Starting phenix.real_space_refine on Fri Sep 11 17:27:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6or5_9032/09_2026/6or5_9032.cif Found real_map, /net/cci-nas-00/data/ceres_data/6or5_9032/09_2026/6or5_9032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6or5_9032/09_2026/6or5_9032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6or5_9032/09_2026/6or5_9032.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6or5_9032/09_2026/6or5_9032.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6or5_9032/09_2026/6or5_9032.cif" model { file = "/net/cci-nas-00/data/ceres_data/6or5_9032/09_2026/6or5_9032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6or5_9032/09_2026/6or5_9032.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.030 sd= 0.761 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 15 5.49 5 C 6143 2.51 5 N 2088 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10364 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2058, 10209 Classifications: {'peptide': 2058} Incomplete info: {'truncation_to_alanine': 1855} Link IDs: {'PTRANS': 74, 'TRANS': 1983} Chain breaks: 55 Unresolved chain link angles: 74 Unresolved non-hydrogen bonds: 6745 Unresolved non-hydrogen angles: 8670 Unresolved non-hydrogen dihedrals: 5586 Unresolved non-hydrogen chiralities: 687 Planarities with less than four sites: {'ASP:plan': 95, 'GLU:plan': 145, 'TRP:plan': 27, 'TYR:plan': 67, 'GLN:plan1': 79, 'HIS:plan': 53, 'ASN:plan1': 97, 'ARG:plan': 110, 'PHE:plan': 98} Unresolved non-hydrogen planarities: 3587 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 155 Unusual residues: {'ANP': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.50, per 1000 atoms: 0.24 Number of scatterers: 10364 At special positions: 0 Unit cell: (136.5, 172.9, 110.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 15 15.00 O 2118 8.00 N 2088 7.00 C 6143 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: 1.64 Conformation dependent library (CDL) restraints added in 857.5 milliseconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 7 sheets defined 56.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.525A pdb=" N ASN A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.532A pdb=" N ALA A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 removed outlier: 3.778A pdb=" N CYS A 58 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.578A pdb=" N LEU A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 136 through 152 Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 164 through 176 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.593A pdb=" N VAL A 297 " --> pdb=" O CYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 304 Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 374 through 381 removed outlier: 3.617A pdb=" N ILE A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 402 Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.522A pdb=" N GLN A 411 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 412 " --> pdb=" O ALA A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 408 through 412' Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.711A pdb=" N THR A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 505 through 510 removed outlier: 3.962A pdb=" N MET A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.846A pdb=" N LEU A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.650A pdb=" N ALA A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 removed outlier: 3.764A pdb=" N ALA A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 616 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 654 through 663 removed outlier: 3.967A pdb=" N SER A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.840A pdb=" N SER A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'A' and resid 777 through 789 Processing helix chain 'A' and resid 795 through 806 removed outlier: 3.586A pdb=" N SER A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 828 Processing helix chain 'A' and resid 833 through 840 Processing helix chain 'A' and resid 877 through 891 Processing helix chain 'A' and resid 906 through 916 Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.673A pdb=" N TYR A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 3.528A pdb=" N ALA A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 973 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1041 through 1053 removed outlier: 3.707A pdb=" N HIS A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A1051 " --> pdb=" O THR A1047 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1074 removed outlier: 4.032A pdb=" N ARG A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1103 through 1116 Processing helix chain 'A' and resid 1121 through 1135 removed outlier: 3.549A pdb=" N MET A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1186 removed outlier: 3.817A pdb=" N ARG A1174 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU A1175 " --> pdb=" O PRO A1171 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU A1178 " --> pdb=" O ARG A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1210 Processing helix chain 'A' and resid 1226 through 1231 removed outlier: 4.017A pdb=" N GLY A1230 " --> pdb=" O GLY