) REVERT: A 916 LYS cc_start: 0.8601 (tmtt) cc_final: 0.8320 (tmtt) REVERT: A 994 LYS cc_start: 0.8664 (mptt) cc_final: 0.8105 (mtmm) REVERT: A 1020 LYS cc_start: 0.8434 (mttt) cc_final: 0.8033 (mttt) REVERT: A 1042 GLU cc_start: 0.8313 (mp0) cc_final: 0.8061 (mm-30) REVERT: A 1054 TYR cc_start: 0.7482 (t80) cc_final: 0.7237 (t80) REVERT: A 1072 GLN cc_start: 0.8297 (mm-40) cc_final: 0.8050 (mm-40) REVERT: A 1122 GLU cc_start: 0.7644 (pp20) cc_final: 0.7308 (pp20) REVERT: A 1129 ILE cc_start: 0.9011 (mm) cc_final: 0.8581 (pp) REVERT: A 1264 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7430 (mm-30) REVERT: A 1366 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8597 (p) REVERT: A 1419 MET cc_start: 0.7739 (mtp) cc_final: 0.7376 (mtt) REVERT: A 1420 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7768 (pt0) REVERT: A 1421 LYS cc_start: 0.7809 (tppt) cc_final: 0.7298 (tppt) REVERT: A 1425 ILE cc_start: 0.8225 (mm) cc_final: 0.8013 (mm) REVERT: A 1441 GLU cc_start: 0.7855 (tp30) cc_final: 0.7413 (tp30) REVERT: A 1620 LEU cc_start: 0.8260 (mp) cc_final: 0.7748 (pp) REVERT: A 1625 ILE cc_start: 0.8700 (mm) cc_final: 0.8458 (mt) REVERT: A 1648 LEU cc_start: 0.8592 (tp) cc_final: 0.8380 (tm) REVERT: A 1667 THR cc_start: 0.8664 (p) cc_final: 0.8100 (p) REVERT: A 1671 ARG cc_start: 0.8731 (ttp80) cc_final: 0.7902 (ttm110) REVERT: A 1675 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7423 (pp20) REVERT: A 1677 LYS cc_start: 0.8637 (tttt) cc_final: 0.8236 (ttpp) REVERT: A 1693 LEU cc_start: 0.7590 (tp) cc_final: 0.7287 (tm) REVERT: A 1696 ILE cc_start: 0.9045 (mt) cc_final: 0.8695 (mm) REVERT: A 1697 ARG cc_start: 0.8096 (mtm110) cc_final: 0.7828 (mtm110) REVERT: A 1799 TYR cc_start: 0.7172 (m-80) cc_final: 0.6816 (m-80) REVERT: A 1850 PHE cc_start: 0.7820 (m-80) cc_final: 0.7599 (m-80) REVERT: A 1945 LYS cc_start: 0.8382 (ttmm) cc_final: 0.7963 (mtpp) REVERT: A 1971 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 1979 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7823 (tp) REVERT: A 2039 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6273 (tt0) REVERT: A 2043 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8185 (tt) REVERT: A 2049 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8452 (ttpp) REVERT: A 2052 SER cc_start: 0.8574 (m) cc_final: 0.8141 (p) REVERT: A 2090 LEU cc_start: 0.8942 (tp) cc_final: 0.8724 (tm) REVERT: A 2094 MET cc_start: 0.8408 (mtt) cc_final: 0.8156 (mtp) REVERT: A 2110 LYS cc_start: 0.8573 (tttt) cc_final: 0.8211 (tptt) REVERT: A 2180 MET cc_start: 0.8372 (mpp) cc_final: 0.8102 (mpp) REVERT: A 2181 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7106 (mt-10) REVERT: A 2184 LYS cc_start: 0.9000 (mppt) cc_final: 0.8652 (mppt) REVERT: A 2193 LYS cc_start: 0.7627 (tppt) cc_final: 0.7358 (mptt) REVERT: A 2219 LYS cc_start: 0.7815 (pttp) cc_final: 0.7594 (pttp) REVERT: A 2220 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7705 (mtm180) REVERT: A 2229 ILE cc_start: 0.8277 (mt) cc_final: 0.7983 (mp) outliers start: 76 outliers final: 21 residues processed: 511 average time/residue: 1.1989 time to fit residues: 701.2015 Evaluate side-chains 478 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 446 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1420 GLU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1780 LEU Chi-restraints excluded: chain A residue 1790 TRP Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1978 ILE Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2039 GLN Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2132 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 201 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 214 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 140 optimal weight: 0.0870 chunk 183 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 914 GLN A1135 ASN A1177 HIS ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1933 GLN A2039 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.128741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.113979 restraints weight = 37370.374| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.94 r_work: 0.3655 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18973 Z= 0.135 Angle : 0.682 13.580 25729 Z= 0.328 Chirality : 0.042 0.235 3019 Planarity : 0.004 0.045 3239 Dihedral : 4.268 54.678 2535 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.77 % Allowed : 28.23 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2309 helix: 1.61 (0.14), residues: 1332 sheet: -0.66 (0.44), residues: 144 loop : -0.24 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1790 HIS 0.014 0.001 HIS B 234 PHE 0.022 0.001 PHE A 394 TYR 0.019 0.001 TYR A1409 ARG 0.010 0.001 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1052) hydrogen bonds : angle 4.47360 ( 3036) metal coordination : bond 0.01512 ( 7) metal coordination : angle 5.65208 ( 1) covalent geometry : bond 0.00312 (18966) covalent geometry : angle 0.68097 (25728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 464 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 251 GLN cc_start: 0.8482 (tp-100) cc_final: 0.7952 (tp-100) REVERT: D 260 LYS cc_start: 0.9024 (tptp) cc_final: 0.8681 (tptp) REVERT: E 234 HIS cc_start: 0.8016 (m-70) cc_final: 0.7717 (m-70) REVERT: E 258 THR cc_start: 0.8304 (m) cc_final: 0.8092 (p) REVERT: B 238 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8514 (mmtt) REVERT: B 284 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8611 (m) REVERT: C 235 LEU cc_start: 0.8521 (mt) cc_final: 0.8277 (mt) REVERT: C 238 LYS cc_start: 0.8721 (mttt) cc_final: 0.8487 (mttt) REVERT: C 280 ASN cc_start: 0.8444 (t0) cc_final: 0.7886 (t0) REVERT: A 65 GLN cc_start: 0.8386 (tp40) cc_final: 0.7977 (tp40) REVERT: A 97 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 184 MET cc_start: 0.8258 (mmm) cc_final: 0.7874 (tpp) REVERT: A 211 ARG cc_start: 0.6960 (ttp80) cc_final: 0.6721 (ttp80) REVERT: A 242 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7342 (ttt) REVERT: A 326 ASP cc_start: 0.7808 (t0) cc_final: 0.7432 (t0) REVERT: A 386 MET cc_start: 0.8059 (mtt) cc_final: 0.7418 (mtt) REVERT: A 414 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8001 (ttp-110) REVERT: A 435 GLU cc_start: 0.7762 (pp20) cc_final: 0.7434 (pp20) REVERT: A 494 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7532 (mtp-110) REVERT: A 498 LYS cc_start: 0.7718 (mttp) cc_final: 0.7281 (mttt) REVERT: A 499 GLN cc_start: 0.7913 (tp40) cc_final: 0.7008 (tm-30) REVERT: A 503 ASP cc_start: 0.8169 (m-30) cc_final: 0.7525 (m-30) REVERT: A 505 ASN cc_start: 0.8479 (t0) cc_final: 0.8094 (t0) REVERT: A 540 TYR cc_start: 0.8626 (p90) cc_final: 0.8310 (p90) REVERT: A 545 GLU cc_start: 0.7920 (mp0) cc_final: 0.7575 (mp0) REVERT: A 588 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8492 (mttp) REVERT: A 601 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7479 (pttp) REVERT: A 672 LYS cc_start: 0.8542 (mppt) cc_final: 0.8042 (ptmm) REVERT: A 715 ASP cc_start: 0.7899 (t0) cc_final: 0.7642 (t0) REVERT: A 817 ASN cc_start: 0.8060 (m-40) cc_final: 0.7845 (m110) REVERT: A 856 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8480 (p) REVERT: A 