Starting phenix.real_space_refine on Sat Oct 24 19:04:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t02_25577/10_2026/7t02_25577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t02_25577/10_2026/7t02_25577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t02_25577/10_2026/7t02_25577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t02_25577/10_2026/7t02_25577.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7t02_25577/10_2026/7t02_25577.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t02_25577/10_2026/7t02_25577.cif" model { file = "/net/cci-nas-00/data/ceres_data/7t02_25577/10_2026/7t02_25577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t02_25577/10_2026/7t02_25577.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 24 5.49 5 S 69 5.16 5 C 8955 2.51 5 N 2597 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14359 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1752, 13843 Classifications: {'peptide': 1752} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 79, 'TRANS': 1672} Chain breaks: 21 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' ZN': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3783 SG CYS A 817 67.269 68.841 59.841 1.00 19.31 S ATOM 3798 SG CYS A 819 64.678 66.345 59.573 1.00 21.74 S ATOM 3952 SG CYS A 840 64.904 68.631 62.673 1.00 21.58 S ATOM 3973 SG CYS A 843 67.375 65.782 62.299 1.00 22.56 S ATOM 6613 SG CYS A1200 40.256 38.972 29.021 1.00 59.05 S ATOM 7154 SG CYS A1271 40.631 35.766 31.022 1.00 58.67 S ATOM 7180 SG CYS A1274 42.883 38.798 31.636 1.00 51.12 S ATOM 3888 SG CYS A 832 74.619 80.216 62.537 1.00 26.03 S ATOM 3912 SG CYS A 835 77.726 79.986 60.191 1.00 27.37 S ATOM 5739 SG CYS A1065 79.129 79.281 63.034 1.00 24.90 S ATOM 12151 SG CYS A2081 84.350 78.363 87.720 1.00 67.71 S ATOM 12313 SG CYS A2104 81.125 79.742 86.428 1.00 67.93 S ATOM 12338 SG CYS A2107 84.246 77.826 84.239 1.00 63.42 S ATOM 12281 SG CYS A2099 82.084 64.922 87.906 1.00 37.84 S ATOM 12413 SG CYS A2117 84.893 66.132 86.436 1.00 40.58 S ATOM 12450 SG CYS A2123 86.160 63.935 86.507 1.00 38.16 S Time building chain proxies: 3.14, per 1000 atoms: 0.22 Number of scatterers: 14359 At special positions: 0 Unit cell: (117.04, 105.336, 123.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 69 16.00 P 24 15.00 O 2709 8.00 N 2597 7.00 C 8955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 623.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2401 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 817 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 840 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 819 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 843 " pdb=" ZN A2402 " pdb="ZN ZN A2402 " - pdb=" ND1 HIS A1348 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1274 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1271 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1200 " pdb=" ZN A2403 " pdb="ZN ZN A2403 " - pdb=" ND1 HIS A 849 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 835 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 832 " pdb="ZN ZN A2403 " - pdb=" SG CYS A1065 " pdb=" ZN A2404 " pdb="ZN ZN A2404 " - pdb=" SG CYS A2081 " pdb="ZN ZN A2404 " - pdb=" SG CYS A2107 " pdb="ZN ZN A2404 " - pdb=" SG CYS A2104 " pdb="ZN ZN A2404 " - pdb=" ND1 HIS A2083 " pdb=" ZN A2405 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2123 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2099 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2117 " pdb="ZN ZN A2405 " - pdb=" ND1 HIS A2101 " Number of angles added : 18 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 17 sheets defined 41.9% alpha, 12.3% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.890A pdb=" N GLN A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 375 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.560A pdb=" N LEU A 412 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 413 " --> pdb=" O THR A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 535 through 546 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 563 through 580 removed outlier: 4.182A pdb=" N LEU A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 4.135A pdb=" N ARG A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 636 through 654 removed outlier: 4.297A pdb=" N ASP A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 654 " --> pdb=" O MET A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 708 Processing helix chain 'A' and resid 722 through 733 Processing helix chain 'A' and resid 735 through 750 Processing helix chain 'A' and resid 759 through 781 Processing helix chain 'A' and resid 802 through 814 removed outlier: 3.562A pdb=" N ARG A 812 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 872 Processing helix chain 'A' and resid 882 through 896 Processing helix chain 'A' and resid 902 through 918 Processing helix chain 'A' and resid 969 through 975 Processing helix chain 'A' and resid 1019 through 1025 Processing helix chain 'A' and resid 1044 through 1051 Processing helix chain 'A' and resid 1189 through 1195 Processing helix