Starting phenix.real_space_refine on Sat Sep 12 06:17:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jxa_9892/09_2026/6jxa_9892.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jxa_9892/09_2026/6jxa_9892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jxa_9892/09_2026/6jxa_9892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jxa_9892/09_2026/6jxa_9892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jxa_9892/09_2026/6jxa_9892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jxa_9892/09_2026/6jxa_9892.map" } resolution = 4.3 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= 0.001 sd= 0.007 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 S 38 5.16 5 C 8748 2.51 5 N 2594 2.21 5 O 2720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 14100 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2244, 14100 Classifications: {'peptide': 2244} Incomplete info: {'truncation_to_alanine': 1183} Link IDs: {'PTRANS': 59, 'TRANS': 2184} Chain breaks: 34 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 4424 Unresolved non-hydrogen angles: 5697 Unresolved non-hydrogen dihedrals: 3750 Unresolved non-hydrogen chiralities: 397 Planarities with less than four sites: {'GLU:plan': 78, 'ASN:plan1': 81, 'PHE:plan': 85, 'ARG:plan': 50, 'ASP:plan': 65, 'HIS:plan': 24, 'TYR:plan': 68, 'GLN:plan1': 45, 'TRP:plan': 21} Unresolved non-hydrogen planarities: 2475 Time building chain proxies: 3.23, per 1000 atoms: 0.23 Number of scatterers: 14100 At special positions: 0 Unit cell: (147.15, 97.2, 191.7, 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) S 38 16.00 O 2720 8.00 N 2594 7.00 C 8748 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: 1.34 Conformation dependent library (CDL) restraints added in 697.2 milliseconds 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4334 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 1 sheets defined 67.1% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 110 through 124 Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 160 through 173 removed outlier: 3.652A pdb=" N SER A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 200 through 205 removed outlier: 5.477A pdb=" N ILE A 205 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.793A pdb=" N ASN A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 260 through 274 Processing helix chain 'A' and resid 281 through 297 Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 327 through 345 removed outlier: 3.792A pdb=" N ARG A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.523A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 521 through 535 Processing helix chain 'A' and resid 546 through 554 Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 597 through 603 Processing helix chain 'A' and resid 627 through 641 Processing helix chain 'A' and resid 668 through 682 Processing helix chain 'A' and resid 707 through 724 removed outlier: 3.543A pdb=" N PHE A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 728 Processing helix chain 'A' and resid 755 through 766 removed outlier: 3.868A pdb=" N LEU A 760 " --> pdb=" O ASP A 756 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASP A 761 " --> pdb=" O HIS A 757 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ASN A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 781 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 865 through 885 Processing helix chain 'A' and resid 890 through 915 Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 926 through 939 Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 948 through 963 removed outlier: 4.210A pdb=" N LEU A 952 " --> pdb=" O PRO A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 978 Processing helix chain 'A' and resid 985 through 996 Processing helix chain 'A' and resid 1003 through 1015 removed outlier: 3.531A pdb=" N ILE A1015 " --> pdb=" O ASN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1022 No H-bonds generated for 'chain 'A' and resid 1020 through 1022' Processing helix chain 'A' and resid 1023 through 1034 removed outlier: 3.714A pdb=" N GLN A1027 " --> pdb=" O PHE A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1051 removed outlier: 3.542A pdb=" N SER A1044 " --> pdb=" O MET A1040 " (cutoff:3.500A) Proline residue: A1049 - end of helix Processing helix chain 'A' and resid 1056 through 1069 Processing helix chain 'A' and resid 1072 through 1078 removed outlier: 6.172A pdb=" N ILE A1078 " --> pdb=" O LEU A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1089 removed outlier: 4.643A pdb=" N GLN A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1096 removed outlier: 4.195A pdb=" N LYS A1095 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A1096 " --> pdb=" O TYR A1093 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1092 through 1096' Processing helix chain 'A' and resid 1097 through 1102 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1136 through 1148 removed outlier: 4.520A pdb=" N GLN A1145 " --> pdb=" O ILE A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1151 No H-bonds generated for 'chain 'A' and resid 1149 through 1151' Processing helix chain 'A' and resid 1153 through 1158 Processing helix chain 'A' and resid 1159 through 1162 Processing helix chain 'A' and resid 1167 through 1172 Processing helix chain 'A' and resid 1174 through 1181 Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1206 through 1211 Processing helix chain 'A' and resid 1214 through 1218 