A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1249 removed outlier: 3.698A pdb=" N ASN A1242 " --> pdb=" O ARG A1238 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A1245 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A1246 " --> pdb=" O ASN A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1272 removed outlier: 3.683A pdb=" N LEU A1272 " --> pdb=" O LYS A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1290 Processing helix chain 'A' and resid 1301 through 1309 Processing helix chain 'A' and resid 1317 through 1321 Processing helix chain 'A' and resid 1323 through 1334 removed outlier: 3.906A pdb=" N GLU A1334 " --> pdb=" O ASN A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1381 Processing helix chain 'A' and resid 1394 through 1404 Processing helix chain 'A' and resid 1411 through 1426 removed outlier: 3.950A pdb=" N GLU A1417 " --> pdb=" O ARG A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1446 removed outlier: 3.595A pdb=" N VAL A1437 " --> pdb=" O SER A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1463 Processing helix chain 'A' and resid 1481 through 1498 Processing helix chain 'A' and resid 1543 through 1557 removed outlier: 3.728A pdb=" N GLN A1557 " --> pdb=" O LEU A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1577 Processing helix chain 'A' and resid 1598 through 1603 Processing helix chain 'A' and resid 1622 through 1629 Processing helix chain 'A' and resid 1637 through 1641 Processing helix chain 'A' and resid 1644 through 1653 Processing helix chain 'A' and resid 1709 through 1718 Processing helix chain 'A' and resid 1725 through 1744 Processing helix chain 'A' and resid 1759 through 1771 removed outlier: 3.602A pdb=" N ASN A1771 " --> pdb=" O LEU A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1788 Processing helix chain 'A' and resid 1795 through 1811 Processing helix chain 'A' and resid 1852 through 1854 No H-bonds generated for 'chain 'A' and resid 1852 through 1854' Processing helix chain 'A' and resid 1855 through 1868 removed outlier: 3.654A pdb=" N GLU A1860 " --> pdb=" O LEU A1856 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER A1861 " --> pdb=" O PRO A1857 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1882 through 1894 Processing helix chain 'A' and resid 1907 through 1912 Processing helix chain 'A' and resid 1920 through 1942 removed outlier: 3.808A pdb=" N LYS A1941 " --> pdb=" O ASN A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1958 Processing helix chain 'A' and resid 1969 through 1980 removed outlier: 3.680A pdb=" N GLN A1973 " --> pdb=" O PHE A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 2003 removed outlier: 4.279A pdb=" N ILE A1995 " --> pdb=" O SER A1991 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A1998 " --> pdb=" O ASP A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2020 through 2025 removed outlier: 3.926A pdb=" N ALA A2024 " --> pdb=" O TYR A2020 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2052 removed outlier: 3.854A pdb=" N LEU A2044 " --> pdb=" O SER A2040 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A2050 " --> pdb=" O ARG A2046 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A2052 " --> pdb=" O ASN A2048 " (cutoff:3.500A) Processing helix chain 'A' and resid 2092 through 2097 Processing helix chain 'A' and resid 2109 through 2117 removed outlier: 3.563A pdb=" N MET A2117 " --> pdb=" O ASP A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2143 removed outlier: 4.055A pdb=" N ILE A2136 " --> pdb=" O LEU A2132 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A2143 " --> pdb=" O ILE A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2167 removed outlier: 4.176A pdb=" N ALA A2159 " --> pdb=" O TYR A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2178 Processing helix chain 'A' and resid 2199 through 2214 removed outlier: 3.787A pdb=" N GLN A2204 " --> pdb=" O LYS A2200 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A2205 " --> pdb=" O ASN A2201 " (cutoff:3.500A) Processing helix chain 'A' and resid 2217 through 2228 Processing helix chain 'A' and resid 2238 through 2245 removed outlier: 3.515A pdb=" N PHE A2245 " --> pdb=" O THR A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2280 removed outlier: 3.928A pdb=" N THR A2259 " --> pdb=" O GLU A2255 " (cutoff:3.500A) Processing helix chain 'A' and resid 2291 through 2298 Processing helix chain 'A' and resid 2312 through 2329 removed outlier: 4.177A pdb=" N PHE A2320 " --> pdb=" O LEU A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2333 through 2337 Processing helix chain 'A' and resid 2342 through 2360 Processing helix chain 'A' and resid 2369 through 2383 Processing helix chain 'A' and resid 2390 through 2407 Proline residue: A2396 - end of helix Processing helix chain 'A' and resid 2759 through 2783 removed outlier: 4.101A pdb=" N LEU A2781 " --> pdb=" O ILE A2777 " (cutoff:3.500A) Processing helix chain 'A' and resid 2788 through 2800 removed outlier: 3.889A pdb=" N ASN A2800 " --> pdb=" O THR A2796 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 182 through 184 Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496 removed outlier: 5.827A pdb=" N TRP A 641 " --> pdb=" O THR A 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 