858 LYS cc_start: 0.8774 (ptpt) cc_final: 0.8432 (ptpp) REVERT: A 892 ASP cc_start: 0.7698 (t0) cc_final: 0.7453 (OUTLIER) REVERT: A 916 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8299 (tmtt) REVERT: A 994 LYS cc_start: 0.8683 (mptt) cc_final: 0.8122 (mtmm) REVERT: A 1020 LYS cc_start: 0.8434 (mttt) cc_final: 0.8149 (mttt) REVERT: A 1042 GLU cc_start: 0.8283 (mp0) cc_final: 0.8042 (mm-30) REVERT: A 1072 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8051 (mm-40) REVERT: A 1122 GLU cc_start: 0.7663 (pp20) cc_final: 0.7325 (pp20) REVERT: A 1129 ILE cc_start: 0.9014 (mm) cc_final: 0.8599 (pp) REVERT: A 1264 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 1419 MET cc_start: 0.7720 (mtp) cc_final: 0.6911 (mpp) REVERT: A 1421 LYS cc_start: 0.7838 (tppt) cc_final: 0.7349 (tppt) REVERT: A 1425 ILE cc_start: 0.8270 (mm) cc_final: 0.8003 (mm) REVERT: A 1441 GLU cc_start: 0.7806 (tp30) cc_final: 0.7299 (tp30) REVERT: A 1530 ARG cc_start: 0.8690 (mtp85) cc_final: 0.8439 (mtp180) REVERT: A 1555 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8833 (mp) REVERT: A 1625 ILE cc_start: 0.8623 (mm) cc_final: 0.8393 (mt) REVERT: A 1671 ARG cc_start: 0.8702 (ttp80) cc_final: 0.7470 (ttp80) REVERT: A 1675 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7495 (pp20) REVERT: A 1677 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8229 (ttpp) REVERT: A 1693 LEU cc_start: 0.7642 (tp) cc_final: 0.7253 (tm) REVERT: A 1696 ILE cc_start: 0.9053 (mt) cc_final: 0.8710 (mm) REVERT: A 1697 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7730 (mtm110) REVERT: A 1945 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7941 (mtpp) REVERT: A 1965 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 1971 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7450 (tm-30) REVERT: A 1979 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7913 (tp) REVERT: A 2023 LEU cc_start: 0.7478 (tm) cc_final: 0.7226 (tt) REVERT: A 2043 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8243 (tt) REVERT: A 2049 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8461 (ttpp) REVERT: A 2052 SER cc_start: 0.8600 (m) cc_final: 0.8149 (p) REVERT: A 2077 LYS cc_start: 0.7848 (mppt) cc_final: 0.7561 (mppt) REVERT: A 2090 LEU cc_start: 0.8931 (tp) cc_final: 0.8681 (tm) REVERT: A 2094 MET cc_start: 0.8384 (mtt) cc_final: 0.8150 (mtp) REVERT: A 2110 LYS cc_start: 0.8538 (tttt) cc_final: 0.8171 (tptt) REVERT: A 2136 LEU cc_start: 0.9009 (mm) cc_final: 0.8771 (mm) REVERT: A 2180 MET cc_start: 0.8399 (mpp) cc_final: 0.8170 (mpp) REVERT: A 2181 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7113 (mt-10) REVERT: A 2184 LYS cc_start: 0.9000 (mppt) cc_final: 0.8664 (mppt) REVERT: A 2220 ARG cc_start: 0.7982 (mtp-110) cc_final: 0.7760 (mtm180) REVERT: A 2229 ILE cc_start: 0.8309 (mt) cc_final: 0.8019 (mp) outliers start: 79 outliers final: 29 residues processed: 501 average time/residue: 1.1983 time to fit residues: 682.2810 Evaluate side-chains 490 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 450 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1677 LYS Chi-restraints excluded: chain A residue 1790 TRP Chi-restraints excluded: chain A residue 1897 THR Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 1978 ILE Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2039 GLN Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 159 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN A 956 ASN A1135 ASN A1138 ASN A1177 HIS ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2039 GLN ** A2091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.126838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111888 restraints weight = 37662.454| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.96 r_work: 0.3616 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18973 Z= 0.177 Angle : 0.702 14.141 25729 Z= 0.341 Chirality : 0.044 0.226 3019 Planarity : 0.005 0.042 3239 Dihedral : 4.243 41.646 2535 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.01 % Allowed : 28.09 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.18), residues: 2309 helix: 1.58 (0.14), residues: 1334 sheet: -0.75 (0.45), residues: 139 loop : -0.36 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1790 HIS 0.011 0.001 HIS B 234 PHE 0.024 0.002 PHE A 394 TYR 0.031 0.002 TYR A1094 ARG 0.010 0.001 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 1052) hydrogen bonds : angle 4.43596 ( 3036) metal coordination : bond 0.02095 ( 7) metal coordination : angle 6.86466 ( 1) covalent geometry : bond 0.00406 (18966) covalent geometry : angle 0.70084 (25728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 476 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 251 GLN cc_start: 0.8476 (tp-100) cc_final: 0.7945 (tp-100) REVERT: D 260 LYS cc_start: 0.9095 (tptp) cc_final: 0.8756 (tptp) REVERT: E 234 HIS cc_start: 0.8081 (m-70) cc_final: 0.7768 (m-70) REVERT: E 252 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8046 (tp) REVERT: E 258 THR cc_start: 0.8355 (m) cc_final: 0.8142 (p) REVERT: B 238 LYS cc_start: 0.8824 (mmtm) cc_final: 0.8576 (mmtm) REVERT: B 284 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8655 (m) REVERT: C 235 LEU cc_start: 0.8555 (mt) cc_final: 0.8301 (mt) REVERT: C 238 LYS cc_start: 0.8809 (mttt) cc_final: 0.8557 (mttt) REVERT: C 280 ASN cc_start: 0.8465 (t0) cc_final: 0.7923 (t0) REVERT: A 65 GLN cc_start: 0.8393 (tp40) cc_final: 0.7964 (tp40) REVERT: A 184 MET cc_start: 0.8337 (tmm) cc_final: 0.7907 (tpp) REVERT: A 386 MET cc_start: 0.7919 (mtt) cc_final: 0.7372 (mtt) REVERT: A 414 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7999 (ttp-110) REVERT: A 435 GLU cc_start: 0.7795 (pp20) cc_final: 0.7455 (pp20) REVERT: A 498 LYS cc_start: 0.7763 (mttp) cc_final: 0.7250 (mttt) REVERT: A 505 ASN cc_start: 0.8532 (t0) cc_final: 0.8151 (t0) REVERT: A 545 GLU cc_start: 0.7976 (mp0) cc_final: 0.7652 (mp0) REVERT: A 588 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8430 (mttm) REVERT: A 601 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7464 (pttp) REVERT: A 672 LYS cc_start: 0.8525 (mppt) cc_final: 0.8061 (ptmm) REVERT: A 715 ASP cc_start: 0.7998 (t0) cc_final: 0.7758 (t0) REVERT: A 856 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8524 (p) REVERT: A 858 LYS cc_start: 0.8791 (ptpt) cc_final: 0.8450 (ptpp) REVERT: A 916 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8312 (tmtt) REVERT: A 994 LYS cc_start: 0.8720 (mptt) cc_final: 0.8153 (mtmm) REVERT: A 1020 LYS cc_start: 0.8444 (mttt) cc_final: 0.8136 (mttt) REVERT: A 1042 GLU cc_start: 0.8351 (mp0) cc_final: 0.8116 (mm-30) REVERT: A 1048 GLU cc_start: 0.7802 (tt0) cc_final: 0.7401 (tm-30) REVERT: A 1072 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8054 (mm-40) REVERT: A 1122 GLU cc_start: 0.7733 (pp20) cc_final: 0.7252 (pm20) REVERT: A 1129 ILE cc_start: 0.8998 (mm) cc_final: 0.8595 (pp) REVERT: A 1135 ASN cc_start: 0.8540 (m-40) cc_final: 0.8217 (m110) REVERT: A 1264 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7382 (mm-30) REVERT: A 1366 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8615 (p) REVERT: A 1421 LYS cc_start: 0.7854 (tppt) cc_final: 0.7410 (tppt) REVERT: A 1425 ILE cc_start: 0.8311 (mm) cc_final: 0.8094 (mm) REVERT: A 1439 LEU cc_start: 0.8875 (tp) cc_final: 0.8619 (tm) REVERT: A 1441 GLU cc_start: 0.7786 (tp30) cc_final: 0.7260 (tp30) REVERT: A 1555 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8866 (mp) REVERT: A 1566 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7761 (mt) REVERT: A 1671 ARG cc_start: 0.8740 (ttp80) cc_final: 0.7747 (ttm110) REVERT: A 1677 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8161 (ttpp) REVERT: A 1693 LEU cc_start: 0.7742 (tp) cc_final: 0.7417 (tm) REVERT: A 1696 ILE cc_start: 0.9098 (mt) cc_final: 0.8784 (mm) REVERT: A 1697 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7857 (mtm110) REVERT: A 1788 THR cc_start: 0.8094 (p) cc_final: 0.7816 (t) REVERT: A 1813 LEU cc_start: 0.8473 (mm) cc_final: 0.7796 (mm) REVERT: A 1832 THR cc_start: 0.8395 (m) cc_final: 0.8148 (p) REVERT: A 1836 ASN cc_start: 0.7566 (t0) cc_final: 0.7208 (p0) REVERT: A 1945 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7892 (mtpp) REVERT: A 1965 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8261 (mp) REVERT: A 1971 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 1979 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7988 (tp) REVERT: A 2043 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8330 (tt) REVERT: A 2049 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8468 (ttpp) REVERT: A 2052 SER cc_start: 0.8632 (m) cc_final: 0.8164 (p) REVERT: A 2064 ASN cc_start: 0.7966 (t0) cc_final: 0.7726 (t0) REVERT: A 2077 LYS cc_start: 0.7875 (mppt) cc_final: 0.7607 (mppt) REVERT: A 2088 ASN cc_start: 0.8898 (t0) cc_final: 0.8614 (t0) REVERT: A 2090 LEU cc_start: 0.8979 (tp) cc_final: 0.8724 (tm) REVERT: A 2094 MET cc_start: 0.8453 (mtt) cc_final: 0.8252 (mtp) REVERT: A 2110 LYS cc_start: 0.8621 (tttt) cc_final: 0.8255 (tptt) REVERT: A 2136 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8783 (mm) REVERT: A 2180 MET cc_start: 0.8477 (mpp) cc_final: 0.8258 (mpp) REVERT: A 2184 LYS cc_start: 0.9026 (mppt) cc_final: 0.8676 (mppt) REVERT: A 2198 GLN cc_start: 0.8472 (mt0) cc_final: 0.8003 (mp10) REVERT: A 2219 LYS cc_start: 0.7924 (pttp) cc_final: 0.7716 (pttp) REVERT: A 2229 ILE cc_start: 0.8355 (mt) cc_final: 0.8131 (mp) outliers start: 84 outliers final: 37 residues processed: 524 average time/residue: 1.1161 time to fit residues: 668.8745 Evaluate side-chains 510 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 459 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1677 LYS Chi-restraints excluded: chain A residue 1780 LEU Chi-restraints excluded: chain A residue 1787 SER Chi-restraints excluded: chain A residue 1790 TRP Chi-restraints excluded: chain A residue 1897 THR Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 1978 ILE Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2039 GLN Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2074 SER Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain A residue 2136 LEU Chi-restraints excluded: chain A residue 2202 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 38 optimal weight: 0.3980 chunk 222 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 210 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 245 GLN ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN A 780 ASN A 823 HIS A 914 GLN A 956 ASN A1138 ASN A1177 HIS A1285 GLN ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2039 GLN A2091 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.128361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.113515 restraints weight = 37383.297| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.96 r_work: 0.3647 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18973 Z= 0.132 Angle : 0.721 15.616 25729 Z= 0.343 Chirality : 0.043 0.246 3019 Planarity : 0.005 0.055 3239 Dihedral : 4.191 35.619 2534 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.86 % Allowed : 29.42 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2309 helix: 1.55 (0.14), residues: 1336 sheet: -0.74 (0.44), residues: 139 loop : -0.34 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1790 HIS 0.013 0.001 HIS B 234 PHE 0.018 0.002 PHE A 319 TYR 0.037 0.002 TYR A 540 ARG 0.010 0.001 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1052) hydrogen bonds : angle 4.39209 ( 3036) metal coordination : bond 0.01246 ( 7) metal coordination : angle 4.85118 ( 1) covalent geometry : bond 0.00305 (18966) covalent geometry : angle 0.72077 (25728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 481 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 251 GLN cc_start: 0.8427 (tp-100) cc_final: 0.7871 (tp-100) REVERT: D 260 LYS cc_start: 0.9044 (tptp) cc_final: 0.8628 (tptp) REVERT: E 234 HIS cc_start: 0.8073 (m-70) cc_final: 0.7741 (m-70) REVERT: E 252 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7980 (tp) REVERT: B 238 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8571 (mmtm) REVERT: B 284 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8650 (m) REVERT: C 235 LEU cc_start: 0.8545 (mt) cc_final: 0.8296 (mt) REVERT: C 238 LYS cc_start: 0.8775 (mttt) cc_final: 0.8569 (mttt) REVERT: C 280 ASN cc_start: 0.8410 (t0) cc_final: 0.7891 (t0) REVERT: A 11 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: A 65 GLN cc_start: 0.8399 (tp40) cc_final: 0.8004 (tp40) REVERT: A 184 MET cc_start: 0.8181 (tmm) cc_final: 0.7782 (tpp) REVERT: A 326 ASP cc_start: 0.7801 (t0) cc_final: 0.7365 (t0) REVERT: A 330 GLU cc_start: 0.7191 (pm20) cc_final: 0.6938 (pm20) REVERT: A 386 MET cc_start: 0.7952 (mtt) cc_final: 0.7413 (mtt) REVERT: A 414 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8012 (ttp-110) REVERT: A 435 GLU cc_start: 0.7751 (pp20) cc_final: 0.7411 (pp20) REVERT: A 498 LYS cc_start: 0.7669 (mttp) cc_final: 0.7234 (mttt) REVERT: A 545 GLU cc_start: 0.7880 (mp0) cc_final: 0.7550 (mp0) REVERT: A 556 GLU cc_start: 0.7765 (mm-30) cc_final: 0.6968 (mm-30) REVERT: A 558 LYS cc_start: 0.7793 (mtmt) cc_final: 0.7281 (pptt) REVERT: A 588 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8428 (mttm) REVERT: A 601 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7460 (pttp) REVERT: A 672 LYS cc_start: 0.8547 (mppt) cc_final: 0.8065 (ptmm) REVERT: A 715 ASP cc_start: 0.7933 (t0) cc_final: 0.7700 (t0) REVERT: A 797 GLU cc_start: 0.7885 (tp30) cc_final: 0.7295 (tm-30) REVERT: A 856 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8414 (p) REVERT: A 858 LYS cc_start: 0.8768 (ptpt) cc_final: 0.8498 (ptpp) REVERT: A 916 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8333 (tmtt) REVERT: A 994 LYS cc_start: 0.8724 (mptt) cc_final: 0.8164 (mtmm) REVERT: A 1020 LYS cc_start: 0.8442 (mttt) cc_final: 0.8127 (mttt) REVERT: A 1042 GLU cc_start: 0.8263 (mp0) cc_final: 0.8034 (mm-30) REVERT: A 1048 GLU cc_start: 0.7819 (tt0) cc_final: 0.7433 (tm-30) REVERT: A 1072 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8015 (mm-40) REVERT: A 1105 LYS cc_start: 0.8297 (mttt) cc_final: 0.8087 (mmmm) REVERT: A 1122 GLU cc_start: 0.7668 (pp20) cc_final: 0.7238 (pm20) REVERT: A 1129 ILE cc_start: 0.9021 (mm) cc_final: 0.8627 (pp) REVERT: A 1264 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 1366 