chain 'A' and resid 1231 through 1240 removed outlier: 7.224A pdb=" N ASN A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR A1238 " --> pdb=" O HIS A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1248 Processing helix chain 'A' and resid 1306 through 1319 Processing helix chain 'A' and resid 1343 through 1354 removed outlier: 3.663A pdb=" N LEU A1354 " --> pdb=" O ALA A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1422 removed outlier: 3.800A pdb=" N LEU A1413 " --> pdb=" O GLN A1409 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP A1415 " --> pdb=" O ARG A1411 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A1418 " --> pdb=" O TRP A1414 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A1419 " --> pdb=" O TRP A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1481 removed outlier: 4.126A pdb=" N ALA A1478 " --> pdb=" O ILE A1474 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLN A1479 " --> pdb=" O ALA A1475 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A1481 " --> pdb=" O VAL A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1519 removed outlier: 3.835A pdb=" N ASN A1513 " --> pdb=" O LYS A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1557 through 1569 removed outlier: 3.959A pdb=" N TRP A1561 " --> pdb=" O SER A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1601 removed outlier: 4.032A pdb=" N ASP A1589 " --> pdb=" O CYS A1585 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A1590 " --> pdb=" O ASP A1586 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1591 " --> pdb=" O ARG A1587 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A1594 " --> pdb=" O ALA A1590 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A1596 " --> pdb=" O MET A1592 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A1597 " --> pdb=" O GLU A1593 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A1598 " --> pdb=" O SER A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1730 Processing helix chain 'A' and resid 1734 through 1741 Processing helix chain 'A' and resid 1757 through 1769 Processing helix chain 'A' and resid 1781 through 1789 Processing helix chain 'A' and resid 1793 through 1803 Processing helix chain 'A' and resid 1806 through 1824 Processing helix chain 'A' and resid 1847 through 1864 Processing helix chain 'A' and resid 1876 through 1888 removed outlier: 4.283A pdb=" N ARG A1882 " --> pdb=" O SER A1878 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1906 Processing helix chain 'A' and resid 1923 through 1961 Processing helix chain 'A' and resid 1971 through 1982 removed outlier: 3.887A pdb=" N GLU A1975 " --> pdb=" O GLN A1971 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A1982 " --> pdb=" O ALA A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2003 Processing helix chain 'A' and resid 2027 through 2068 removed outlier: 3.872A pdb=" N GLY A2068 " --> pdb=" O LYS A2064 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2078 removed outlier: 4.171A pdb=" N VAL A2075 " --> pdb=" O ASP A2071 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A2076 " --> pdb=" O ALA A2072 " (cutoff:3.500A) Processing helix chain 'A' and resid 2105 through 2114 removed outlier: 3.959A pdb=" N LYS A2110 " --> pdb=" O LYS A2106 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A2111 " --> pdb=" O CYS A2107 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2139 removed outlier: 3.910A pdb=" N GLY A2139 " --> pdb=" O VAL A2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2135 through 2139' Processing helix chain 'A' and resid 2150 through 2163 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2202 through 2211 Processing helix chain 'A' and resid 2251 through 2267 removed outlier: 4.117A pdb=" N VAL A2266 " --> pdb=" O ALA A2262 " (cutoff:3.500A) Processing helix chain 'A' and resid 2285 through 2303 removed outlier: 3.843A pdb=" N GLU A2300 " --> pdb=" O THR A2296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.223A pdb=" N LEU A 347 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 383 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 349 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A 385 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR A 351 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N PHE A 406 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER A 385 " --> pdb=" O PHE A 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 434 through 435 removed outlier: 6.400A pdb=" N LEU A 434 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU A 481 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 521 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 663 through 665 Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 783 removed outlier: 3.921A pdb=" N ASP A 792 " --> pdb=" O PHE A1182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 782 through 783 removed outlier: 6.534A pdb=" N ILE A1339 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A1208 " --> pdb=" O PHE A1337 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE A1337 " --> pdb=" O SER A1208 