Starting phenix.real_space_refine on Sat Aug 8 05:23:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygj_72927/08_2026/9ygj_72927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygj_72927/08_2026/9ygj_72927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ygj_72927/08_2026/9ygj_72927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygj_72927/08_2026/9ygj_72927.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ygj_72927/08_2026/9ygj_72927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygj_72927/08_2026/9ygj_72927.map" } resolution = 3.7 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= 0.019 sd= 0.077 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 143 5.16 5 C 16030 2.51 5 N 4236 2.21 5 O 4696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25105 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1256, 10272 Classifications: {'peptide': 1256} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 1217} Chain breaks: 3 Chain: "B" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3441 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 418} Chain: "C" Number of atoms: 8164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 8164 Classifications: {'peptide': 1003} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 981} Chain breaks: 4 Chain: "D" Number of atoms: 3228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3228 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Time building chain proxies: 5.03, per 1000 atoms: 0.20 Number of scatterers: 25105 At special positions: 0 Unit cell: (118.512, 202.458, 196.697, 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 143 16.00 O 4696 8.00 N 4236 7.00 C 16030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 961 " - pdb=" SG CYS A1062 " distance=2.03 Simple disulfide: pdb=" SG CYS A1166 " - pdb=" SG CYS A1203 " distance=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1262 " distance=2.03 Simple disulfide: pdb=" SG CYS A1867 " - pdb=" SG CYS A1871 " distance=2.03 Simple disulfide: pdb=" SG CYS A2037 " - pdb=" SG CYS A2049 " distance=2.03 Simple disulfide: pdb=" SG CYS B 888 " - pdb=" SG CYS B1083 " distance=2.03 Simple disulfide: pdb=" SG CYS B 935 " - pdb=" SG CYS B 998 " distance=2.03 Simple disulfide: pdb=" SG CYS B1071 " - pdb=" SG CYS B1131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 337 " - pdb=" SG CYS C 341 " distance=2.03 Simple disulfide: pdb=" SG CYS C 706 " - pdb=" SG CYS C 777 " distance=2.03 Simple disulfide: pdb=" SG CYS C 717 " - pdb=" SG CYS C 737 " distance=2.03 Simple disulfide: pdb=" SG CYS C 812 " - pdb=" SG CYS C 866 " distance=2.03 Simple disulfide: pdb=" SG CYS D 149 " - pdb=" SG CYS D 302 " distance=2.03 Simple disulfide: pdb=" SG CYS D 217 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 263 " - pdb=" SG CYS D 275 " distance=2.03 Simple disulfide: pdb=" SG CYS D 320 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 337 " - pdb=" SG CYS D 409 " distance=2.03 Simple disulfide: pdb=" SG CYS D 490 " - pdb=" SG CYS D 507 " distance=2.03 Simple disulfide: pdb=" SG CYS D 492 " - pdb=" SG CYS D 509 " distance=2.03 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5930 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 21 sheets defined 61.6% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.524A pdb=" N ARG A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 931 Processing helix chain 'A' and resid 933 through 935 No H-bonds generated for 'chain 'A' and resid 933 through 935' Processing helix chain 'A' and resid 936 through 947 removed outlier: 3.581A pdb=" N ILE A 943 " --> pdb=" O PRO A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 964 Processing helix chain 'A' and resid 972 through 997 Processing helix chain 'A' and resid 1008 through 1021 Processing helix chain 'A' and resid 1033 through 1039 removed outlier: 3.590A pdb=" N ASN A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1067 Processing helix chain 'A' and resid 1072 through 1086 Processing helix chain 'A' and resid 1088 through 1095 Processing helix chain 'A' and resid 1095 through 1100 removed outlier: 3.687A pdb=" N SER A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1113 Processing helix chain 'A' and resid 1116 through 1132 Processing helix chain 'A' and resid 1132 through 1138 Processing helix chain 'A' and resid 1146 through 1154 removed outlier: 3.717A pdb=" N ASN A1154 " --> pdb=" O ILE A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1166 removed outlier: 3.947A pdb=" N PHE A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 3.732A pdb=" N ARG A1188 " --> pdb=" O ILE A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1221 Processing helix chain 'A' and resid 1221 through 1228 Processing helix chain 'A' and resid 1238 through 1251 removed outlier: 3.596A pdb=" N LYS A1249 " --> pdb=" O ARG A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1305 Processing helix chain 'A' and resid 1306 through 1308 No H-bonds generated for 'chain 'A' and resid 1306 through 1308' Processing helix chain 'A' and resid 1311 through 1319 Processing helix chain 'A' and resid 1324 through 1333 removed outlier: 3.998A pdb=" N TYR A1328 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP A1333 " --> pdb=" O TYR A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1349 Processing helix chain 'A' and resid 1357 through 1367 removed outlier: 3.623A pdb=" N SER A1366 " --> pdb=" O PHE A1362 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A1367 " --> pdb=" O MET A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1431 removed outlier: 3.693A pdb=" N ARG A1419 " --> pdb=" O THR A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1437 removed outlier: 3.520A pdb=" N TYR A1435 " --> pdb=" O SER A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1451 removed outlier: 4.530A pdb=" N VAL A1442 " --> pdb=" O ILE A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.832A pdb=" N LEU A1457 " --> pdb=" O PRO A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1471 Processing helix chain 'A' and resid 1475 through 1488 removed outlier: 3.512A pdb=" N ARG A1488 " --> pdb=" O THR A1484 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1504 Processing helix chain 'A' and resid 1506 through 1513 Processing helix chain 'A' and resid 1520 through 1532 Processing helix chain 'A' and resid 1533 through 1535 No H-bonds generated for 'chain 'A' and resid 1533 through 1535' Processing helix chain 'A' and resid 1536 through 1550 Processing helix chain 'A' and resid 1553 through 1557 Processing helix chain 'A' and resid 1558 through 1563 Processing helix chain 'A' and resid 1569 through 1575 Processing helix chain 'A' and resid 1579 through 1586 removed outlier: 3.866A pdb=" N LYS A1585 " --> pdb=" O TYR A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1594 through 1602 removed outlier: 3.597A pdb=" N GLN A1600 " --> pdb=" O MET A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1622 removed outlier: 3.550A pdb=" N SER A1620 " --> pdb=" O ALA A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1648 Processing helix chain 'A' and resid 1658 through 1684 Processing helix chain 'A' and resid 1685 through 1687 No H-bonds generated for 'chain 'A' and resid 1685 through 1687' Processing helix chain 'A' and resid 1688 through 1708 Processing helix chain 'A' and resid 1710 through 1715 removed outlier: 4.195A pdb=" N SER A1715 " --> pdb=" O PRO A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1716 through 1731 Processing helix chain 'A' and resid 1749 through 1766 removed outlier: 3.621A pdb=" N GLY A1762 " --> pdb=" O ILE A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1784 through 1801 removed outlier: 3.575A pdb=" N LEU A1791 " --> pdb=" O LYS A1787 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1809 removed outlier: 3.669A pdb=" N TRP A1809 " --> pdb=" O ASP A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1827 Processing helix chain 'A' and resid 1828 through 1833 removed outlier: 4.004A pdb=" N ARG A1832 " --> pdb=" O TYR A1828 " (cutoff:3.500A) Processing helix chain 'A' and resid 1849 through 1853 Processing helix chain 'A' and resid 1854 through 1888 removed outlier: 3.804A pdb=" N ASP A1869 " --> pdb=" O SER A1865 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N SER A1872 " --> pdb=" O ALA A1868 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER A1873 " --> pdb=" O ASP A1869 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N HIS A1884 " --> pdb=" O SER A1880 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N HIS A1885 " --> pdb=" O PHE A1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1900 Processing helix chain 'A' and resid 1901 through 1906 Processing helix chain 'A' and resid 1912 through 1915 Processing helix chain 'A' and