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8615 (p) REVERT: A 1419 MET cc_start: 0.7623 (mtp) cc_final: 0.7006 (mpp) REVERT: A 1421 LYS cc_start: 0.7882 (tppt) cc_final: 0.7455 (tppt) REVERT: A 1425 ILE cc_start: 0.8303 (mm) cc_final: 0.8102 (mm) REVERT: A 1441 GLU cc_start: 0.7682 (tp30) cc_final: 0.7136 (tp30) REVERT: A 1635 LYS cc_start: 0.8510 (tmmt) cc_final: 0.8307 (ttpp) REVERT: A 1648 LEU cc_start: 0.8575 (tp) cc_final: 0.8189 (mt) REVERT: A 1671 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7382 (ttm110) REVERT: A 1675 GLU cc_start: 0.7712 (pm20) cc_final: 0.7368 (pm20) REVERT: A 1677 LYS cc_start: 0.8591 (tttt) cc_final: 0.8149 (ttpp) REVERT: A 1693 LEU cc_start: 0.7673 (tp) cc_final: 0.7344 (tm) REVERT: A 1696 ILE cc_start: 0.9078 (mt) cc_final: 0.8778 (mm) REVERT: A 1697 ARG cc_start: 0.8127 (mtm110) cc_final: 0.7816 (mtm110) REVERT: A 1788 THR cc_start: 0.7951 (p) cc_final: 0.7719 (t) REVERT: A 1813 LEU cc_start: 0.8442 (mm) cc_final: 0.7735 (mm) REVERT: A 1832 THR cc_start: 0.8333 (m) cc_final: 0.8105 (p) REVERT: A 1836 ASN cc_start: 0.7483 (t0) cc_final: 0.7208 (p0) REVERT: A 1900 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7846 (mp0) REVERT: A 1945 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7894 (mtpp) REVERT: A 1971 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7400 (tm-30) REVERT: A 1979 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7955 (tp) REVERT: A 1980 ARG cc_start: 0.5940 (tpp-160) cc_final: 0.5678 (tpt170) REVERT: A 2043 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8340 (tt) REVERT: A 2049 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8474 (ttpp) REVERT: A 2052 SER cc_start: 0.8638 (m) cc_final: 0.8092 (p) REVERT: A 2064 ASN cc_start: 0.7948 (t0) cc_final: 0.7698 (t0) REVERT: A 2077 LYS cc_start: 0.7824 (mppt) cc_final: 0.7547 (mppt) REVERT: A 2090 LEU cc_start: 0.8957 (tp) cc_final: 0.8683 (tm) REVERT: A 2110 LYS cc_start: 0.8588 (tttt) cc_final: 0.8214 (tptt) REVERT: A 2136 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8761 (mm) REVERT: A 2142 ARG cc_start: 0.8037 (tpt170) cc_final: 0.7655 (tpp-160) REVERT: A 2193 LYS cc_start: 0.7473 (tppt) cc_final: 0.7132 (mptt) REVERT: A 2229 ILE cc_start: 0.8361 (mt) cc_final: 0.8109 (mp) outliers start: 81 outliers final: 31 residues processed: 516 average time/residue: 1.2253 time to fit residues: 721.8404 Evaluate side-chains 502 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 460 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1440 LEU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1790 TRP Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1978 ILE Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2039 GLN Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain A residue 2136 LEU Chi-restraints excluded: chain A residue 2162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 105 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 188 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 100 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 245 GLN ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 GLN A 395 GLN A 780 ASN A 823 HIS A 956 ASN A1138 ASN A1177 HIS ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2039 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.128540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113760 restraints weight = 37289.350| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.95 r_work: 0.3652 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18973 Z= 0.136 Angle : 0.754 16.926 25729 Z= 0.356 Chirality : 0.043 0.293 3019 Planarity : 0.005 0.064 3239 Dihedral : 4.177 40.271 2534 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.77 % Allowed : 30.47 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.18), residues: 2309 helix: 1.54 (0.14), residues: 1335 sheet: -0.69 (0.45), residues: 139 loop : -0.36 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1790 HIS 0.014 0.001 HIS B 234 PHE 0.025 0.002 PHE A1309 TYR 0.044 0.001 TYR A2191 ARG 0.014 0.001 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 1052) hydrogen bonds : angle 4.35607 ( 3036) metal coordination : bond 0.01414 ( 7) metal coordination : angle 5.72534 ( 1) covalent geometry : bond 0.00317 (18966) covalent geometry : angle 0.75279 (25728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 475 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 251 GLN cc_start: 0.8448 (tp-100) cc_final: 0.7909 (tp-100) REVERT: D 260 LYS cc_start: 0.9015 (tptp) cc_final: 0.8670 (tptp) REVERT: E 234 HIS cc_start: 0.8099 (m-70) cc_final: 0.7734 (m-70) REVERT: E 252 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7969 (tp) REVERT: B 238 LYS cc_start: 0.8809 (mmtm) cc_final: 0.8583 (mmtm) REVERT: B 284 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8625 (m) REVERT: C 233 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7448 (mp10) REVERT: C 235 LEU cc_start: 0.8542 (mt) cc_final: 0.8286 (mt) REVERT: C 238 LYS cc_start: 0.8777 (mttt) cc_final: 0.8573 (mttt) REVERT: C 248 MET cc_start: 0.7804 (mtt) cc_final: 0.7473 (mpp) REVERT: C 280 ASN cc_start: 0.8374 (t0) cc_final: 0.7857 (t0) REVERT: A 11 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: A 65 GLN cc_start: 0.8401 (tp40) cc_final: 0.8001 (tp40) REVERT: A 184 MET cc_start: 0.8134 (tmm) cc_final: 0.7743 (tpp) REVERT: A 323 GLU cc_start: 0.8161 (tp30) cc_final: 0.7692 (tp30) REVERT: A 326 ASP cc_start: 0.7818 (t0) cc_final: 0.7255 (t0) REVERT: A 330 GLU cc_start: 0.7164 (pm20) cc_final: 0.6896 (pm20) REVERT: A 365 MET cc_start: 0.7661 (mpp) cc_final: 0.7360 (mmt) REVERT: A 414 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8013 (ttp-110) REVERT: A 431 LYS cc_start: 0.8476 (mmmm) cc_final: 0.8054 (mppt) REVERT: A 435 GLU cc_start: 0.7744 (pp20) cc_final: 0.7399 (pp20) REVERT: A 498 LYS cc_start: 0.7620 (mttp) cc_final: 0.7202 (mttt) REVERT: A 519 ASN cc_start: 0.7937 (t0) cc_final: 0.7698 (m-40) REVERT: A 536 THR cc_start: 0.8917 (m) cc_final: 0.8590 (p) REVERT: A 545 GLU cc_start: 0.7895 (mp0) cc_final: 0.7553 (mp0) REVERT: A 556 GLU cc_start: 0.7787 (mm-30) cc_final: 0.6969 (mm-30) REVERT: A 558 LYS cc_start: 0.7828 (mtmt) cc_final: 0.7319 (pptt) REVERT: A 588 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8436 (mttp) REVERT: A 601 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7457 (pttp) REVERT: A 672 LYS cc_start: 0.8521 (mppt) cc_final: 0.8053 (ptmm) REVERT: A 715 ASP cc_start: 0.7929 (t0) cc_final: 0.7703 (t0) REVERT: A 856 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 858 LYS cc_start: 0.8744 (ptpt) cc_final: 0.8428 (ptpp) REVERT: A 916 LYS cc_start: 0.8588 (tmtt) cc_final: 0.8311 (tmtt) REVERT: A 994 LYS cc_start: 0.8720 (mptt) cc_final: 0.8160 (mtmm) REVERT: A 1020 LYS cc_start: 0.8420 (mttt) cc_final: 0.8086 (mttt) REVERT: A 1048 GLU cc_start: 0.7835 (tt0) cc_final: 0.7467 (tm-30) REVERT: A 1072 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7995 (mm-40) REVERT: A 1122 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7267 (pm20) REVERT: A 1129 ILE cc_start: 0.9027 (mm) cc_final: 0.8642 (pp) REVERT: A 1223 ILE cc_start: 0.8092 (pt) cc_final: 0.7885 (pt) REVERT: A 1264 