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG A1210 " --> pdb=" O GLY A1335 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A1335 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 838 through 840 Processing sheet with id=AA7, first strand: chain 'A' and resid 1147 through 1148 removed outlier: 3.879A pdb=" N TYR A 926 " --> pdb=" O VAL A 936 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU A 938 " --> pdb=" O PHE A 924 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N PHE A 924 " --> pdb=" O GLU A 938 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1004 through 1007 removed outlier: 3.793A pdb=" N ARG A1124 " --> pdb=" O ASP A1142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1009 through 1010 removed outlier: 3.871A pdb=" N GLU A1009 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A1042 " --> pdb=" O GLU A1009 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU A1015 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL A1039 " --> pdb=" O LYS A1013 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS A1013 " --> pdb=" O VAL A1039 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1009 through 1010 removed outlier: 3.871A pdb=" N GLU A1009 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A1042 " --> pdb=" O GLU A1009 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER A1037 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A1060 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1088 through 1092 removed outlier: 3.507A pdb=" N ASP A1092 " --> pdb=" O ARG A1103 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A1103 " --> pdb=" O ASP A1092 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1364 through 1366 removed outlier: 3.637A pdb=" N GLU A1451 " --> pdb=" O SER A1364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1369 through 1371 Processing sheet with id=AB5, first strand: chain 'A' and resid 1429 through 1430 Processing sheet with id=AB6, first strand: chain 'A' and resid 1550 through 1551 removed outlier: 6.537A pdb=" N LEU A1500 " --> pdb=" O ILE A1723 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A1722 " --> pdb=" O TRP A1747 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU A1749 " --> pdb=" O VAL A1722 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA A1724 " --> pdb=" O LEU A1749 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY A1459 " --> pdb=" O ILE A1748 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N SER A1750 " --> pdb=" O GLY A1459 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE A1461 " --> pdb=" O SER A1750 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A1460 " --> pdb=" O ARG A1826 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1837 through 1844 removed outlier: 6.403A pdb=" N VAL A1838 " --> pdb=" O ILE A2277 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ARG A2279 " --> pdb=" O VAL A1838 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS A1840 " --> pdb=" O ARG A2279 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A2281 " --> pdb=" O HIS A1840 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N HIS A1842 " --> pdb=" O LEU A2281 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A2278 " --> pdb=" O ALA A2241 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A2168 " --> pdb=" O ALA A2238 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS A2240 " --> pdb=" O ARG A2168 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL A2169 " --> pdb=" O LEU A2221 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N LEU A2223 " --> pdb=" O VAL A2169 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A2171 " --> pdb=" O LEU A2223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2102 through 2104 573 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2362 1.31 - 1.44: 3906 1.44 - 1.57: 8269 1.57 - 1.70: 50 1.70 - 1.82: 98 Bond restraints: 14685 Sorted by residual: bond pdb=" C2' 5CM B 30 " pdb=" C1' 5CM B 30 " ideal model delta sigma weight residual 1.530 1.307 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" O4' 5CM B 30 " pdb=" C1' 5CM B 30 " ideal model delta sigma weight residual 1.400 1.620 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C4' 5CM B 30 " pdb=" O4' 5CM B 30 " ideal model delta sigma weight residual 1.432 1.278 0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C2 5CM B 30 " pdb=" N3 5CM B 30 " ideal model delta sigma weight residual 1.348 1.480 -0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" C5 5CM B 30 " pdb=" C6 5CM B 30 " ideal model delta sigma weight residual 1.353 1.478 -0.125 2.00e-02 2.50e+03 3.88e+01 ... (remaining 14680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 19076 2.19 - 4.37: 755 4.37 - 6.56: 110 6.56 - 8.75: 17 8.75 - 10.94: 10 Bond angle restraints: 19968 Sorted by residual: angle pdb=" C GLN A1731 " pdb=" N LYS A1732 " pdb=" CA LYS A1732 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C GLN A1332 " pdb=" N ASP A1333 " pdb=" CA ASP A1333 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C4' DC B 27 " pdb=" O4' DC B 27 " pdb=" C1' DC B 27 " ideal model delta sigma weight