resid 1916 through 1923 removed outlier: 3.528A pdb=" N GLY A1923 " --> pdb=" O MET A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1932 Processing helix chain 'A' and resid 1935 through 1945 removed outlier: 3.562A pdb=" N ASP A1941 " --> pdb=" O THR A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1948 through 1967 Processing helix chain 'A' and resid 1969 through 1979 Processing helix chain 'A' and resid 1979 through 2030 removed outlier: 3.751A pdb=" N GLY A1988 " --> pdb=" O GLY A1984 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A2030 " --> pdb=" O ALA A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2059 Processing helix chain 'A' and resid 2064 through 2070 Processing helix chain 'A' and resid 2071 through 2073 No H-bonds generated for 'chain 'A' and resid 2071 through 2073' Processing helix chain 'A' and resid 2085 through 2099 removed outlier: 3.525A pdb=" N ALA A2090 " --> pdb=" O MET A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2099 through 2124 Processing helix chain 'A' and resid 2125 through 2152 removed outlier: 4.028A pdb=" N LEU A2129 " --> pdb=" O GLY A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2156 Processing helix chain 'B' and resid 751 through 756 removed outlier: 3.641A pdb=" N PHE B 755 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 778 Processing helix chain 'B' and resid 779 through 785 removed outlier: 3.555A pdb=" N LEU B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 788 No H-bonds generated for 'chain 'B' and resid 786 through 788' Processing helix chain 'B' and resid 792 through 803 Processing helix chain 'B' and resid 806 through 813 Processing helix chain 'B' and resid 818 through 841 removed outlier: 3.636A pdb=" N TYR B 822 " --> pdb=" O SER B 818 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR B 839 " --> pdb=" O GLU B 835 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 840 " --> pdb=" O MET B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 847 Processing helix chain 'B' and resid 851 through 856 removed outlier: 3.822A pdb=" N LEU B 855 " --> pdb=" O LYS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 871 Processing helix chain 'B' and resid 898 through 914 removed outlier: 3.709A pdb=" N LYS B 912 " --> pdb=" O ILE B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 922 Processing helix chain 'B' and resid 924 through 927 Processing helix chain 'B' and resid 928 through 952 Proline residue: B 939 - end of helix Processing helix chain 'B' and resid 961 through 971 removed outlier: 3.782A pdb=" N LEU B 965 " --> pdb=" O ALA B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 975 removed outlier: 3.643A pdb=" N ARG B 975 " --> pdb=" O MET B 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 972 through 975' Processing helix chain 'B' and resid 979 through 991 Processing helix chain 'B' and resid 992 through 1009 removed outlier: 3.628A pdb=" N ILE B1004 " --> pdb=" O LYS B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1034 Processing helix chain 'B' and resid 1040 through 1059 Processing helix chain 'B' and resid 1062 through 1083 Processing helix chain 'B' and resid 1094 through 1102 removed outlier: 3.588A pdb=" N LEU B1102 " --> pdb=" O GLN B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1115 removed outlier: 3.793A pdb=" N VAL B1109 " --> pdb=" O LYS B1105 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B1112 " --> pdb=" O MET B1108 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS B1115 " --> pdb=" O GLN B1111 " (cutoff:3.500A) Processing helix chain 'B' and resid 1124 through 1131 Processing helix chain 'B' and resid 1135 through 1147 removed outlier: 3.899A pdb=" N ASP B1139 " --> pdb=" O ASN B1135 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET B1145 " --> pdb=" O THR B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1151 removed outlier: 6.466A pdb=" N THR B1151 " --> pdb=" O LEU B1148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1148 through 1151' Processing helix chain 'B' and resid 1152 through 1165 removed outlier: 3.730A pdb=" N LEU B1156 " --> pdb=" O ASP B1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 129 removed outlier: 3.604A pdb=" N ARG C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C 118 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 161 removed outlier: 3.986A pdb=" N GLU