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7379 (mm-30) REVERT: A 1310 THR cc_start: 0.8551 (p) cc_final: 0.8251 (p) REVERT: A 1366 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8608 (p) REVERT: A 1419 MET cc_start: 0.7586 (mtp) cc_final: 0.7379 (mtt) REVERT: A 1420 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: A 1421 LYS cc_start: 0.7899 (tppt) cc_final: 0.7365 (tppt) REVERT: A 1425 ILE cc_start: 0.8295 (mm) cc_final: 0.7951 (mt) REVERT: A 1441 GLU cc_start: 0.7621 (tp30) cc_final: 0.7062 (tp30) REVERT: A 1666 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7868 (mmpt) REVERT: A 1671 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7306 (ttm110) REVERT: A 1675 GLU cc_start: 0.7714 (pm20) cc_final: 0.7333 (pm20) REVERT: A 1677 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8189 (ttpp) REVERT: A 1693 LEU cc_start: 0.7683 (tp) cc_final: 0.7348 (tm) REVERT: A 1696 ILE cc_start: 0.9091 (mt) cc_final: 0.8786 (mm) REVERT: A 1697 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7827 (mtm110) REVERT: A 1788 THR cc_start: 0.7985 (p) cc_final: 0.7753 (t) REVERT: A 1813 LEU cc_start: 0.8444 (mm) cc_final: 0.7718 (mm) REVERT: A 1832 THR cc_start: 0.8359 (m) cc_final: 0.8122 (p) REVERT: A 1836 ASN cc_start: 0.7463 (t0) cc_final: 0.7224 (p0) REVERT: A 1887 ASN cc_start: 0.8430 (t0) cc_final: 0.8154 (m110) REVERT: A 1945 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7853 (mttp) REVERT: A 1971 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 1979 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 2023 LEU cc_start: 0.7571 (tm) cc_final: 0.7289 (tt) REVERT: A 2043 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8332 (tt) REVERT: A 2049 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8494 (ttpp) REVERT: A 2052 SER cc_start: 0.8646 (m) cc_final: 0.8184 (p) REVERT: A 2064 ASN cc_start: 0.7877 (t0) cc_final: 0.7624 (t0) REVERT: A 2077 LYS cc_start: 0.7815 (mppt) cc_final: 0.7521 (mppt) REVERT: A 2078 TRP cc_start: 0.7427 (t60) cc_final: 0.7189 (t60) REVERT: A 2090 LEU cc_start: 0.8979 (tp) cc_final: 0.8702 (tm) REVERT: A 2110 LYS cc_start: 0.8583 (tttt) cc_final: 0.8234 (tptt) REVERT: A 2136 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8757 (mm) REVERT: A 2184 LYS cc_start: 0.9003 (tppt) cc_final: 0.8790 (tmmt) REVERT: A 2192 LEU cc_start: 0.7870 (mt) cc_final: 0.7607 (mm) REVERT: A 2193 LYS cc_start: 0.7446 (tppt) cc_final: 0.7130 (mptt) REVERT: A 2220 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7649 (mtm180) REVERT: A 2229 ILE cc_start: 0.8380 (mt) cc_final: 0.8165 (mp) outliers start: 79 outliers final: 34 residues processed: 513 average time/residue: 1.1822 time to fit residues: 690.8155 Evaluate side-chains 510 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 461 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1122 GLU Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1420 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1677 LYS Chi-restraints excluded: chain A residue 1790 TRP Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1978 ILE Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 1980 ARG Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2039 GLN Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain A residue 2136 LEU Chi-restraints excluded: chain A residue 2162 LEU Chi-restraints excluded: chain A residue 2202 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 44 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 108 optimal weight: 0.0070 chunk 18 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 245 GLN A 395 GLN A 505 ASN A 780 ASN A 817 ASN A 876 ASN A 956 ASN A1138 ASN A1177 HIS ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2039 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.127923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.113148 restraints weight = 37395.578| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.95 r_work: 0.3643 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18973 Z= 0.149 Angle : 0.774 16.039 25729 Z= 0.368 Chirality : 0.044 0.284 3019 Planarity : 0.005 0.054 3239 Dihedral : 4.175 42.589 2533 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.48 % Allowed : 30.57 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2309 helix: 1.47 (0.14), residues: 1336 sheet: -0.66 (0.45), residues: 139 loop : -0.35 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1790 HIS 0.015 0.001 HIS B 234 PHE 0.039 0.002 PHE A1880 TYR 0.037 0.002 TYR A 540 ARG 0.012 0.001 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 1052) hydrogen bonds : angle 4.36103 ( 3036) metal coordination : bond 0.01553 ( 7) metal coordination : angle 6.14525 ( 1) covalent geometry : bond 0.00347 (18966) covalent geometry : angle 0.77349 (25728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 474 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 251 GLN cc_start: 0.8449 (tp-100) cc_final: 0.7916 (tp-100) REVERT: D 260 LYS cc_start: 0.8977 (tptp) cc_final: 0.8668 (tptp) REVERT: E 234 HIS cc_start: 0.8142 (m-70) cc_final: 0.7787 (m-70) REVERT: E 252 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7964 (tp) REVERT: B 238 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8615 (mmtm) REVERT: B 260 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7361 (mmpt) REVERT: B 284 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8649 (m) REVERT: C 235 LEU cc_start: 0.8548 (mt) cc_final: 0.8278 (mt) REVERT: C 238 LYS cc_start: 0.8811 (mttt) cc_final: 0.8602 (mttt) REVERT: C 248 MET cc_start: 0.7813 (mtt) cc_final: 0.7487 (mpp) REVERT: C 280 ASN cc_start: 0.8344 (t0) cc_final: 0.7784 (t0) REVERT: A 11 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: A 65 GLN cc_start: 0.8383 (tp40) cc_final: 0.7986 (tp40) REVERT: A 184 MET cc_start: 0.8131 (tmm) cc_final: 0.7702 (tpp) REVERT: A 323 GLU cc_start: 0.8162 (tp30) cc_final: 0.7742 (tp30) REVERT: A 326 ASP cc_start: 0.7819 (t0) cc_final: 0.7225 (t0) REVERT: A 330 GLU cc_start: 0.7175 (pm20) cc_final: 0.6883 (pm20) REVERT: A 365 MET cc_start: 0.7688 (mpp) cc_final: 0.7427 (mmt) REVERT: A 414 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8047 (ttp-110) REVERT: A 431 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8075 (mppt) REVERT: A 435 GLU cc_start: 0.7746 (pp20) cc_final: 0.7414 (pp20) REVERT: A 436 MET cc_start: 0.8178 (mtt) cc_final: 0.7686 (mtm) REVERT: A 498 LYS cc_start: 0.7699 (mttp) cc_final: 0.7284 (mmtt) REVERT: A 519 ASN cc_start: 0.7986 (t0) cc_final: 0.7709 (m-40) REVERT: A 536 THR cc_start: 0.8912 (m) cc_final: 0.8589 (p) REVERT: A 545 GLU cc_start: 0.7913 (mp0) cc_final: 0.7583 (mp0) REVERT: A 556 GLU cc_start: 0.7771 (mm-30) cc_final: 0.6878 (mm-30) REVERT: A 558 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7351 (pptt) REVERT: A 601 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7458 (pttp) REVERT: A 672 LYS cc_start: 0.8482 (mppt) cc_final: 0.8050 (ptmm) REVERT: A 715 ASP cc_start: 0.7945 (t0) cc_final: 0.7729 (t0) REVERT: A 856 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8541 (p) REVERT: A 858 LYS cc_start: 0.8751 (ptpt) cc_final: 0.8441 (ptpp) REVERT: A 916 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8313 (tmtt) REVERT: A 994 LYS