residual 110.10 105.61 4.49 1.00e+00 1.00e+00 2.02e+01 angle pdb=" N3 DT D 9 " pdb=" C4 DT D 9 " pdb=" O4 DT D 9 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT D 4 " pdb=" C4 DT D 4 " pdb=" O4 DT D 4 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 19963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7778 17.80 - 35.59: 818 35.59 - 53.39: 195 53.39 - 71.19: 61 71.19 - 88.98: 26 Dihedral angle restraints: 8878 sinusoidal: 3789 harmonic: 5089 Sorted by residual: dihedral pdb=" CA GLN A2124 " pdb=" C GLN A2124 " pdb=" N ALA A2125 " pdb=" CA ALA A2125 " ideal model delta harmonic sigma weight residual -180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA HIS A 849 " pdb=" C HIS A 849 " pdb=" N VAL A 850 " pdb=" CA VAL A 850 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA MET A 734 " pdb=" C MET A 734 " pdb=" N THR A 735 " pdb=" CA THR A 735 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 8875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1790 0.066 - 0.133: 389 0.133 - 0.199: 56 0.199 - 0.265: 5 0.265 - 0.332: 3 Chirality restraints: 2243 Sorted by residual: chirality pdb=" C3' 5CM B 30 " pdb=" C4' 5CM B 30 " pdb=" O3' 5CM B 30 " pdb=" C2' 5CM B 30 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB ILE A 952 " pdb=" CA ILE A 952 " pdb=" CG1 ILE A 952 " pdb=" CG2 ILE A 952 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2240 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A2304 " 0.025 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP A2304 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A2304 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A2304 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A2304 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A2304 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A2304 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2304 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2304 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A2304 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A2284 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ASP A2284 " -0.062 2.00e-02 2.50e+03 pdb=" O ASP A2284 " 0.024 2.00e-02 2.50e+03 pdb=" N THR A2285 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1332 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.62e+00 pdb=" C GLN A1332 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN A1332 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A1333 " 0.018 2.00e-02 2.50e+03 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 163 2.59 - 3.16: 12354 3.16 - 3.74: 21312 3.74 - 4.32: 28410 4.32 - 4.90: 47442 Nonbonded interactions: 109681 Sorted by model distance: nonbonded pdb=" O GLU A 834 " pdb="ZN ZN A2403 " model vdw 2.007 2.230 nonbonded pdb=" O GLU A 834 " pdb=" SG CYS A 835 " model vdw 2.211 3.400 nonbonded pdb=" O SER A1071 " pdb=" OG SER A1071 " model vdw 2.246 3.040 nonbonded pdb=" NH2 ARG A1802 " pdb=" OE1 GLU A1803 " model vdw 2.247 3.120 nonbonded pdb=" O LEU A 347 " pdb=" N GLU A 381 " model vdw 2.248 3.120 ... (remaining 109676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.620 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.012 0.532 14705 Z= 0.530 Angle : 1.170 44.988 19986 Z= 0.589 Chirality : 0.056 0.332 2243 Planarity : 0.006 0.070 2483 Dihedral : 16.674 88.983 5546 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.27 % Allowed : 0.53 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.19), residues: 1708 helix: 0.12 (0.19), residues: 698 sheet: -1.15 (0.31), residues: 277 loop : -2.32 (0.19), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 858 TYR 0.034 0.003 TYR A 851 PHE 0.031 0.003 PHE A1106 TRP 0.064 0.003 TRP A2304 HIS 0.010 0.002 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.01066 / 0.52 (14685) covalent geometry : angle 1.01143 / 0.57 (19968) hydrogen bonds : bond 0.15354 / 10.97 ( 575) hydrogen bonds : angle 6.82705 / 4.82 ( 1658) metal coordination : bond 0.15174 / 9.89 ( 20) metal coordination : angle 19.61930 / 11.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8869 (mtt) cc_final: 0.8533 (mtt) REVERT: A 1125 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8817 (tt) REVERT: A 1240 PHE cc_start: 0.7597 (m-80) cc_final: 0.7349 (m-80) REVERT: A 1975 GLU cc_start: 0.7475 (mp0) cc_final: 0.7210 (mp0) outliers start: 4 outliers final: 2 residues processed: 109 average time/residue: 0.1102 time to fit residues: 18.7938 Evaluate side-chains 80 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN A1883 ASN A1927 HIS A2254 ASN ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115224 restraints weight = 24290.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115270 restraints weight = 22942.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116380 restraints weight = 22119.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116663 restraints weight = 14516.