C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER C 148 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 178 through 197 removed outlier: 3.736A pdb=" N ILE C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 242 Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.638A pdb=" N VAL C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 279 removed outlier: 4.554A pdb=" N ASN C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 5.264A pdb=" N LYS C 287 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Proline residue: C 290 - end of helix Processing helix chain 'C' and resid 292 through 303 Processing helix chain 'C' and resid 309 through 328 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 379 through 402 Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.817A pdb=" N SER C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 430 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 451 through 455 Processing helix chain 'C' and resid 466 through 483 Processing helix chain 'C' and resid 490 through 510 removed outlier: 3.758A pdb=" N TYR C 510 " --> pdb=" O TYR C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 removed outlier: 3.741A pdb=" N LYS C 516 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS C 517 " --> pdb=" O GLN C 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 517' Processing helix chain 'C' and resid 528 through 538 removed outlier: 4.149A pdb=" N PHE C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 573 removed outlier: 3.548A pdb=" N SER C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 584 removed outlier: 4.045A pdb=" N PHE C 584 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 611 Processing helix chain 'C' and resid 619 through 640 Processing helix chain 'C' and resid 647 through 663 Processing helix chain 'C' and resid 677 through 689 Processing helix chain 'C' and resid 693 through 706 Processing helix chain 'C' and resid 745 through 760 removed outlier: 3.550A pdb=" N LYS C 751 " --> pdb=" O ARG C 747 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 755 " --> pdb=" O LYS C 751 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER C 759 " --> pdb=" O LYS C 755 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 760 " --> pdb=" O LEU C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 785 removed outlier: 4.079A pdb=" N ASN C 785 " --> pdb=" O ASN C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 803 Processing helix chain 'C' and resid 804 through 829 removed outlier: 3.565A pdb=" N ARG C 829 " --> pdb=" O ARG C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 834 No H-bonds generated for 'chain 'C' and resid 832 through 834' Processing helix chain 'C' and resid 835 through 845 Processing helix chain 'C' and resid 873 through 892 Processing helix chain 'C' and resid 971 through 979 removed outlier: 3.573A pdb=" N LEU C 975 " --> pdb=" O GLU C 971 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 977 " --> pdb=" O GLU C 973 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP C 978 " --> pdb=" O ILE C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1013 Processing helix chain 'C' and resid 1029 through 1035 Processing helix chain 'C' and resid 1056 through 1061 removed outlier: 3.842A pdb=" N ILE C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1085 Processing helix chain 'C' and resid 1090 through 1097 removed outlier: 3.781A pdb=" N VAL C1093 " --> pdb=" O PRO C1090 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN C1094 " --> pdb=" O SER C1091 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C1097 " --> pdb=" O ASN C1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 1122 through 1126 Processing helix chain 'D' and resid 110 through 116 removed outlier: 3.866A pdb=" N LYS D 116 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 195 through 202 removed outlier: 3.681A pdb=" N ARG D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 211 Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.520A pdb=" N ALA D 221 " --> pdb=" O CYS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 333 through 344 Processing helix chain 'D' and resid 358 through 366 Processing helix chain 'D' and resid 371 through 380 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 442 through 459 removed outlier: 4.270A pdb=" N TYR D 446 " --> pdb=" O PRO D 442 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 450 " --> pdb=" O TYR D 446 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET D 451 " --> pdb=" O LYS D 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D 454 " --> pdb=" O ILE D 450 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 455 " --> pdb=" O MET D 451 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER D 458 " --> pdb=" O ILE D 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 61 removed outlier: 3.602A pdb=" N GLU A 57 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 59 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1168 through 1170 Processing sheet with id=AA3, first strand: chain 'A' and resid 1564 through 1568 removed outlier: 6.370A pdb=" N GLY A1780 " --> pdb=" O THR A1567 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 186 through 187 Processing sheet with id=AA5, first strand: chain 'B' and resid 759 through 761 removed outlier: 6.154A pdb=" N GLY B 759 " --> pdb=" O MET B1092 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 881 through 883 Processing sheet with id=AA7, first strand: chain 'B' and resid 1013 through 1015 Processing sheet with id=AA8, first strand: chain 'C' and resid 712 through 714 Processing sheet with id=AA9, first strand: chain 'C' and resid 717 through 718 removed outlier: 4.499A pdb=" N THR C 863 " --> pdb=" O ILE C 922 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 930 through 931 Processing sheet with id=AB2, first strand: chain 'C' and resid 968 through 970 removed outlier: 6.902A pdb=" N LYS C 961 " --> pdb=" O TYR C1026 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N SER C1028 " --> pdb=" O LYS C 961 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR C 963 " --> pdb=" O SER C1028 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 984 through 985 Processing sheet with id=AB4, first strand: chain 'C' and resid 1050 through 1053 removed outlier: 4.310A pdb=" N TRP C1073 " --> pdb=" O ILE C1042 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1113 through 1117 removed outlier: 6.612A pdb=" N ILE C1106 " --> pdb=" O ILE C1114 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS C1116 " --> pdb=" O PHE C1104 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE C1104 " --> pdb=" O LYS C1116 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLU C1148 " --> pdb=" O LYS C1143 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LYS C1143 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE C1150 " --> pdb=" O ALA C1141 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA C1141 " --> pdb=" O ILE C1150 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N HIS C1152 " --> pdb=" O ILE C1139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 133 through 137 Processing sheet with id=AB7, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AB8, first strand: chain 'D' and resid 154 through 158 Processing sheet with id=AB9, first strand: chain 'D' and resid 306 through 307 removed outlier: 5.537A pdb=" N ASN D 306 " --> pdb=" O GLU D 438 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 310 through 313 Processing sheet with id=AC2, first strand: chain 'D' and resid 327 through 330 removed outlier: 3.865A pdb=" N LYS D 408 " --> pdb=" O ASN D 403 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP D 399 " --> pdb=" O PHE D 412 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 514 through 516 1322 hydrogen bonds defined for protein. 3768 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: 6.02 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8015 1.34 - 1.46: 5864 1.46 - 1.58: 11469 1.58 - 1.70: 0 1.70 - 1.82: 244 Bond restraints: 25592 Sorted by residual: bond pdb=" CA LYS C 981 " pdb=" CB LYS C 981 " ideal model delta sigma weight residual 1.531 1.572 -0.042 3.12e-02 1.03e+03 1.78e+00 bond pdb=" CG LYS B 790 " pdb=" CD LYS B 790 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" N GLN B 744 " pdb=" CA GLN B 744 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.65e+00 bond pdb=" CB LYS B 852 " pdb=" CG LYS B 852 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB LYS B 790 " pdb=" CG LYS B 790 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.39e+00 ... (remaining 25587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 34201 2.45 - 4.91: 170 4.91 - 7.36: 28 7.36 - 9.82: 8 9.82 - 12.27: 4 Bond angle restraints: 34411 Sorted by residual: angle pdb=" N ILE A1180 " pdb=" CA