Processing helix chain 'A' and resid 1226 through 1234 Processing helix chain 'A' and resid 1240 through 1249 removed outlier: 3.581A pdb=" N TYR A1244 " --> pdb=" O TYR A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1277 Processing helix chain 'A' and resid 1286 through 1298 Processing helix chain 'A' and resid 1302 through 1320 Processing helix chain 'A' and resid 1324 through 1328 Processing helix chain 'A' and resid 1332 through 1336 Processing helix chain 'A' and resid 1343 through 1358 Processing helix chain 'A' and resid 1369 through 1381 Processing helix chain 'A' and resid 1388 through 1400 removed outlier: 3.665A pdb=" N GLN A1392 " --> pdb=" O SER A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1414 Processing helix chain 'A' and resid 1439 through 1446 removed outlier: 4.078A pdb=" N SER A1446 " --> pdb=" O VAL A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1451 Processing helix chain 'A' and resid 1466 through 1475 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1494 through 1499 Processing helix chain 'A' and resid 1516 through 1522 Processing helix chain 'A' and resid 1529 through 1542 Processing helix chain 'A' and resid 1549 through 1560 Processing helix chain 'A' and resid 1599 through 1605 Processing helix chain 'A' and resid 1611 through 1616 Processing helix chain 'A' and resid 1619 through 1625 Processing helix chain 'A' and resid 1626 through 1628 No H-bonds generated for 'chain 'A' and resid 1626 through 1628' Processing helix chain 'A' and resid 1641 through 1652 Proline residue: A1650 - end of helix Processing helix chain 'A' and resid 1659 through 1667 removed outlier: 3.591A pdb=" N LEU A1663 " --> pdb=" O CYS A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1683 Processing helix chain 'A' and resid 1692 through 1697 Processing helix chain 'A' and resid 1704 through 1723 removed outlier: 3.838A pdb=" N VAL A1708 " --> pdb=" O MET A1704 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1734 Processing helix chain 'A' and resid 1742 through 1746 Processing helix chain 'A' and resid 1750 through 1757 removed outlier: 3.657A pdb=" N MET A1757 " --> pdb=" O GLU A1753 " (cutoff:3.500A) Processing helix chain 'A' and resid 1765 through 1775 Processing helix chain 'A' and resid 1776 through 1780 removed outlier: 3.708A pdb=" N ASP A1779 " --> pdb=" O ASN A1776 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A1780 " --> pdb=" O ASP A1777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1776 through 1780' Processing helix chain 'A' and resid 1808 through 1819 removed outlier: 3.834A pdb=" N ALA A1813 " --> pdb=" O LEU A1809 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A1814 " --> pdb=" O PHE A1810 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A1819 " --> pdb=" O PHE A1815 " (cutoff:3.500A) Processing helix chain 'A' and resid 1828 through 1836 removed outlier: 4.707A pdb=" N ALA A1833 " --> pdb=" O SER A1829 " (cutoff:3.500A) Processing helix chain 'A' and resid 1839 through 1847 removed outlier: 4.984A pdb=" N LEU A1845 " --> pdb=" O GLY A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1864 Processing helix chain 'A' and resid 1876 through 1887 Processing helix chain 'A' and resid 1894 through 1910 removed outlier: 4.061A pdb=" N SER A1898 " --> pdb=" O PHE A1894 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A1901 " --> pdb=" O LYS A1897 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1913 No H-bonds generated for 'chain 'A' and resid 1911 through 1913' Processing helix chain 'A' and resid 1918 through 1920 No H-bonds generated for 'chain 'A' and resid 1918 through 1920' Processing helix chain 'A' and resid 1921 through 1933 removed outlier: 4.135A pdb=" N ALA A1925 " --> pdb=" O ASP A1921 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A1926 " --> pdb=" O THR A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1945 through 1955 Processing helix chain 'A' and resid 1963 through 1966 Processing helix chain 'A' and resid 1967 through 1984 Processing helix chain 'A' and resid 1987 through 2009 Processing helix chain 'A' and resid 2014 through 2021 Processing helix chain 'A' and resid 2040 through 2058 removed outlier: 4.269A pdb=" N ALA A2056 " --> pdb=" O THR A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2080 Processing helix chain 'A' and resid 2081 through 2084 removed outlier: 3.784A pdb=" N SER A2084 " --> pdb=" O ILE A2081 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2081 through 2084' Processing helix chain 'A' and resid 2089 through 2094 Processing helix chain 'A' and resid 2101 through 2113 removed outlier: 3.909A pdb=" N ARG A2113 " --> pdb=" O SER A2109 " (cutoff:3.500A) Processing helix chain 'A' and resid 2115 through 2119 removed outlier: 3.589A pdb=" N ALA A2119 " --> pdb=" O PRO A2116 " (cutoff:3.500A) Processing helix chain 'A' and resid 2122 through 2127 removed outlier: 4.138A pdb=" N VAL A2126 " --> pdb=" O GLU A2122 " (cutoff:3.500A) Processing helix chain 'A' and resid 2138 through 2155 removed outlier: 3.571A pdb=" N PHE A2142 " --> pdb=" O CYS A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2161 through 2175 removed outlier: 4.350A pdb=" N ARG A2165 " --> pdb=" O GLU A2161 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A2166 " --> pdb=" O ILE A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2199 through 2212 Processing helix chain 'A' and resid 2214 through 2235 removed outlier: 3.806A pdb=" N LEU A2225 " --> pdb=" O