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.116923 restraints weight = 13833.801| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 14705 Z= 0.154 Angle : 0.700 13.020 19986 Z= 0.355 Chirality : 0.043 0.233 2243 Planarity : 0.005 0.059 2483 Dihedral : 13.929 87.948 2168 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.80 % Allowed : 7.09 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.20), residues: 1708 helix: 0.80 (0.20), residues: 698 sheet: -0.93 (0.32), residues: 263 loop : -2.04 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 858 TYR 0.013 0.001 TYR A 851 PHE 0.021 0.002 PHE A1767 TRP 0.017 0.002 TRP A1511 HIS 0.020 0.001 HIS A1373 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (14685) covalent geometry : angle 0.67188 / 0.35 (19968) hydrogen bonds : bond 0.05187 / 3.60 ( 575) hydrogen bonds : angle 5.48547 / 3.81 ( 1658) metal coordination : bond 0.02596 / 1.77 ( 20) metal coordination : angle 6.54535 / 3.97 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.496 Fit side-chains REVERT: A 650 MET cc_start: 0.8802 (ttm) cc_final: 0.8479 (ttm) REVERT: A 1125 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8658 (tt) REVERT: A 1304 PHE cc_start: 0.6500 (m-80) cc_final: 0.6280 (m-80) REVERT: A 1332 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 1975 GLU cc_start: 0.7336 (mp0) cc_final: 0.7065 (mp0) outliers start: 12 outliers final: 7 residues processed: 116 average time/residue: 0.1051 time to fit residues: 19.5620 Evaluate side-chains 90 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 2177 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [22, 136, 83, 7, 151, 74, 167, 119, 24, 115, 121] chunk 22 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 7 optimal weight: 0.0370 chunk 151 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 HIS A1049 ASN ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 HIS ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 ASN ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2278 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118136 restraints weight = 24489.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118383 restraints weight = 24000.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119582 restraints weight = 20563.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120180 restraints weight = 15562.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120414 restraints weight = 15749.298| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14705 Z= 0.125 Angle : 0.628 13.942 19986 Z= 0.317 Chirality : 0.040 0.197 2243 Planarity : 0.005 0.069 2483 Dihedral : 13.446 85.678 2166 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.54 % Allowed : 10.29 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1708 helix: 1.23 (0.20), residues: 699 sheet: -0.81 (0.31), residues: 263 loop : -1.80 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 345 TYR 0.024 0.001 TYR A 522 PHE 0.020 0.002 PHE A1767 TRP 0.018 0.001 TRP A1511 HIS 0.019 0.001 HIS A1373 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (14685) covalent geometry : angle 0.60315 / 0.31 (19968) hydrogen bonds : bond 0.04448 / 3.11 ( 575) hydrogen bonds : angle 4.99660 / 3.49 ( 1658) metal coordination : bond 0.01492 / 0.90 ( 20) metal coordination : angle 5.90711 / 3.49 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.373 Fit side-chains REVERT: A 594 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7545 (tm-30) REVERT: A 650 MET cc_start: 0.8787 (ttm) cc_final: 0.8308 (ttm) REVERT: A 1113 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8548 (pp) REVERT: A 1125 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8614 (tt) REVERT: A 1304 PHE cc_start: 0.6417 (m-80) cc_final: 0.6204 (m-80) REVERT: A 1373 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7277 (p90) REVERT: A 1883 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8640 (t0) REVERT: A 1975 GLU cc_start: 0.7274 (mp0) cc_final: 0.7033 (mp0) outliers start: 23 outliers final: 8 residues processed: 119 average time/residue: 0.0955 time to fit residues: 18.2953 Evaluate side-chains 99 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 2177 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [67, 60, 76, 118, 64, 70, 158, 13, 44, 0, 160] chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 HIS ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113279 restraints weight = 24709.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113346 restraints weight = 26775.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114148 restraints weight = 26034.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114661 restraints weight = 16772.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115158 restraints weight = 15026.889| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14705 Z= 0.262 Angle : 0.713 14.666 19986 Z= 0.361 Chirality : 0.044 0.208 2243 Planarity : 0.005 0.068 2483 Dihedral : 13.665 88.452 2162 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.94 % Allowed : 13.44 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1708 helix: 1.01 (0.20), residues: 711 sheet: -0.93 (0.32), residues: 268 loop : -1.93 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 548 TYR 0.023 0.002 TYR A 522 PHE 0.017 0.002 PHE A1798 TRP 0.016 0.002 TRP A1511 HIS 0.031 0.002 HIS A1373 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.26 (14685) covalent geometry : angle 0.69337 / 0.36 (19968) hydrogen bonds : bond 0.05071 / 3.57 ( 575) hydrogen bonds : angle 5.13695 / 3.62 ( 1658) metal coordination : bond 0.01733 / 1.03 ( 20) metal coordination : angle 5.59567 / 3.