cc_start: 0.8743 (mptt) cc_final: 0.8192 (mtmm) REVERT: A 1020 LYS cc_start: 0.8426 (mttt) cc_final: 0.8075 (mttt) REVERT: A 1042 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7926 (mm-30) REVERT: A 1048 GLU cc_start: 0.7837 (tt0) cc_final: 0.7467 (tm-30) REVERT: A 1072 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7986 (mm-40) REVERT: A 1122 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: A 1129 ILE cc_start: 0.9015 (mm) cc_final: 0.8652 (pp) REVERT: A 1250 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7302 (tmt-80) REVERT: A 1264 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 1310 THR cc_start: 0.8584 (p) cc_final: 0.8285 (p) REVERT: A 1366 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 1419 MET cc_start: 0.7608 (mtp) cc_final: 0.7052 (mpp) REVERT: A 1420 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7743 (pt0) REVERT: A 1421 LYS cc_start: 0.7907 (tppt) cc_final: 0.7370 (tppt) REVERT: A 1425 ILE cc_start: 0.8291 (mm) cc_final: 0.7911 (mm) REVERT: A 1441 GLU cc_start: 0.7546 (tp30) cc_final: 0.6985 (tp30) REVERT: A 1648 LEU cc_start: 0.8573 (tp) cc_final: 0.8192 (mt) REVERT: A 1654 GLN cc_start: 0.7468 (mt0) cc_final: 0.7104 (mt0) REVERT: A 1671 ARG cc_start: 0.8478 (ttp80) cc_final: 0.7311 (ttm110) REVERT: A 1675 GLU cc_start: 0.7698 (pm20) cc_final: 0.7278 (pm20) REVERT: A 1677 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8217 (ttpp) REVERT: A 1692 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7944 (mm) REVERT: A 1693 LEU cc_start: 0.7697 (tp) cc_final: 0.7422 (tm) REVERT: A 1696 ILE cc_start: 0.9095 (mt) cc_final: 0.8792 (mm) REVERT: A 1697 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7901 (mtm110) REVERT: A 1788 THR cc_start: 0.7986 (p) cc_final: 0.7769 (t) REVERT: A 1813 LEU cc_start: 0.8423 (mm) cc_final: 0.7653 (mm) REVERT: A 1823 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8495 (tm) REVERT: A 1832 THR cc_start: 0.8413 (m) cc_final: 0.8206 (p) REVERT: A 1836 ASN cc_start: 0.7496 (t0) cc_final: 0.7286 (p0) REVERT: A 1887 ASN cc_start: 0.8420 (t0) cc_final: 0.8122 (m110) REVERT: A 1900 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7937 (mp0) REVERT: A 1965 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8215 (mp) REVERT: A 1971 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7566 (tm-30) REVERT: A 1979 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7955 (tp) REVERT: A 1980 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.5769 (tpt170) REVERT: A 2043 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8348 (tt) REVERT: A 2049 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8489 (ttpp) REVERT: A 2052 SER cc_start: 0.8662 (m) cc_final: 0.8202 (p) REVERT: A 2064 ASN cc_start: 0.7900 (t0) cc_final: 0.7657 (t0) REVERT: A 2077 LYS cc_start: 0.7827 (mppt) cc_final: 0.7520 (mppt) REVERT: A 2090 LEU cc_start: 0.8984 (tp) cc_final: 0.8716 (tm) REVERT: A 2110 LYS cc_start: 0.8662 (tttt) cc_final: 0.8308 (tptt) REVERT: A 2193 LYS cc_start: 0.7360 (tppt) cc_final: 0.7068 (mptt) REVERT: A 2229 ILE cc_start: 0.8406 (mt) cc_final: 0.8166 (mp) outliers start: 73 outliers final: 33 residues processed: 509 average time/residue: 1.2223 time to fit residues: 711.4951 Evaluate side-chains 507 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 457 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1122 GLU Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1420 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1677 LYS Chi-restraints excluded: chain A residue 1692 LEU Chi-restraints excluded: chain A residue 1780 LEU Chi-restraints excluded: chain A residue 1790 TRP Chi-restraints excluded: chain A residue 1820 SER Chi-restraints excluded: chain A residue 1823 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 1978 ILE Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 1980 ARG Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2039 GLN Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain A residue 2162 LEU Chi-restraints excluded: chain A residue 2202 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 180 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 100 optimal weight: 0.0170 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 0.0040 chunk 140 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 0.0970 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 245 GLN ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 780 ASN A 956 ASN A1138 ASN A1177 HIS ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1810 HIS A1847 GLN A2039 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.129415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114611 restraints weight = 37781.690| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.00 r_work: 0.3670 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18973 Z= 0.136 Angle : 0.789 16.379 25729 Z= 0.374 Chirality : 0.043 0.287 3019 Planarity : 0.005 0.064 3239 Dihedral : 4.202 43.835 2533 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.10 % Allowed : 31.71 % Favored : 65.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.18), residues: 2309 helix: 1.47 (0.14), residues: 1334 sheet: -0.65 (0.45), residues: 139 loop : -0.29 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1790 HIS 0.013 0.001 HIS B 234 PHE 0.031 0.001 PHE A1880 TYR 0.030 0.001 TYR A2191 ARG 0.014 0.001 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 1052) hydrogen bonds : angle 4.36947 ( 3036) metal coordination : bond 0.01082 ( 7) metal coordination : angle 4.88840 ( 1) covalent geometry : bond 0.00309 (18966) covalent geometry : angle 0.78892 (25728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 480 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 222 MET cc_start: 0.8840 (pp-130) cc_final: 0.8572 (pmm) REVERT: D 251 GLN cc_start: 0.8448 (tp-100) cc_final: 0.7917 (tp-100) REVERT: D 260 LYS cc_start: 0.8975 (tptp) cc_final: 0.8662 (tptp) REVERT: E 234 HIS cc_start: 0.8100 (m-70) cc_final: 0.7724 (m-70) REVERT: E 248 MET cc_start: 0.8587 (tpp) cc_final: 0.8295 (tmm) REVERT: E 252 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7894 (tp) REVERT: B 238 LYS cc_start: 0.8839 (mmtm) cc_final: 0.8588 (mmtm) REVERT: C 235 LEU cc_start: 0.8537 (mt) cc_final: 0.8270 (mt) REVERT: C 238 LYS cc_start: 0.8803 (mttt) cc_final: 0.8595 (mttt) REVERT: C 248 MET cc_start: 0.7810 (mtt) cc_final: 0.7542 (ptp) REVERT: C 280 ASN cc_start: 0.8277 (t0) cc_final: 0.7693 (t0) REVERT: A 11 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: A 65 GLN cc_start: 0.8379 (tp40) cc_final: 0.7961 (tp40) REVERT: A 184 MET cc_start: 0.8124 (tmm) cc_final: 0.7706 (tpp) REVERT: A 323 GLU cc_start: 0.8175 (tp30) cc_final: 0.7712 (tp30) REVERT: A 326 ASP cc_start: 0.7812 (t0) cc_final: 0.7196 (t0) REVERT: A 330 GLU cc_start: 0.7171 (pm20) cc_final: 0.6862 (pm20) REVERT: A 365 MET cc_start: 0.7651 (mpp) cc_final: 0.7422 (mmt) REVERT: A 414 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7999 (ttp-110) REVERT: A 431 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8070 (mppt) REVERT: A 435 GLU cc_start: 0.7730 (pp20) cc_final: 0.7401 (pp20) REVERT: A 436 MET cc_start: 0.8204 (mtt) cc_final: 0.7714 (mtm) REVERT: A 457 