LYS A2221 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP A2226 " --> pdb=" O GLU A2222 " (cutoff:3.500A) Processing helix chain 'A' and resid 2243 through 2257 removed outlier: 3.548A pdb=" N LYS A2249 " --> pdb=" O ASP A2245 " (cutoff:3.500A) Processing helix chain 'A' and resid 2263 through 2274 removed outlier: 3.592A pdb=" N LEU A2267 " --> pdb=" O ILE A2263 " (cutoff:3.500A) Processing helix chain 'A' and resid 2282 through 2290 Processing helix chain 'A' and resid 2297 through 2312 Processing helix chain 'A' and resid 2313 through 2316 Processing helix chain 'A' and resid 2317 through 2330 Processing helix chain 'A' and resid 2335 through 2352 removed outlier: 3.572A pdb=" N GLY A2352 " --> pdb=" O LEU A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2358 No H-bonds generated for 'chain 'A' and resid 2356 through 2358' Processing helix chain 'A' and resid 2359 through 2379 Proline residue: A2365 - end of helix Processing helix chain 'A' and resid 2426 through 2430 Processing helix chain 'A' and resid 2468 through 2472 Processing helix chain 'A' and resid 2474 through 2491 removed outlier: 3.642A pdb=" N GLU A2478 " --> pdb=" O ASP A2474 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2495 Processing helix chain 'A' and resid 2506 through 2510 Processing helix chain 'A' and resid 2525 through 2533 Processing helix chain 'A' and resid 2539 through 2549 removed outlier: 3.788A pdb=" N MET A2547 " --> pdb=" O ALA A2543 " (cutoff:3.500A) Processing helix chain 'A' and resid 2574 through 2580 Processing helix chain 'A' and resid 2584 through 2606 removed outlier: 3.666A pdb=" N PHE A2588 " --> pdb=" O PRO A2584 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A2589 " --> pdb=" O LEU A2585 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE A2603 " --> pdb=" O ALA A2599 " (cutoff:3.500A) Processing helix chain 'A' and resid 2654 through 2665 removed outlier: 4.684A pdb=" N THR A2663 " --> pdb=" O GLY A2659 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A2665 " --> pdb=" O GLY A2661 " (cutoff:3.500A) Processing helix chain 'A' and resid 2668 through 2679 removed outlier: 4.283A pdb=" N SER A2672 " --> pdb=" O LEU A2668 " (cutoff:3.500A) Processing helix chain 'A' and resid 2679 through 2684 removed outlier: 4.047A pdb=" N ASP A2683 " --> pdb=" O VAL A2679 " (cutoff:3.500A) Processing helix chain 'A' and resid 2684 through 2692 removed outlier: 3.908A pdb=" N VAL A2690 " --> pdb=" O LYS A2686 " (cutoff:3.500A) Processing helix chain 'A' and resid 2739 through 2753 Processing sheet with id=AA1, first strand: chain 'A' and resid 2523 through 2524 882 hydrogen bonds defined for protein. 2541 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: 2.97 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3048 1.32 - 1.45: 4066 1.45 - 1.58: 7001 1.58 - 1.72: 21 1.72 - 1.85: 60 Bond restraints: 14196 Sorted by residual: bond pdb=" CB LEU A1899 " pdb=" CG LEU A1899 " ideal model delta sigma weight residual 1.530 1.392 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CB LEU A1975 " pdb=" CG LEU A1975 " ideal model delta sigma weight residual 1.530 1.395 0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" NE ARG A1972 " pdb=" CZ ARG A1972 " ideal model delta sigma weight residual 1.326 1.385 -0.059 1.10e-02 8.26e+03 2.85e+01 bond pdb=" CB LEU A1562 " pdb=" CG LEU A1562 " ideal model delta sigma weight residual 1.530 1.629 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CA ILE A 87 " pdb=" CB ILE A 87 " ideal model delta sigma weight residual 1.540 1.476 0.064 1.29e-02 6.01e+03 2.43e+01 ... (remaining 14191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 17284 2.73 - 5.47: 1790 5.47 - 8.20: 275 8.20 - 10.93: 32 10.93 - 13.67: 10 Bond angle restraints: 19391 Sorted by residual: angle pdb=" N MET A1691 " pdb=" CA MET A1691 " pdb=" C MET A1691 " ideal model delta sigma weight residual 114.62 100.95 13.67 1.14e+00 7.69e-01 1.44e+02 angle pdb=" N ARG A1382 " pdb=" CA ARG A1382 " pdb=" C ARG A1382 " ideal model delta sigma weight residual 108.75 98.10 10.65 9.60e-01 1.09e+00 1.23e+02 angle pdb=" CA PHE A1962 " pdb=" CB PHE A1962 " pdb=" CG PHE A1962 " ideal model delta sigma weight residual 113.80 103.05 10.75 1.00e+00 1.00e+00 1.16e+02 angle pdb=" N ILE A1331 " pdb=" CA ILE A1331 " pdb=" C ILE A1331 " ideal model delta sigma weight residual 111.58 100.69 10.89 1.06e+00 8.90e-01 1.06e+02 angle pdb=" N ASN A 22 " pdb=" CA ASN A 22 " pdb=" C ASN A 22 " ideal model delta sigma weight residual 112.90 100.84 12.06 1.31e+00 5.83e-01 8.47e+01 ... (remaining 19386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.86: 8233 12.86 - 25.72: 246 25.72 - 38.57: 61 38.57 - 51.43: 28 51.43 - 64.29: 25 Dihedral angle restraints: 8593 sinusoidal: 2022 harmonic: 6571 Sorted by residual: dihedral pdb=" C PHE A1894 " pdb=" N PHE A1894 " pdb=" CA PHE A1894 " pdb=" CB PHE A1894 " ideal model delta harmonic sigma weight residual -122.60 -111.15 -11.45 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" C TRP A2587 " pdb=" N TRP A2587 " pdb=" CA TRP A2587 " pdb=" CB TRP A2587 " ideal model delta harmonic sigma weight residual -122.60 -112.05 -10.55 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" N PRO A1237 " pdb=" C PRO A1237 " pdb=" CA PRO A1237 " pdb=" CB PRO A1237 " ideal model delta harmonic sigma weight residual 115.10 125.17 -10.07 0 2.50e+00 1.60e-01 1.62e+01 ... (remaining 8590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1737 0.085 - 