923 through 926 removed outlier: 6.625A pdb=" N VAL A 923 " --> pdb=" O VAL A 966 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP A 968 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 925 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 967 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A1010 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1215 through 1218 removed outlier: 7.308A pdb=" N HIS A1215 " --> pdb=" O LEU A1314 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASP A1316 " --> pdb=" O HIS A1215 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A1217 " --> pdb=" O ASP A1316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1587 through 1591 removed outlier: 6.158A pdb=" N ILE A1562 " --> pdb=" O ALA A1678 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A1563 " --> pdb=" O VAL A1703 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1822 through 1823 Processing sheet with id=AA7, first strand: chain 'A' and resid 1897 through 1901 removed outlier: 6.429A pdb=" N LYS A1898 " --> pdb=" O VAL A2032 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP A2034 " --> pdb=" O LYS A1898 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N MET A1900 " --> pdb=" O ASP A2034 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A2031 " --> pdb=" O PHE A2081 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR A2083 " --> pdb=" O PHE A2031 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A2033 " --> pdb=" O THR A2083 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS A1872 " --> pdb=" O LEU A2082 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.31: 2071 1.31 - 1.41: 2045 1.41 - 1.50: 2115 1.50 - 1.60: 4077 1.60 - 1.69: 10 Bond restraints: 10318 Sorted by residual: bond pdb=" O3A ANP A7204 " pdb=" PB ANP A7204 " ideal model delta sigma weight residual 1.700 1.534 0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" O3A ANP A7203 " pdb=" PB ANP A7203 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" O3A ANP A7201 " pdb=" PB ANP A7201 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" O3A ANP A7205 " pdb=" PB ANP A7205 " ideal model delta sigma weight residual 1.700 1.545 0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" O3A ANP A7202 " pdb=" PB ANP A7202 " ideal model delta sigma weight residual 1.700 1.562 0.138 2.00e-02 2.50e+03 4.74e+01 ... (remaining 10313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.31: 14259 5.31 - 10.61: 63 10.61 - 15.92: 9 15.92 - 21.22: 2 21.22 - 26.53: 3 Bond angle restraints: 14336 Sorted by residual: angle pdb=" PB ANP A7201 " pdb=" N3B ANP A7201 " pdb=" PG ANP A7201 " ideal model delta sigma weight residual 126.95 100.42 26.53 3.00e+00 1.11e-01 7.82e+01 angle pdb=" PB ANP A7205 " pdb=" N3B ANP A7205 " pdb=" PG ANP A7205 " ideal model delta sigma weight residual 126.95 101.31 25.64 3.00e+00 1.11e-01 7.31e+01 angle pdb=" PB ANP A7204 " pdb=" N3B ANP A7204 " pdb=" PG ANP A7204 " ideal model delta sigma weight residual 126.95 103.33 23.62 3.00e+00 1.11e-01 6.20e+01 angle pdb=" N ILE A1055 " pdb=" CA ILE A1055 " pdb=" C ILE A1055 " ideal model delta sigma weight residual 108.17 119.01 -10.84 1.40e+00 5.10e-01 5.99e+01 angle pdb=" PA ANP A7205 " pdb=" O3A ANP A7205 " pdb=" PB ANP A7205 " ideal model delta sigma weight residual 125.41 107.68 17.73 3.00e+00 1.11e-01 3.49e+01 ... (remaining 14331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 5964 35.14 - 70.29: 6 70.29 - 105.43: 2 105.43 - 140.58: 3 140.58 - 175.72: 1 Dihedral angle restraints: 5976 sinusoidal: 20 harmonic: 5956 Sorted by residual: dihedral pdb=" CA HIS A 424 " pdb=" C HIS A 424 " pdb=" N ASN A 425 " pdb=" CA ASN A 425 " ideal model delta harmonic sigma weight residual 180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ILE A1661 " pdb=" C ILE A1661 " pdb=" N PRO A1662 " pdb=" CA PRO A1662 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLY A 794 " pdb=" C GLY A 794 " pdb=" N LEU A 795 " pdb=" CA LEU A 795 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 5973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1682 0.066 - 0.132: 286 0.132 - 0.198: 22 0.198 - 0.263: 5 0.263 - 0.329: 2 Chirality restraints: 1997 Sorted by residual: chirality pdb=" C3' ANP A7202 " pdb=" C2' ANP A7202 " pdb=" C4' ANP A7202 " pdb=" O3' ANP A7202 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3' ANP A7204 " pdb=" C2' ANP A7204 " pdb=" C4' ANP A7204 " pdb=" O3' ANP A7204 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C3' ANP A7203 " pdb=" C2' ANP A7203 " pdb=" C4' ANP A7203 " pdb=" O3' ANP A7203 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1994 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A2223 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C MET A2223 " -0.063 2.00e-02 2.50e+03 pdb=" O MET A2223 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A2224 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 46 " -0.012 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C TRP A 46 " 0.039 2.00e-02 2.50e+03 pdb=" O TRP A 46 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 47 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 54 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ILE A 54 