MET cc_start: 0.8826 (mtm) cc_final: 0.8431 (mtm) REVERT: A 498 LYS cc_start: 0.7583 (mttp) cc_final: 0.7172 (mmtt) REVERT: A 519 ASN cc_start: 0.7965 (t0) cc_final: 0.7742 (m-40) REVERT: A 536 THR cc_start: 0.8903 (m) cc_final: 0.8576 (p) REVERT: A 540 TYR cc_start: 0.8257 (p90) cc_final: 0.8045 (p90) REVERT: A 545 GLU cc_start: 0.7890 (mp0) cc_final: 0.7636 (mp0) REVERT: A 588 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8416 (mttp) REVERT: A 601 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7427 (pttp) REVERT: A 608 THR cc_start: 0.8450 (m) cc_final: 0.8220 (t) REVERT: A 672 LYS cc_start: 0.8473 (mppt) cc_final: 0.8070 (ptmt) REVERT: A 715 ASP cc_start: 0.7939 (t0) cc_final: 0.7717 (t0) REVERT: A 856 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8508 (p) REVERT: A 916 LYS cc_start: 0.8545 (tmtt) cc_final: 0.8251 (tmtt) REVERT: A 994 LYS cc_start: 0.8730 (mptt) cc_final: 0.8168 (mtmm) REVERT: A 1020 LYS cc_start: 0.8427 (mttt) cc_final: 0.7975 (mttt) REVERT: A 1048 GLU cc_start: 0.7840 (tt0) cc_final: 0.7468 (tm-30) REVERT: A 1054 TYR cc_start: 0.7285 (t80) cc_final: 0.7082 (t80) REVERT: A 1072 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7997 (mm-40) REVERT: A 1122 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7267 (pm20) REVERT: A 1129 ILE cc_start: 0.9019 (mm) cc_final: 0.8662 (pp) REVERT: A 1264 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7369 (mm-30) REVERT: A 1267 GLN cc_start: 0.7440 (tp40) cc_final: 0.6859 (tm-30) REVERT: A 1310 THR cc_start: 0.8601 (p) cc_final: 0.8301 (p) REVERT: A 1419 MET cc_start: 0.7635 (mtp) cc_final: 0.7422 (mtt) REVERT: A 1420 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: A 1421 LYS cc_start: 0.7909 (tppt) cc_final: 0.7374 (tppt) REVERT: A 1425 ILE cc_start: 0.8283 (mm) cc_final: 0.7940 (mt) REVERT: A 1441 GLU cc_start: 0.7538 (tp30) cc_final: 0.6955 (tp30) REVERT: A 1562 ASN cc_start: 0.7745 (m110) cc_final: 0.5331 (m110) REVERT: A 1635 LYS cc_start: 0.8324 (tmmt) cc_final: 0.8050 (tptp) REVERT: A 1654 GLN cc_start: 0.7421 (mt0) cc_final: 0.7062 (mt0) REVERT: A 1666 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7860 (mmpt) REVERT: A 1671 ARG cc_start: 0.8425 (ttp80) cc_final: 0.7198 (ttm110) REVERT: A 1675 GLU cc_start: 0.7557 (pm20) cc_final: 0.7148 (pm20) REVERT: A 1677 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8201 (ttpp) REVERT: A 1692 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7913 (mm) REVERT: A 1693 LEU cc_start: 0.7679 (tp) cc_final: 0.7303 (tm) REVERT: A 1696 ILE cc_start: 0.9093 (mt) cc_final: 0.8788 (mm) REVERT: A 1697 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7777 (mtm110) REVERT: A 1788 THR cc_start: 0.7978 (p) cc_final: 0.7762 (t) REVERT: A 1798 ASN cc_start: 0.7994 (t0) cc_final: 0.7535 (t0) REVERT: A 1813 LEU cc_start: 0.8376 (mm) cc_final: 0.7581 (mm) REVERT: A 1887 ASN cc_start: 0.8395 (t0) cc_final: 0.8101 (m110) REVERT: A 1900 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7920 (mp0) REVERT: A 1971 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 1979 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7868 (tp) REVERT: A 1980 ARG cc_start: 0.5892 (OUTLIER) cc_final: 0.5626 (tpt170) REVERT: A 2039 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6387 (tt0) REVERT: A 2043 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8349 (tt) REVERT: A 2049 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8484 (ttpp) REVERT: A 2052 SER cc_start: 0.8678 (m) cc_final: 0.8211 (p) REVERT: A 2064 ASN cc_start: 0.7880 (t0) cc_final: 0.7636 (t0) REVERT: A 2077 LYS cc_start: 0.7791 (mppt) cc_final: 0.7489 (mppt) REVERT: A 2090 LEU cc_start: 0.8984 (tp) cc_final: 0.8709 (tm) REVERT: A 2110 LYS cc_start: 0.8621 (tttt) cc_final: 0.8304 (tptt) REVERT: A 2142 ARG cc_start: 0.8008 (tpt170) cc_final: 0.7608 (tpp-160) REVERT: A 2198 GLN cc_start: 0.8326 (mt0) cc_final: 0.8000 (mt0) REVERT: A 2229 ILE cc_start: 0.8397 (mt) cc_final: 0.8167 (mp) outliers start: 65 outliers final: 26 residues processed: 513 average time/residue: 1.1772 time to fit residues: 689.6642 Evaluate side-chains 507 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 467 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 1122 GLU Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1420 GLU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1677 LYS Chi-restraints excluded: chain A residue 1692 LEU Chi-restraints excluded: chain A residue 1790 TRP Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1978 ILE Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 1980 ARG Chi-restraints excluded: chain A residue 2039 GLN Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain A residue 2132 ILE Chi-restraints excluded: chain A residue 2202 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 144 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 0.0010 chunk 12 optimal weight: 0.5980 chunk 213 optimal weight: 0.4980 chunk 198 optimal weight: 5.9990 chunk 160 optimal weight: 0.2980 chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 ASN ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 505 ASN A 780 ASN A 956 ASN A1138 ASN A1177 HIS A1358 ASN ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1810 HIS A2039 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.129925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.115179 restraints weight = 37468.980| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.98 r_work: 0.3674 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18973 Z= 0.141 Angle : 0.815 16.984 25729 Z= 0.388 Chirality : 0.044 0.293 3019 Planarity : 0.005 0.064 3239 Dihedral : 4.190 45.641 2533 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.48 % Allowed : 32.90 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 2309 helix: 1.40 (0.14), residues: 1339 sheet: -0.71 (0.45), residues: 139 loop : -0.29 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1481 HIS 0.012 0.001 HIS B 234 PHE 0.031 0.002 PHE A1880 TYR 0.031 0.001 TYR A1094 ARG 0.015 0.001 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 1052) hydrogen bonds : angle 4.40912 ( 3036) metal coordination : bond 0.01225 ( 7) metal coordination : angle 5.04435 ( 1) covalent geometry : bond 0.00327 (18966) covalent geometry : angle 0.81459 (25728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 475 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 222 MET cc_start: 0.8827 (pp-130) cc_final: 0.8602 (pmm) REVERT: D 235 LEU cc_start: 0.9129 (tp) cc_final: 0.8114 (mp) REVERT: D 251 GLN cc_start: 0.8448 (tp-100) cc_final: 0.7924 (tp-100) REVERT: D 260 LYS cc_start: 0.8957 (tptp) cc_final: 0.8638 (tptp) REVERT: E 234 HIS cc_start: 0.8107 (m-70) cc_final: 0.7740 (m-70) REVERT: E 248 MET cc_start: 0.8593 (tpp) cc_final: 0.8283 (tmm) REVERT: E 252 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7900 (tp) REVERT: B 238 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8604 (mmtm) REVERT: C 235 LEU cc_start: 0.8547 (mt) cc_final: 0.8273 (mt) REVERT: C 238 LYS cc_start: 0.8799 (mttt) cc_final: 0.8560 (mttt) REVERT: C 248 MET cc_start: 0.7846 (mtt) cc_final: 0.7569 (ptp) REVERT: C 280 ASN cc_start: 0.8258 (t0) cc_final: 0.7677 (t0) REVERT: A 11 