0.170: 532 0.170 - 0.256: 140 0.256 - 0.341: 47 0.341 - 0.426: 11 Chirality restraints: 2467 Sorted by residual: chirality pdb=" CA GLU A1018 " pdb=" N GLU A1018 " pdb=" C GLU A1018 " pdb=" CB GLU A1018 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CG LEU A1562 " pdb=" CB LEU A1562 " pdb=" CD1 LEU A1562 " pdb=" CD2 LEU A1562 " both_signs ideal model delta sigma weight residual False -2.59 -3.01 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA TRP A2587 " pdb=" N TRP A2587 " pdb=" C TRP A2587 " pdb=" CB TRP A2587 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 2464 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A2268 " -0.095 2.00e-02 2.50e+03 5.20e-02 5.41e+01 pdb=" CG TYR A2268 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A2268 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR A2268 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR A2268 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A2268 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A2268 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A2268 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1380 " 0.071 2.00e-02 2.50e+03 4.03e-02 3.24e+01 pdb=" CG TYR A1380 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A1380 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A1380 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A1380 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR A1380 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A1380 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A1380 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1489 " 0.072 2.00e-02 2.50e+03 3.50e-02 3.07e+01 pdb=" CG TRP A1489 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A1489 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A1489 " -0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP A1489 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A1489 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A1489 " -0.045 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1489 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1489 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A1489 " 0.037 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 227 2.52 - 3.12: 12856 3.12 - 3.71: 22394 3.71 - 4.31: 29199 4.31 - 4.90: 43430 Nonbonded interactions: 108106 Sorted by model distance: nonbonded pdb=" O LEU A 386 " pdb=" O PHE A 387 " model vdw 1.926 3.040 nonbonded pdb=" O ASP A1855 " pdb=" CG2 VAL A1856 " model vdw 2.001 3.460 nonbonded pdb=" O ILE A1635 " pdb=" O HIS A1636 " model vdw 2.050 3.040 nonbonded pdb=" O ASN A1795 " pdb=" NH1 ARG A1807 " model vdw 2.063 3.120 nonbonded pdb=" O PHE A2452 " pdb=" O ASN A2453 " model vdw 2.084 3.040 ... (remaining 108101 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: 1.110 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.410 Find NCS groups from input model: 0.070 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4236 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 : 0.017 0.138 14196 Z= 1.019 Angle : 1.811 13.665 19391 Z= 1.248 Chirality : 0.096 0.426 2467 Planarity : 0.011 0.108 2582 Dihedral : 9.079 64.292 4259 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 29.80 Ramachandran Plot: Outliers : 8.46 % Allowed : 12.24 % Favored : 79.30 % Rotamer: Outliers : 2.04 % Allowed : 1.25 % Favored : 96.71 % Cbeta Deviations : 0.14 % 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 (0.17), residues: 2174 helix: -0.73 (0.13), residues: 1324 sheet: -3.39 (1.14), residues: 10 loop : -3.60 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2071 TYR 0.095 0.008 TYR A2268 PHE 0.049 0.006 PHE A1962 TRP 0.072 0.011 TRP A1489 HIS 0.007 0.002 HIS A1530 Details of bonding type rmsd/Z covalent geometry : bond 0.01686 / 1.02 (14196) covalent geometry : angle 1.81067 / 1.25 (19391) hydrogen bonds : bond 0.19290 / 14.36 ( 882) hydrogen bonds : angle 7.74815 / 5.80 ( 2541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1717 ARG cc_start: 0.6037 (ttt90) cc_final: 0.5554 (tpt-90) REVERT: A 1935 ILE cc_start: 0.4646 (OUTLIER) cc_final: 0.4445 (tt) outliers start: 18 outliers final: 6 residues processed: 225 average time/residue: 0.1366 time to fit residues: 43.3459 Evaluate side-chains 136 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.0470 chunk 212 optimal weight: 6.9990 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1475 HIS A1528 GLN ** A1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1759 ASN A1764 ASN ** A1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2533 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 = 0.4030 r_free = 0.4030 target = 0.081470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.072333 restraints weight = 159419.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.072258 restraints weight = 157848.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.072211 restraints weight = 157792.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.072301 restraints weight = 157556.