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.559 Fit side-chains REVERT: A 1113 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8677 (pp) REVERT: A 1883 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8720 (t0) outliers start: 29 outliers final: 16 residues processed: 105 average time/residue: 0.1024 time to fit residues: 17.3824 Evaluate side-chains 101 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2254 ASN Chi-restraints excluded: chain A residue 2296 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [34, 114, 152, 91, 46, 39, 69, 21, 153, 48, 127] chunk 34 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 127 optimal weight: 0.0030 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115805 restraints weight = 24289.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115770 restraints weight = 24446.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116398 restraints weight = 23640.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117180 restraints weight = 17228.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117391 restraints weight = 15514.959| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14705 Z= 0.148 Angle : 0.624 14.635 19986 Z= 0.315 Chirality : 0.041 0.195 2243 Planarity : 0.005 0.069 2483 Dihedral : 13.446 88.498 2160 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.27 % Allowed : 14.30 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1708 helix: 1.27 (0.20), residues: 710 sheet: -0.84 (0.32), residues: 265 loop : -1.84 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 858 TYR 0.021 0.001 TYR A 522 PHE 0.016 0.002 PHE A 864 TRP 0.017 0.001 TRP A1511 HIS 0.004 0.001 HIS A1373 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (14685) covalent geometry : angle 0.60532 / 0.31 (19968) hydrogen bonds : bond 0.04371 / 3.05 ( 575) hydrogen bonds : angle 4.86499 / 3.41 ( 1658) metal coordination : bond 0.01149 / 0.76 ( 20) metal coordination : angle 5.06963 / 2.97 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.493 Fit side-chains REVERT: A 650 MET cc_start: 0.8792 (ttm) cc_final: 0.8410 (ttm) REVERT: A 1113 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8605 (pp) REVERT: A 1883 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8662 (t0) REVERT: A 1971 GLN cc_start: 0.7316 (mt0) cc_final: 0.6639 (mt0) REVERT: A 2153 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7709 (mt) outliers start: 34 outliers final: 18 residues processed: 114 average time/residue: 0.0925 time to fit residues: 17.1107 Evaluate side-chains 106 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2289 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [2, 65, 55, 174, 163, 99, 45, 97, 170, 78, 124] chunk 2 optimal weight: 0.0370 chunk 65 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.137614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114910 restraints weight = 24142.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113877 restraints weight = 26966.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115252 restraints weight = 25158.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115666 restraints weight = 16550.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115944 restraints weight = 15838.339| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14705 Z= 0.174 Angle : 0.636 13.974 19986 Z= 0.321 Chirality : 0.041 0.200 2243 Planarity : 0.004 0.057 2483 Dihedral : 13.471 89.839 2160 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.81 % Allowed : 15.11 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.20), residues: 1708 helix: 1.36 (0.20), residues: 702 sheet: -0.83 (0.32), residues: 270 loop : -1.80 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 858 TYR 0.023 0.002 TYR A 522 PHE 0.015 0.002 PHE A 864 TRP 0.019 0.001 TRP A1511 HIS 0.006 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (14685) covalent geometry : angle 0.61623 / 0.32 (19968) hydrogen bonds : bond 0.04413 / 3.09 ( 575) hydrogen bonds : angle 4.83590 / 3.40 ( 1658) metal coordination : bond 0.01597 / 1.00 ( 20) metal coordination : angle 5.23905 / 3.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 0.546 Fit side-chains REVERT: A 650 MET cc_start: 0.8869 (ttm) cc_final: 0.8434 (ttm) REVERT: A 1113 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8638 (pp) REVERT: A 1883 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8707 (t0) REVERT: A 1971 GLN cc_start: 0.7300 (mt0) cc_final: 0.6628 (mt0) REVERT: A 2081 CYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6941 (t) outliers start: 42 outliers final: 22 residues processed: 121 average time/residue: 0.1026 time to fit residues: 19.7128 Evaluate side-chains 111 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 2081 CYS Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2296 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [111, 20, 75, 71, 118, 66, 39, 73, 134, 95, 107] chunk 111 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 118 optimal weight: 0.0070 chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116569 restraints weight = 24053.