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: A 48 ASN cc_start: 0.8432 (t0) cc_final: 0.7963 (t0) REVERT: A 65 GLN cc_start: 0.8409 (tp40) cc_final: 0.7990 (tp40) REVERT: A 184 MET cc_start: 0.8114 (tmm) cc_final: 0.7800 (tpp) REVERT: A 323 GLU cc_start: 0.8147 (tp30) cc_final: 0.7858 (tp30) REVERT: A 326 ASP cc_start: 0.7794 (t0) cc_final: 0.7189 (t0) REVERT: A 327 LEU cc_start: 0.8410 (mp) cc_final: 0.7935 (mt) REVERT: A 330 GLU cc_start: 0.7187 (pm20) cc_final: 0.6862 (pm20) REVERT: A 414 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7973 (ttp-110) REVERT: A 431 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8072 (mppt) REVERT: A 435 GLU cc_start: 0.7726 (pp20) cc_final: 0.7388 (pp20) REVERT: A 436 MET cc_start: 0.8191 (mtt) cc_final: 0.7708 (mtm) REVERT: A 457 MET cc_start: 0.8841 (mtm) cc_final: 0.8454 (mtm) REVERT: A 498 LYS cc_start: 0.7693 (mttp) cc_final: 0.7314 (mttt) REVERT: A 514 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.8123 (mmm-85) REVERT: A 519 ASN cc_start: 0.8005 (t0) cc_final: 0.7640 (m-40) REVERT: A 536 THR cc_start: 0.8899 (m) cc_final: 0.8567 (p) REVERT: A 540 TYR cc_start: 0.8293 (p90) cc_final: 0.8037 (p90) REVERT: A 545 GLU cc_start: 0.7882 (mp0) cc_final: 0.7564 (mp0) REVERT: A 588 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8379 (mttp) REVERT: A 601 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7411 (pttp) REVERT: A 672 LYS cc_start: 0.8469 (mppt) cc_final: 0.8039 (ptmm) REVERT: A 707 MET cc_start: 0.7818 (mtp) cc_final: 0.7413 (mmm) REVERT: A 856 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8500 (p) REVERT: A 858 LYS cc_start: 0.8740 (ptpt) cc_final: 0.8404 (ptpp) REVERT: A 916 LYS cc_start: 0.8549 (tmtt) cc_final: 0.8266 (tmtt) REVERT: A 994 LYS cc_start: 0.8773 (mptt) cc_final: 0.8218 (mtmm) REVERT: A 1020 LYS cc_start: 0.8434 (mttt) cc_final: 0.7994 (mttt) REVERT: A 1048 GLU cc_start: 0.7860 (tt0) cc_final: 0.7493 (tm-30) REVERT: A 1072 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7997 (mm-40) REVERT: A 1105 LYS cc_start: 0.8292 (mmtm) cc_final: 0.8087 (mmmm) REVERT: A 1122 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: A 1129 ILE cc_start: 0.9024 (mm) cc_final: 0.8676 (pp) REVERT: A 1264 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 1267 GLN cc_start: 0.7449 (tp40) cc_final: 0.6887 (tm-30) REVERT: A 1310 THR cc_start: 0.8628 (p) cc_final: 0.8325 (p) REVERT: A 1419 MET cc_start: 0.7615 (mtp) cc_final: 0.6834 (tpp) REVERT: A 1420 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: A 1421 LYS cc_start: 0.7887 (tppt) cc_final: 0.7349 (tppt) REVERT: A 1425 ILE cc_start: 0.8275 (mm) cc_final: 0.7892 (mm) REVERT: A 1441 GLU cc_start: 0.7524 (tp30) cc_final: 0.6948 (tp30) REVERT: A 1648 LEU cc_start: 0.8580 (mt) cc_final: 0.8141 (mt) REVERT: A 1654 GLN cc_start: 0.7400 (mt0) cc_final: 0.7062 (mt0) REVERT: A 1666 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7816 (mmpt) REVERT: A 1671 ARG cc_start: 0.8428 (ttp80) cc_final: 0.7176 (ttm110) REVERT: A 1675 GLU cc_start: 0.7544 (pm20) cc_final: 0.7153 (pm20) REVERT: A 1677 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8237 (ttpp) REVERT: A 1690 ARG cc_start: 0.6611 (pmm150) cc_final: 0.5431 (mpt90) REVERT: A 1692 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7938 (mm) REVERT: A 1693 LEU cc_start: 0.7672 (tp) cc_final: 0.7401 (tm) REVERT: A 1696 ILE cc_start: 0.9081 (mt) cc_final: 0.8782 (mm) REVERT: A 1697 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7850 (mtm110) REVERT: A 1788 THR cc_start: 0.7957 (p) cc_final: 0.7748 (t) REVERT: A 1798 ASN cc_start: 0.7824 (t0) cc_final: 0.7365 (t0) REVERT: A 1823 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8503 (tp) REVERT: A 1887 ASN cc_start: 0.8346 (t0) cc_final: 0.8050 (m110) REVERT: A 1900 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7893 (mp0) REVERT: A 1945 LYS cc_start: 0.8336 (mtmt) cc_final: 0.7770 (mttp) REVERT: A 1971 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 1979 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7862 (tp) REVERT: A 1980 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.5622 (tpt170) REVERT: A 2039 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: A 2043 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8365 (tt) REVERT: A 2049 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8495 (ttpp) REVERT: A 2052 SER cc_start: 0.8693 (m) cc_final: 0.8228 (p) REVERT: A 2064 ASN cc_start: 0.7880 (t0) cc_final: 0.7632 (t0) REVERT: A 2077 LYS cc_start: 0.7777 (mppt) cc_final: 0.7488 (mppt) REVERT: A 2088 ASN cc_start: 0.8797 (t0) cc_final: 0.8463 (t0) REVERT: A 2090 LEU cc_start: 0.8976 (tp) cc_final: 0.8655 (tm) REVERT: A 2110 LYS cc_start: 0.8653 (tttt) cc_final: 0.8279 (tptt) REVERT: A 2142 ARG cc_start: 0.8022 (tpt170) cc_final: 0.7651 (tpp-160) REVERT: A 2198 GLN cc_start: 0.8222 (mt0) cc_final: 0.7992 (mt0) REVERT: A 2205 MET cc_start: 0.6516 (mmp) cc_final: 0.6313 (tpt) REVERT: A 2229 ILE cc_start: 0.8416 (mt) cc_final: 0.8193 (mp) outliers start: 52 outliers final: 25 residues processed: 502 average time/residue: 1.2362 time to fit residues: 705.8421 Evaluate side-chains 499 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 459 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1122 GLU Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1420 GLU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1677 LYS Chi-restraints excluded: chain A residue 1692 LEU Chi-restraints excluded: chain A residue 1790 TRP Chi-restraints excluded: chain A residue 1823 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1978 ILE Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 1980 ARG Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2039 GLN Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain A residue 2132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 GLN ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 780 ASN A 956 ASN A1177 HIS ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1802 HIS A1810 HIS A2039 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.129234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.114507 restraints weight = 37265.921| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.95 r_work: 0.3663 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18973 Z= 0.155 Angle : 0.830 17.117 25729 Z= 0.398 Chirality : 0.045 0.374 3019 Planarity : 0.005 0.087 3239 Dihedral : 4.267 46.535 2533 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.48 % Allowed : 33.09 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2309 helix: 1.35 (0.14), residues: 1336 sheet: -0.69 (0.45), residues: 139 loop : -0.28 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 488 HIS 0.012 0.001 HIS B 234 PHE 0.031 0.002 PHE A1880 TYR 0.018 0.001 TYR A 838 ARG 0.020 0.001 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 1052) hydrogen bonds : angle 4.47356 ( 3036) metal coordination : bond 0.01571 ( 7) metal coordination : angle 5.59756 ( 1) covalent geometry : bond 0.00363 (18966) covalent geometry : angle 0.82954 (25728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15272.22 seconds wall clock time: 264 minutes 23.04 seconds (15863.04 seconds total)