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 54 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 55 " 0.012 2.00e-02 2.50e+03 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2780 2.78 - 3.31: 10352 3.31 - 3.84: 15288 3.84 - 4.37: 15546 4.37 - 4.90: 24049 Nonbonded interactions: 68015 Sorted by model distance: nonbonded pdb=" O2B ANP A7205 " pdb=" O2G ANP A7205 " model vdw 2.245 3.040 nonbonded pdb=" O1B ANP A7201 " pdb=" O2A ANP A7201 " model vdw 2.261 3.040 nonbonded pdb=" O ALA A 50 " pdb=" CB ARG A 55 " model vdw 2.264 3.440 nonbonded pdb=" O PHE A2222 " pdb=" CB TYR A2226 " model vdw 2.282 2.752 nonbonded pdb=" C ALA A1659 " pdb=" O ASP A1665 " model vdw 2.282 3.270 ... (remaining 68010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.340 Find NCS groups from input model: 0.060 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.166 10318 Z= 0.464 Angle : 1.123 26.527 14336 Z= 0.624 Chirality : 0.050 0.329 1997 Planarity : 0.005 0.037 2007 Dihedral : 10.845 175.724 2022 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 17.32 % Favored : 82.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.53 (0.14), residues: 1946 helix: -2.84 (0.11), residues: 1059 sheet: -4.87 (0.34), residues: 102 loop : -4.63 (0.18), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.46 (10318) covalent geometry : angle 1.12293 / 0.62 (14336) hydrogen bonds : bond 0.18340 / 13.60 ( 724) hydrogen bonds : angle 8.18329 / 5.85 ( 2124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.363 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0441 time to fit residues: 3.5531 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.045612 restraints weight = 94159.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.046211 restraints weight = 68061.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.046640 restraints weight = 52696.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.046963 restraints weight = 43282.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.047234 restraints weight = 37164.554| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10318 Z= 0.225 Angle : 0.612 10.200 14336 Z= 0.365 Chirality : 0.040 0.137 1997 Planarity : 0.003 0.026 2007 Dihedral : 9.210 165.749 2022 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.29 % Favored : 83.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.17), residues: 1946 helix: -0.98 (0.14), residues: 1125 sheet: -4.74 (0.35), residues: 103 loop : -4.62 (0.19), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.22 (10318) covalent geometry : angle 0.61245 / 0.37 (14336) hydrogen bonds : bond 0.04277 / 3.22 ( 724) hydrogen bonds : angle 5.70340 / 4.03 ( 2124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.338 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0444 time to fit residues: 3.5649 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 113 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 104 optimal weight: 0.0070 chunk 20 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.052764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.045656 restraints weight = 93832.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.046231 restraints weight = 68115.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.046687 restraints weight = 53494.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.047023 restraints weight = 43738.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.047204 restraints weight = 37429.229| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10318 Z= 0.194 Angle : 0.548 8.601 14336 Z= 0.324 Chirality : 0.040 0.133 1997 Planarity : 0.002 0.019 2007 Dihedral : 8.646 162.975 2022 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.93 % Favored : 84.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.19), residues: 1946 helix: 0.04 (0.16), residues: 1119 sheet: -4.61 (0.38), residues: 102 loop : -4.51 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.19 (10318) covalent geometry : angle 0.54795 / 0.32 (14336) hydrogen bonds : bond 0.03683 / 2.77 ( 724) hydrogen bonds : angle 5.11707 / 3.60 ( 2124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.310 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0442 time to fit residues: 3.5446 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 77 optimal weight: 0.5980 chunk 29 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 170 optimal weight: 20.0000 chunk 196 optimal weight: 5.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.052397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.045318 restraints weight = 94894.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.045885 restraints weight = 69403.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.046268 restraints weight = 54162.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.046645 restraints weight = 44855.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.046888 restraints weight = 38139.173| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10318 Z= 0.232 Angle : 0.580 8.819 14336 Z= 0.344 Chirality : 0.040 0.133 1997 Planarity : 0.003 0.019 2007 Dihedral : 8.666 159.868 2022 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.42 % Favored : 82.