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115554 restraints weight = 25539.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116407 restraints weight = 24730.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117259 restraints weight = 17643.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117630 restraints weight = 15754.737| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14705 Z= 0.129 Angle : 0.608 15.936 19986 Z= 0.304 Chirality : 0.040 0.193 2243 Planarity : 0.004 0.053 2483 Dihedral : 13.327 87.751 2160 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.27 % Allowed : 16.38 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.21), residues: 1708 helix: 1.49 (0.20), residues: 703 sheet: -0.83 (0.32), residues: 275 loop : -1.69 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 858 TYR 0.020 0.001 TYR A 522 PHE 0.017 0.001 PHE A 864 TRP 0.019 0.001 TRP A1511 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14685) covalent geometry : angle 0.58771 / 0.30 (19968) hydrogen bonds : bond 0.04073 / 2.84 ( 575) hydrogen bonds : angle 4.68769 / 3.28 ( 1658) metal coordination : bond 0.01272 / 0.88 ( 20) metal coordination : angle 5.25199 / 3.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.641 Fit side-chains REVERT: A 650 MET cc_start: 0.8871 (ttm) cc_final: 0.8439 (ttm) REVERT: A 1113 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8590 (pp) REVERT: A 1240 PHE cc_start: 0.7375 (m-80) cc_final: 0.7145 (m-80) REVERT: A 1883 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8681 (t0) REVERT: A 1971 GLN cc_start: 0.7315 (mt0) cc_final: 0.6586 (mt0) REVERT: A 2081 CYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6746 (t) outliers start: 34 outliers final: 21 residues processed: 115 average time/residue: 0.0979 time to fit residues: 18.4090 Evaluate side-chains 109 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 2081 CYS Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2223 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [160, 152, 174, 132, 125, 20, 149, 121, 138, 69, 140] chunk 160 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114806 restraints weight = 24154.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114613 restraints weight = 26049.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115166 restraints weight = 24101.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115945 restraints weight = 18620.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116155 restraints weight = 16561.295| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14705 Z= 0.192 Angle : 0.646 15.545 19986 Z= 0.324 Chirality : 0.041 0.199 2243 Planarity : 0.005 0.053 2483 Dihedral : 13.419 89.662 2160 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.14 % Allowed : 17.11 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.20), residues: 1708 helix: 1.44 (0.20), residues: 701 sheet: -0.84 (0.32), residues: 275 loop : -1.74 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 858 TYR 0.022 0.002 TYR A 522 PHE 0.016 0.002 PHE A1555 TRP 0.019 0.001 TRP A1511 HIS 0.007 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (14685) covalent geometry : angle 0.62734 / 0.32 (19968) hydrogen bonds : bond 0.04416 / 3.08 ( 575) hydrogen bonds : angle 4.78097 / 3.35 ( 1658) metal coordination : bond 0.01429 / 0.87 ( 20) metal coordination : angle 5.18057 / 2.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.554 Fit side-chains REVERT: A 650 MET cc_start: 0.8876 (ttm) cc_final: 0.8426 (ttm) REVERT: A 1113 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8664 (pp) REVERT: A 1240 PHE cc_start: 0.7503 (m-80) cc_final: 0.7264 (m-80) REVERT: A 1883 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8729 (t0) REVERT: A 1971 GLN cc_start: 0.7296 (mt0) cc_final: 0.6661 (mt0) outliers start: 32 outliers final: 23 residues processed: 107 average time/residue: 0.0973 time to fit residues: 16.6975 Evaluate side-chains 108 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 2081 CYS Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2223 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [53, 22, 174, 108, 140, 161, 27, 14, 84, 23, 134] chunk 53 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 174 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.117801 restraints weight = 24120.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117232 restraints weight = 24817.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118576 restraints weight = 24079.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118878 restraints weight = 15909.