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.072308 restraints weight = 152721.262| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14196 Z= 0.211 Angle : 0.945 10.428 19391 Z= 0.512 Chirality : 0.047 0.358 2467 Planarity : 0.006 0.091 2582 Dihedral : 6.492 42.170 2278 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 3.73 % Allowed : 13.25 % Favored : 83.03 % Rotamer: Outliers : 0.34 % Allowed : 3.86 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.32 (0.18), residues: 2174 helix: -0.14 (0.14), residues: 1316 sheet: -2.53 (1.21), residues: 12 loop : -3.94 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1721 TYR 0.023 0.002 TYR A1857 PHE 0.024 0.002 PHE A2224 TRP 0.030 0.003 TRP A2128 HIS 0.009 0.002 HIS A1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.21 (14196) covalent geometry : angle 0.94461 / 0.51 (19391) hydrogen bonds : bond 0.06085 / 4.53 ( 882) hydrogen bonds : angle 6.09934 / 4.56 ( 2541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1673 TYR cc_start: 0.8801 (m-80) cc_final: 0.8182 (m-10) REVERT: A 1977 ASN cc_start: 0.8764 (m-40) cc_final: 0.8158 (p0) REVERT: A 2152 GLN cc_start: 0.9000 (mp10) cc_final: 0.8646 (mp10) REVERT: A 2307 ARG cc_start: 0.7936 (tpt170) cc_final: 0.7716 (ptt180) REVERT: A 2477 MET cc_start: 0.8267 (ptm) cc_final: 0.7750 (ptt) REVERT: A 2687 VAL cc_start: 0.8800 (t) cc_final: 0.8462 (p) outliers start: 3 outliers final: 1 residues processed: 159 average time/residue: 0.1202 time to fit residues: 28.1778 Evaluate side-chains 115 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 79 optimal weight: 40.0000 chunk 28 optimal weight: 30.0000 chunk 175 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 196 optimal weight: 40.0000 chunk 62 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1776 ASN A1811 ASN ** A1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1911 GLN A1937 GLN ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2044 GLN ** A2230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2302 GLN A2490 ASN ** A2533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.074500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.061391 restraints weight = 150126.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.061396 restraints weight = 145061.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.061396 restraints weight = 144703.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.061396 restraints weight = 144703.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.061396 restraints weight = 144703.883| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14196 Z= 0.263 Angle : 0.962 10.250 19391 Z= 0.525 Chirality : 0.048 0.308 2467 Planarity : 0.006 0.107 2582 Dihedral : 6.583 35.277 2278 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 3.36 % Allowed : 16.15 % Favored : 80.50 % Rotamer: Outliers : 0.34 % Allowed : 4.09 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.87 (0.18), residues: 2174 helix: -0.62 (0.14), residues: 1321 sheet: -3.24 (1.47), residues: 10 loop : -4.09 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1995 TYR 0.025 0.003 TYR A2063 PHE 0.027 0.003 PHE A1839 TRP 0.038 0.003 TRP A2226 HIS 0.012 0.003 HIS A2526 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.26 (14196) covalent geometry : angle 0.96165 / 0.53 (19391) hydrogen bonds : bond 0.06297 / 4.70 ( 882) hydrogen bonds : angle 6.13658 / 4.60 ( 2541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1330 PHE cc_start: 0.8910 (m-80) cc_final: 0.8601 (m-80) REVERT: A 2070 MET cc_start: 0.7183 (ttt) cc_final: 0.6623 (tmm) REVERT: A 2152 GLN cc_start: 0.8938 (mp10) cc_final: 0.8700 (mp10) REVERT: A 2477 MET cc_start: 0.8378 (ptm) cc_final: 0.8134 (ptm) REVERT: A 2684 TYR cc_start: 0.7692 (t80) cc_final: 0.6977 (t80) outliers start: 3 outliers final: 0 residues processed: 134 average time/residue: 0.1294 time to fit residues: 25.3513 Evaluate side-chains 104 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 145 optimal weight: 0.9990 chunk 55 optimal weight: 50.0000 chunk 208 optimal weight: 0.0870 chunk 65 optimal weight: 50.0000 chunk 134 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 203 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 overall best weight: 3.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1400 HIS ** A1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2490 ASN A2533 HIS A2617 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.075926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.062527 restraints weight = 147324.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.062525 restraints weight = 141964.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.062525 restraints weight = 141163.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.062525 restraints weight = 141163.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.062525 restraints weight = 141163.395| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14196 Z= 0.175 Angle : 0.808 10.366 19391 Z= 0.437 Chirality : 0.043 0.275 2467 Planarity : 0.005 0.105 2582 Dihedral : 6.083 36.571 2278 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 3.36 % Allowed : 13.71 % Favored : 82.93 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.21 (0.18), residues: 2174 helix: -0.09 (0.14), residues: 1313 sheet: -2.76 (1.64), residues: 10 loop : -3.80 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1453 TYR 0.018 0.001 TYR A2063 PHE 0.021 0.002 PHE A2224 TRP 0.026 0.002 TRP A2226 HIS 0.006 0.001 HIS A1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (14196) covalent geometry : angle 0.80807 / 0.44 (19391) hydrogen bonds : bond 0.04971 / 3.69 ( 882) hydrogen bonds : angle 5.66100 / 4.21 ( 2541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1330 PHE cc_start: 0.8858 (m-80) cc_final: 0.8573 (m-80) REVERT: A 1378 PHE cc_start: 0.9026 (m-80) cc_final: 0.8681 (m-10) REVERT: A 2477 MET cc_start: 0.8442 (ptm) cc_final: 0.8190 (ptm) REVERT: A 2684 TYR cc_start: 0.7551 (t80) cc_final: 0.7011 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1093 time to fit residues: 21.8457 Evaluate side-chains 110 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 85 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 120 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.9726 > 50:) chunk 95 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2284 ASN A2285 GLN A2490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.075837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.062349 restraints weight = 156763.