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.19), residues: 1946 helix: 0.13 (0.16), residues: 1119 sheet: -4.61 (0.38), residues: 102 loop : -4.47 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.23 (10318) covalent geometry : angle 0.57971 / 0.34 (14336) hydrogen bonds : bond 0.03953 / 2.96 ( 724) hydrogen bonds : angle 5.30527 / 3.74 ( 2124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.399 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0410 time to fit residues: 3.2375 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 4 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 0.0050 chunk 96 optimal weight: 0.0870 chunk 134 optimal weight: 30.0000 chunk 122 optimal weight: 0.7980 chunk 140 optimal weight: 20.0000 chunk 117 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.055025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047690 restraints weight = 92154.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.048309 restraints weight = 66892.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.048781 restraints weight = 52066.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.049148 restraints weight = 42665.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.049419 restraints weight = 36292.644| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 10318 Z= 0.073 Angle : 0.416 5.445 14336 Z= 0.239 Chirality : 0.038 0.139 1997 Planarity : 0.002 0.013 2007 Dihedral : 7.693 155.540 2022 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.23 (0.21), residues: 1946 helix: 1.35 (0.16), residues: 1126 sheet: -4.25 (0.40), residues: 107 loop : -4.08 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00101 / 0.07 (10318) covalent geometry : angle 0.41614 / 0.24 (14336) hydrogen bonds : bond 0.02579 / 1.95 ( 724) hydrogen bonds : angle 3.89961 / 2.71 ( 2124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.310 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0422 time to fit residues: 3.3555 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.051998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.044975 restraints weight = 96671.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.045539 restraints weight = 70137.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.045967 restraints weight = 54787.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.046294 restraints weight = 45132.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.046535 restraints weight = 38669.518| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10318 Z= 0.308 Angle : 0.651 10.149 14336 Z= 0.391 Chirality : 0.041 0.148 1997 Planarity : 0.003 0.016 2007 Dihedral : 8.599 158.319 2022 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.99 % Favored : 82.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.19), residues: 1946 helix: 0.22 (0.16), residues: 1123 sheet: -4.46 (0.40), residues: 101 loop : -4.34 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.31 (10318) covalent geometry : angle 0.65073 / 0.39 (14336) hydrogen bonds : bond 0.04448 / 3.32 ( 724) hydrogen bonds : angle 5.55776 / 3.93 ( 2124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.404 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0428 time to fit residues: 3.4817 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 160 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 134 optimal weight: 30.0000 chunk 75 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.051696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.044721 restraints weight = 95399.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.045300 restraints weight = 68852.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.045726 restraints weight = 53373.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046024 restraints weight = 43750.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.046277 restraints weight = 37715.641| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10318 Z= 0.353 Angle : 0.704 11.283 14336 Z= 0.424 Chirality : 0.042 0.146 1997 Planarity : 0.004 0.020 2007 Dihedral : 8.961 153.281 2022 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 19.48 % Favored : 80.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.18), residues: 1946 helix: -0.52 (0.15), residues: 1121 sheet: -4.36 (0.44), residues: 93 loop : -4.53 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.35 (10318) covalent geometry : angle 0.70379 / 0.42 (14336) hydrogen bonds : bond 0.04903 / 3.66 ( 724) hydrogen bonds : angle 6.05990 / 4.29 ( 2124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.330 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0425 time to fit residues: 3.3970 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 123 optimal weight: 0.0170 chunk 1 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 96 optimal weight: 0.0970 chunk 163 optimal weight: 0.9980 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.054638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.047320 restraints weight = 92461.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.047960 restraints weight = 66707.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.048418 restraints weight = 51632.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.048767 restraints weight = 42292.