ILE A1180 " pdb=" C ILE A1180 " ideal model delta sigma weight residual 113.53 108.22 5.31 9.80e-01 1.04e+00 2.93e+01 angle pdb=" N ILE C1122 " pdb=" CA ILE C1122 " pdb=" C ILE C1122 " ideal model delta sigma weight residual 113.20 109.07 4.13 9.60e-01 1.09e+00 1.85e+01 angle pdb=" CB MET B 797 " pdb=" CG MET B 797 " pdb=" SD MET B 797 " ideal model delta sigma weight residual 112.70 124.97 -12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" CB LYS B 790 " pdb=" CG LYS B 790 " pdb=" CD LYS B 790 " ideal model delta sigma weight residual 111.30 120.47 -9.17 2.30e+00 1.89e-01 1.59e+01 angle pdb=" CB MET D 114 " pdb=" CG MET D 114 " pdb=" SD MET D 114 " ideal model delta sigma weight residual 112.70 123.74 -11.04 3.00e+00 1.11e-01 1.35e+01 ... (remaining 34406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 14064 17.79 - 35.58: 1337 35.58 - 53.36: 285 53.36 - 71.15: 63 71.15 - 88.94: 15 Dihedral angle restraints: 15764 sinusoidal: 6608 harmonic: 9156 Sorted by residual: dihedral pdb=" CB CYS D 320 " pdb=" SG CYS D 320 " pdb=" SG CYS D 418 " pdb=" CB CYS D 418 " ideal model delta sinusoidal sigma weight residual -86.00 -152.57 66.57 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CA PRO D 491 " pdb=" C PRO D 491 " pdb=" N CYS D 492 " pdb=" CA CYS D 492 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA MET B 743 " pdb=" C MET B 743 " pdb=" N GLN B 744 " pdb=" CA GLN B 744 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 15761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2746 0.039 - 0.077: 821 0.077 - 0.116: 168 0.116 - 0.154: 31 0.154 - 0.193: 2 Chirality restraints: 3768 Sorted by residual: chirality pdb=" CB ILE D 323 " pdb=" CA ILE D 323 " pdb=" CG1 ILE D 323 " pdb=" CG2 ILE D 323 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CG LEU C1085 " pdb=" CB LEU C1085 " pdb=" CD1 LEU C1085 " pdb=" CD2 LEU C1085 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ILE A2048 " pdb=" N ILE A2048 " pdb=" C ILE A2048 " pdb=" CB ILE A2048 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 3765 not shown) Planarity restraints: 4367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 451 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO C 452 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 452 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 452 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1429 " 0.009 2.00e-02 2.50e+03 1.26e-02 2.78e+00 pdb=" CG PHE A1429 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A1429 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A1429 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A1429 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1429 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A1429 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C1063 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO C1064 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C1064 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C1064 " -0.023 5.00e-02 4.00e+02 ... (remaining 4364 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 13103 3.01 - 3.48: 26480 3.48 - 3.95: 41950 3.95 - 4.43: 50257 4.43 - 4.90: 77989 Nonbonded interactions: 209779 Sorted by model distance: nonbonded pdb=" N ASN A1003 " pdb=" OD1 ASN A1003 " model vdw 2.531 3.120 nonbonded pdb=" N ILE C1122 " pdb=" N ASN C1123 " model vdw 2.599 2.560 nonbonded pdb=" N MET A1801 " pdb=" O MET A1801 " model vdw 2.603 2.496 nonbonded pdb=" O ASN D 371 " pdb=" OD1 ASN D 371 " model vdw 2.612 3.040 nonbonded pdb=" O LYS D 370 " pdb=" OD1 ASN D 371 " model vdw 2.621 3.040 ... (remaining 209774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.520 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.003 0.042 25611 Z= 0.110 Angle : 0.499 12.269 34449 Z= 0.262 Chirality : 0.038 0.193 3768 Planarity : 0.003 0.046 4367 Dihedral : 14.623 88.941 9777 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.88 % Allowed : 12.25 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 3063 helix: 0.81 (0.12), residues: 1673 sheet: 0.42 (0.40), residues: 169 loop : -0.20 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2149 TYR 0.016 0.001 TYR A2014 PHE 0.029 0.001 PHE A1429 TRP 0.015 0.001 TRP C1044 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (25592) covalent geometry : angle 0.49883 / 0.26 (34411) SS BOND : bond 0.00204 / 0.09 ( 19) SS BOND : angle 