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.062391 restraints weight = 151976.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.062453 restraints weight = 149926.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.062463 restraints weight = 150126.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.062464 restraints weight = 149695.255| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14196 Z= 0.167 Angle : 0.779 10.122 19391 Z= 0.422 Chirality : 0.043 0.267 2467 Planarity : 0.005 0.105 2582 Dihedral : 5.840 35.178 2278 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 3.17 % Allowed : 14.72 % Favored : 82.11 % Rotamer: Outliers : 0.23 % Allowed : 3.29 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.93 (0.19), residues: 2174 helix: 0.18 (0.15), residues: 1297 sheet: -2.39 (1.82), residues: 10 loop : -3.71 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2104 TYR 0.016 0.001 TYR A2063 PHE 0.019 0.002 PHE A2224 TRP 0.025 0.002 TRP A2226 HIS 0.004 0.001 HIS A1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (14196) covalent geometry : angle 0.77941 / 0.42 (19391) hydrogen bonds : bond 0.04688 / 3.48 ( 882) hydrogen bonds : angle 5.44971 / 4.05 ( 2541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1330 PHE cc_start: 0.8877 (m-80) cc_final: 0.8599 (m-80) REVERT: A 1378 PHE cc_start: 0.9010 (m-80) cc_final: 0.8793 (m-80) REVERT: A 1412 CYS cc_start: 0.7900 (m) cc_final: 0.7504 (m) REVERT: A 1535 ARG cc_start: 0.5100 (mtt-85) cc_final: 0.4763 (mtt180) REVERT: A 1835 GLU cc_start: 0.8669 (tt0) cc_final: 0.8376 (tp30) REVERT: A 1977 ASN cc_start: 0.8997 (m-40) cc_final: 0.8381 (p0) REVERT: A 2001 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8612 (pp30) REVERT: A 2221 LYS cc_start: 0.9259 (mttm) cc_final: 0.8936 (mmtt) REVERT: A 2477 MET cc_start: 0.8635 (ptm) cc_final: 0.8331 (ptt) REVERT: A 2684 TYR cc_start: 0.7624 (t80) cc_final: 0.7342 (t80) outliers start: 2 outliers final: 1 residues processed: 133 average time/residue: 0.1083 time to fit residues: 22.0221 Evaluate side-chains 112 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 142 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 118 optimal weight: 40.0000 chunk 119 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1965 HIS ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.077029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063145 restraints weight = 149107.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063145 restraints weight = 147410.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063145 restraints weight = 147378.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063145 restraints weight = 147379.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063145 restraints weight = 147379.270| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14196 Z= 0.141 Angle : 0.754 11.471 19391 Z= 0.402 Chirality : 0.042 0.306 2467 Planarity : 0.004 0.105 2582 Dihedral : 5.591 35.455 2278 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 2.99 % Allowed : 13.94 % Favored : 83.07 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.57 (0.19), residues: 2174 helix: 0.51 (0.15), residues: 1307 sheet: -2.10 (1.97), residues: 10 loop : -3.69 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2104 TYR 0.016 0.001 TYR A2684 PHE 0.016 0.002 PHE A1391 TRP 0.021 0.002 TRP A2226 HIS 0.014 0.001 HIS A2533 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (14196) covalent geometry : angle 0.75362 / 0.40 (19391) hydrogen bonds : bond 0.04226 / 3.14 ( 882) hydrogen bonds : angle 5.16722 / 3.83 ( 2541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1330 PHE cc_start: 0.8793 (m-80) cc_final: 0.8406 (m-80) REVERT: A 1412 CYS cc_start: 0.7914 (m) cc_final: 0.7496 (m) REVERT: A 1479 LYS cc_start: 0.6807 (tmtt) cc_final: 0.5585 (mtmt) REVERT: A 1535 ARG cc_start: 0.5032 (mtt-85) cc_final: 0.4757 (mtt180) REVERT: A 1977 ASN cc_start: 0.8993 (m-40) cc_final: 0.8393 (p0) REVERT: A 2221 LYS cc_start: 0.9208 (mttm) cc_final: 0.8886 (mmtt) REVERT: A 2477 MET cc_start: 0.8607 (ptm) cc_final: 0.8310 (ptt) REVERT: A 2498 ASP cc_start: 0.8933 (m-30) cc_final: 0.8587 (p0) REVERT: A 2684 TYR cc_start: 0.7700 (t80) cc_final: 0.7330 (t80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1127 time to fit residues: 23.1172 Evaluate side-chains 111 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 220 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 56 optimal weight: 40.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.075123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.061484 restraints weight = 152408.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.061496 restraints weight = 149996.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.061497 restraints weight = 149398.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.061497 restraints weight = 149352.