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119285 restraints weight = 14866.443| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14705 Z= 0.118 Angle : 0.592 14.968 19986 Z= 0.296 Chirality : 0.039 0.191 2243 Planarity : 0.004 0.055 2483 Dihedral : 13.140 85.583 2160 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.67 % Allowed : 17.85 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1708 helix: 1.69 (0.20), residues: 701 sheet: -0.80 (0.31), residues: 275 loop : -1.57 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 518 TYR 0.013 0.001 TYR A 522 PHE 0.019 0.001 PHE A 864 TRP 0.020 0.001 TRP A1511 HIS 0.005 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14685) covalent geometry : angle 0.57399 / 0.29 (19968) hydrogen bonds : bond 0.03795 / 2.63 ( 575) hydrogen bonds : angle 4.57117 / 3.18 ( 1658) metal coordination : bond 0.01262 / 0.86 ( 20) metal coordination : angle 4.86070 / 2.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.527 Fit side-chains REVERT: A 650 MET cc_start: 0.8844 (ttm) cc_final: 0.8402 (ttm) REVERT: A 1240 PHE cc_start: 0.7397 (m-80) cc_final: 0.7182 (m-80) REVERT: A 1883 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8670 (t0) REVERT: A 1971 GLN cc_start: 0.7210 (mt0) cc_final: 0.6207 (mt0) REVERT: A 1975 GLU cc_start: 0.7470 (mp0) cc_final: 0.7167 (mp0) REVERT: A 2261 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8290 (tt0) outliers start: 25 outliers final: 20 residues processed: 115 average time/residue: 0.1058 time to fit residues: 19.3729 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 2081 CYS Chi-restraints excluded: chain A residue 2177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [84, 120, 91, 114, 132, 108, 172, 139, 136, 75, 77] chunk 84 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 114 optimal weight: 0.0980 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.139804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117093 restraints weight = 24019.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116441 restraints weight = 25901.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117800 restraints weight = 25471.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118107 restraints weight = 16445.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118438 restraints weight = 15171.286| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14705 Z= 0.135 Angle : 0.604 15.153 19986 Z= 0.301 Chirality : 0.040 0.192 2243 Planarity : 0.004 0.057 2483 Dihedral : 13.140 86.803 2160 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.67 % Allowed : 18.11 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1708 helix: 1.69 (0.20), residues: 701 sheet: -0.83 (0.31), residues: 275 loop : -1.54 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 340 TYR 0.026 0.001 TYR A 522 PHE 0.016 0.001 PHE A 864 TRP 0.041 0.001 TRP A1511 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (14685) covalent geometry : angle 0.58678 / 0.30 (19968) hydrogen bonds : bond 0.03888 / 2.70 ( 575) hydrogen bonds : angle 4.56407 / 3.19 ( 1658) metal coordination : bond 0.01264 / 0.83 ( 20) metal coordination : angle 4.76727 / 2.75 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.576 Fit side-chains REVERT: A 650 MET cc_start: 0.8857 (ttm) cc_final: 0.8383 (ttm) REVERT: A 1240 PHE cc_start: 0.7451 (m-80) cc_final: 0.7204 (m-80) REVERT: A 1883 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8673 (t0) outliers start: 25 outliers final: 21 residues processed: 110 average time/residue: 0.1056 time to fit residues: 18.4898 Evaluate side-chains 111 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 2081 CYS Chi-restraints excluded: chain A residue 2177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [161, 8, 100, 63, 5, 79, 143, 47, 85, 99, 74] chunk 161 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.141680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118660 restraints weight = 23947.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119134 restraints weight = 23859.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120236 restraints weight = 22587.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120584 restraints weight = 15530.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120810 restraints weight = 15291.861| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14705 Z= 0.111 Angle : 0.588 16.269 19986 Z= 0.292 Chirality : 0.039 0.189 2243 Planarity : 0.004 0.058 2483 Dihedral : 12.962 84.267 2160 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.54 % Allowed : 18.45 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1708 helix: 1.84 (0.20), residues: 701 sheet: -0.68 (0.32), residues: 261 loop : -1.47 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 340 TYR 0.019 0.001 TYR A 522 PHE 0.018 0.001 PHE A 864 TRP 0.029 0.001 TRP A1511 HIS 0.005 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14685) covalent geometry : angle 0.57094 / 0.29 (19968) hydrogen bonds : bond 0.03575 / 2.49 ( 575) hydrogen bonds : angle 4.44246 / 3.10 ( 1658) metal coordination : bond 0.01286 / 0.89 ( 20) metal coordination : angle 4.68689 / 2.71 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1678.62 seconds wall clock time: 30 minutes 3.51 seconds (1803.51 seconds total)