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.049007 restraints weight = 36041.479| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 10318 Z= 0.081 Angle : 0.436 5.628 14336 Z= 0.250 Chirality : 0.039 0.137 1997 Planarity : 0.002 0.014 2007 Dihedral : 7.596 148.130 2022 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.21 (0.21), residues: 1946 helix: 1.35 (0.16), residues: 1126 sheet: -4.45 (0.39), residues: 116 loop : -3.95 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00114 / 0.08 (10318) covalent geometry : angle 0.43612 / 0.25 (14336) hydrogen bonds : bond 0.02769 / 2.09 ( 724) hydrogen bonds : angle 4.01217 / 2.79 ( 2124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.417 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0461 time to fit residues: 3.7356 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 36 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.052111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.045090 restraints weight = 94722.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.045646 restraints weight = 70721.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046089 restraints weight = 54902.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046406 restraints weight = 45036.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.046638 restraints weight = 38589.709| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10318 Z= 0.290 Angle : 0.620 9.070 14336 Z= 0.372 Chirality : 0.041 0.147 1997 Planarity : 0.003 0.015 2007 Dihedral : 8.294 151.196 2022 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.60 % Favored : 81.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.19), residues: 1946 helix: 0.40 (0.16), residues: 1124 sheet: -4.21 (0.46), residues: 93 loop : -4.32 (0.20), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.29 (10318) covalent geometry : angle 0.61993 / 0.37 (14336) hydrogen bonds : bond 0.04182 / 3.13 ( 724) hydrogen bonds : angle 5.38008 / 3.80 ( 2124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.411 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0441 time to fit residues: 3.5168 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 76 optimal weight: 20.0000 chunk 77 optimal weight: 0.0770 chunk 53 optimal weight: 0.0670 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 0.0270 chunk 93 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 overall best weight: 3.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.045854 restraints weight = 92477.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.046443 restraints weight = 67205.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.046887 restraints weight = 52522.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.047222 restraints weight = 43082.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.047442 restraints weight = 36894.257| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10318 Z= 0.172 Angle : 0.510 6.948 14336 Z= 0.300 Chirality : 0.039 0.130 1997 Planarity : 0.002 0.015 2007 Dihedral : 7.970 147.443 2022 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.34 % Favored : 85.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.81 (0.20), residues: 1946 helix: 0.80 (0.16), residues: 1123 sheet: -4.13 (0.47), residues: 94 loop : -4.22 (0.20), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.17 (10318) covalent geometry : angle 0.51022 / 0.30 (14336) hydrogen bonds : bond 0.03392 / 2.55 ( 724) hydrogen bonds : angle 4.76016 / 3.34 ( 2124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.405 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0452 time to fit residues: 3.6192 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 1 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 164 optimal weight: 30.0000 chunk 53 optimal weight: 0.5980 chunk 110 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 overall best weight: 5.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.052393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.045303 restraints weight = 95001.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.045888 restraints weight = 68716.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.046326 restraints weight = 53561.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.046627 restraints weight = 43989.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.046901 restraints weight = 37927.484| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10318 Z= 0.235 Angle : 0.562 7.654 14336 Z= 0.335 Chirality : 0.040 0.137 1997 Planarity : 0.002 0.015 2007 Dihedral : 8.093 145.293 2022 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.04 % Favored : 81.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.20), residues: 1946 helix: 0.52 (0.16), residues: 1125 sheet: -4.13 (0.48), residues: 94 loop : -4.30 (0.20), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 47 TRP 0.000 0.000 TRP A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.23 (10318) covalent geometry : angle 0.56198 / 0.34 (14336) hydrogen bonds : bond 0.03831 / 2.87 ( 724) hydrogen bonds : angle 5.12841 / 3.61 ( 2124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1571.67 seconds wall clock time: 27 minutes 31.52 seconds (1651.52 seconds total)