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.061497 restraints weight = 149352.877| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14196 Z= 0.186 Angle : 0.786 9.854 19391 Z= 0.426 Chirality : 0.043 0.274 2467 Planarity : 0.005 0.104 2582 Dihedral : 5.728 33.658 2278 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 3.17 % Allowed : 14.90 % Favored : 81.92 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.69 (0.19), residues: 2174 helix: 0.36 (0.15), residues: 1301 sheet: -2.29 (1.91), residues: 10 loop : -3.61 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1453 TYR 0.029 0.002 TYR A2268 PHE 0.022 0.002 PHE A1839 TRP 0.027 0.002 TRP A2226 HIS 0.004 0.001 HIS A2230 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.19 (14196) covalent geometry : angle 0.78598 / 0.43 (19391) hydrogen bonds : bond 0.04622 / 3.42 ( 882) hydrogen bonds : angle 5.41809 / 4.00 ( 2541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1330 PHE cc_start: 0.8940 (m-80) cc_final: 0.8630 (m-80) REVERT: A 1412 CYS cc_start: 0.7634 (m) cc_final: 0.7263 (m) REVERT: A 1479 LYS cc_start: 0.6871 (tmtt) cc_final: 0.5786 (mtmt) REVERT: A 1531 MET cc_start: 0.2651 (mtm) cc_final: 0.2214 (mtp) REVERT: A 1717 ARG cc_start: 0.8749 (tpt-90) cc_final: 0.8421 (tpt170) REVERT: A 1977 ASN cc_start: 0.8991 (m-40) cc_final: 0.8490 (p0) REVERT: A 2001 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8644 (pp30) REVERT: A 2221 LYS cc_start: 0.9104 (mttm) cc_final: 0.8757 (mmtt) REVERT: A 2477 MET cc_start: 0.8549 (ptm) cc_final: 0.8269 (ptt) REVERT: A 2684 TYR cc_start: 0.7552 (t80) cc_final: 0.7171 (t80) REVERT: A 2781 MET cc_start: 0.6490 (mtm) cc_final: 0.5926 (ptp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1113 time to fit residues: 21.7515 Evaluate side-chains 106 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 44 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 209 optimal weight: 0.0870 chunk 222 optimal weight: 0.0870 chunk 114 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 ASN ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.077679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.063512 restraints weight = 154517.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.063603 restraints weight = 152676.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.063603 restraints weight = 150705.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.063603 restraints weight = 150705.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.063603 restraints weight = 150705.587| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14196 Z= 0.139 Angle : 0.737 9.773 19391 Z= 0.392 Chirality : 0.042 0.292 2467 Planarity : 0.004 0.104 2582 Dihedral : 5.338 34.627 2278 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 2.99 % Allowed : 12.37 % Favored : 84.64 % Rotamer: Outliers : 0.11 % Allowed : 1.48 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.34 (0.19), residues: 2174 helix: 0.78 (0.15), residues: 1305 sheet: -1.94 (1.89), residues: 10 loop : -3.73 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1535 TYR 0.038 0.002 TYR A2268 PHE 0.018 0.001 PHE A1391 TRP 0.023 0.002 TRP A2226 HIS 0.004 0.001 HIS A1965 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (14196) covalent geometry : angle 0.73727 / 0.39 (19391) hydrogen bonds : bond 0.04001 / 2.97 ( 882) hydrogen bonds : angle 4.96816 / 3.68 ( 2541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1330 PHE cc_start: 0.8892 (m-80) cc_final: 0.8514 (m-80) REVERT: A 1412 CYS cc_start: 0.7593 (m) cc_final: 0.7169 (m) REVERT: A 1479 LYS cc_start: 0.6750 (tmtt) cc_final: 0.5658 (mtmt) REVERT: A 1860 ASN cc_start: 0.5079 (OUTLIER) cc_final: 0.4813 (m110) REVERT: A 1976 MET cc_start: 0.6700 (ttp) cc_final: 0.6373 (ptm) REVERT: A 1977 ASN cc_start: 0.9042 (m-40) cc_final: 0.8402 (p0) REVERT: A 2221 LYS cc_start: 0.9054 (mttm) cc_final: 0.8703 (mmtt) REVERT: A 2477 MET cc_start: 0.8354 (ptm) cc_final: 0.8050 (ptt) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1135 time to fit residues: 23.0666 Evaluate side-chains 106 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 100 optimal weight: 0.8980 chunk 5 optimal weight: 40.0000 chunk 157 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 50.0000 chunk 66 optimal weight: 30.0000 chunk 2 optimal weight: 0.0030 chunk 154 optimal weight: 6.9990 chunk 84 optimal weight: 0.0770 overall best weight: 3.5952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1965 HIS A2044 GLN ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.076181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.062433 restraints weight = 153398.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.062438 restraints weight = 150421.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.062439 restraints weight = 149789.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.062439 restraints weight = 149731.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.062439 restraints weight = 149731.946| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14196 Z= 0.162 Angle : 0.747 10.210 19391 Z= 0.404 Chirality : 0.042 0.325 2467 Planarity : 0.005 0.102 2582 Dihedral : 5.385 33.175 2278 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 2.85 % Allowed : 14.17 % Favored : 82.98 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.35 (0.19), residues: 2174 helix: 0.74 (0.15), residues: 1310 sheet: -2.09 (1.87), residues: 10 loop : -3.69 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2104 TYR 0.032 0.002 TYR A2268 PHE 0.019 0.002 PHE A1338 TRP 0.023 0.002 TRP A2226 HIS 0.004 0.001 HIS A1525 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (14196) covalent geometry : angle 0.74750 / 0.40 (19391) hydrogen bonds : bond 0.04252 / 3.16 ( 882) hydrogen bonds : angle 5.07092 / 3.76 ( 2541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1412 CYS cc_start: 0.7673 (m) cc_final: 0.7310 (m) REVERT: A 1479 LYS cc_start: 0.6552 (tmtt) cc_final: 0.5450 (mtmt) REVERT: A 1531 MET cc_start: 0.0851 (mtm) cc_final: 0.0606 (mtt) REVERT: A 1717 ARG cc_start: 0.8394 (tpt-90) cc_final: 0.8158 (tpt170) REVERT: A 1977 ASN cc_start: 0.9052 (m-40) cc_final: 0.8500 (p0) REVERT: A 2001 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8631 (pp30) REVERT: A 2152 GLN cc_start: 0.8923 (mp10) cc_final: 0.8468 (mp-120) REVERT: A 2221 LYS cc_start: 0.9040 (mttm) cc_final: 0.8713 (mmtt) REVERT: A 2477 MET cc_start: 0.8425 (ptm) cc_final: 0.8077 (ptt) REVERT: A 2742 TYR cc_start: 0.9605 (m-80) cc_final: 0.9380 (m-80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1046 time to fit residues: 21.1071 Evaluate side-chains 109 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 55 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 40.0000 chunk 208 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 182 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2044 GLN ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2479 GLN ** A2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.076177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.062390 restraints weight = 153708.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.062435 restraints weight = 153484.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.062435 restraints weight = 152017.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.062435 restraints weight = 151909.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.062435 restraints weight = 151909.311| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14196 Z= 0.151 Angle : 0.733 9.773 19391 Z= 0.395 Chirality : 0.042 0.344 2467 Planarity : 0.005 0.102 2582 Dihedral : 5.370 32.723 2278 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 2.85 % Allowed : 14.40 % Favored : 82.75 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.32 (0.19), residues: 2174 helix: 0.80 (0.15), residues: 1306 sheet: -2.03 (1.88), residues: 10 loop : -3.74 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2495 TYR 0.034 0.001 TYR A2268 PHE 0.020 0.002 PHE A1374 TRP 0.029 0.002 TRP A2226 HIS 0.005 0.001 HIS A1525 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (14196) covalent geometry : angle 0.73267 / 0.40 (19391) hydrogen bonds : bond 0.04123 / 3.06 ( 882) hydrogen bonds : angle 5.04003 / 3.74 ( 2541) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1412 CYS cc_start: 0.7672 (m) cc_final: 0.7301 (m) REVERT: A 1479 LYS cc_start: 0.6565 (tmtt) cc_final: 0.5585 (mtmt) REVERT: A 1531 MET cc_start: 0.1268 (mtm) cc_final: 0.0896 (mtt) REVERT: A 1717 ARG cc_start: 0.8536 (tpt-90) cc_final: 0.8227 (tpt170) REVERT: A 1977 ASN cc_start: 0.9037 (m-40) cc_final: 0.8548 (p0) REVERT: A 2001 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8572 (pp30) REVERT: A 2152 GLN cc_start: 0.8905 (mp10) cc_final: 0.8514 (mp10) REVERT: A 2221 LYS cc_start: 0.9071 (mttm) cc_final: 0.8779 (mmtt) REVERT: A 2477 MET cc_start: 0.8276 (ptm) cc_final: 0.7916 (ptt) REVERT: A 2742 TYR cc_start: 0.9635 (m-80) cc_final: 0.9422 (m-80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1103 time to fit residues: 22.0284 Evaluate side-chains 109 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 158 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 26 optimal weight: 30.0000 chunk 192 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 3 optimal weight: 40.0000 chunk 124 optimal weight: 0.9990 chunk 170 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 chunk 50 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2044 GLN ** A2230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.073908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.060508 restraints weight = 156922.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.060508 restraints weight = 158130.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.060508 restraints weight = 158130.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.060508 restraints weight = 158130.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.060508 restraints weight = 158130.834| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14196 Z= 0.219 Angle : 0.833 12.293 19391 Z= 0.450 Chirality : 0.045 0.316 2467 Planarity : 0.005 0.103 2582 Dihedral : 5.940 30.774 2278 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 2.81 % Allowed : 16.33 % Favored : 80.86 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.98 (0.18), residues: 2174 helix: 0.18 (0.14), residues: 1304 sheet: -2.52 (1.70), residues: 10 loop : -3.82 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2495 TYR 0.033 0.002 TYR A2268 PHE 0.022 0.002 PHE A2577 TRP 0.039 0.003 TRP A2226 HIS 0.005 0.002 HIS A1475 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.22 (14196) covalent geometry : angle 0.83258 / 0.45 (19391) hydrogen bonds : bond 0.04921 / 3.65 ( 882) hydrogen bonds : angle 5.58008 / 4.15 ( 2541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2644.29 seconds wall clock time: 46 minutes 13.51 seconds (2773.51 seconds total)