0.54252 / 0.32 ( 38) hydrogen bonds : bond 0.20922 / 13.77 ( 1322) hydrogen bonds : angle 6.58464 / 4.74 ( 3768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TYR cc_start: 0.5539 (m-80) cc_final: 0.5337 (m-80) REVERT: A 1006 ASP cc_start: 0.8424 (m-30) cc_final: 0.7611 (t0) REVERT: A 1017 GLU cc_start: 0.8405 (tt0) cc_final: 0.8160 (tt0) REVERT: A 1596 MET cc_start: 0.8735 (ppp) cc_final: 0.8493 (ppp) REVERT: A 1641 ASP cc_start: 0.8391 (m-30) cc_final: 0.8141 (t0) REVERT: A 1670 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8290 (tm-30) REVERT: A 1771 PHE cc_start: 0.8378 (t80) cc_final: 0.7857 (p90) REVERT: A 1992 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8080 (tptt) REVERT: A 2078 ILE cc_start: 0.7599 (tp) cc_final: 0.7333 (tp) REVERT: A 2151 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7486 (tpt) REVERT: B 774 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8465 (tm-30) REVERT: C 103 GLU cc_start: 0.8580 (mp0) cc_final: 0.8283 (mp0) REVERT: C 125 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8736 (mptt) REVERT: C 529 ARG cc_start: 0.8270 (mtt180) cc_final: 0.6378 (mtm180) REVERT: C 747 ARG cc_start: 0.8967 (ptp-110) cc_final: 0.8473 (ttp80) REVERT: C 785 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.6843 (p0) REVERT: C 981 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6702 (tptt) REVERT: C 984 TYR cc_start: 0.6357 (m-80) cc_final: 0.5960 (m-80) REVERT: C 1022 ASP cc_start: 0.7083 (m-30) cc_final: 0.6848 (m-30) REVERT: C 1034 ASN cc_start: 0.8205 (m-40) cc_final: 0.7978 (m110) REVERT: D 110 TRP cc_start: 0.7454 (m100) cc_final: 0.6786 (m100) REVERT: D 190 MET cc_start: 0.5405 (tpp) cc_final: 0.5117 (tpt) REVERT: D 399 TRP cc_start: 0.6014 (m-90) cc_final: 0.4960 (m-90) REVERT: D 439 ASN cc_start: 0.7478 (m-40) cc_final: 0.7190 (m110) outliers start: 25 outliers final: 14 residues processed: 271 average time/residue: 0.1923 time to fit residues: 80.3637 Evaluate side-chains 239 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1723 GLU Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 2151 MET Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 785 ASN Chi-restraints excluded: chain C residue 981 LYS Chi-restraints excluded: chain C residue 1020 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 857 GLN C 124 ASN C 297 GLN C1152 HIS ** D 371 ASN ** 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 = 0.3209 r_free = 0.3209 target = 0.074541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.051328 restraints weight = 65790.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.050646 restraints weight = 45804.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.050995 restraints weight = 42804.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.051249 restraints weight = 37165.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.051237 restraints weight = 34920.003| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25611 Z= 0.235 Angle : 0.558 7.016 34449 Z= 0.298 Chirality : 0.043 0.185 3768 Planarity : 0.004 0.043 4367 Dihedral : 5.136 59.303 3374 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.19 % Allowed : 11.68 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.17 (0.15), residues: 3063 helix: 1.53 (0.12), residues: 1677 sheet: 0.05 (0.39), residues: 169 loop : -0.09 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 599 TYR 0.018 0.002 TYR A1034 PHE 0.020 0.002 PHE A1717 TRP 0.030 0.002 TRP C1044 HIS 0.009 0.001 HIS D 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 (25592) covalent geometry : angle 0.55750 / 0.30 (34411) SS BOND : bond 0.00334 / 0.14 ( 19) SS BOND : angle 1.13435 / 0.67 ( 38) hydrogen bonds : bond 0.05358 / 3.47 ( 1322) hydrogen bonds : angle 4.54663 / 3.28 ( 3768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TYR cc_start: 0.6240 (m-80) cc_final: 0.5982 (m-80) REVERT: A 53 MET cc_start: 0.6992 (mpp) cc_final: 0.6676 (mpp) REVERT: A 1017 GLU cc_start: 0.7646 (tt0) cc_final: 0.7387 (tt0) REVERT: A 1354 LYS cc_start: 0.8300 (mmmt) cc_final: 0.7675 (mtpp) REVERT: A 1594 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7925 (ttmm) REVERT: A 1843 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7874 (mtt) REVERT: A 1919 MET cc_start: 0.8752 (ttp) cc_final: 0.8479 (ttp) REVERT: A 2006 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7748 (mpp) REVERT: A 2078 ILE cc_start: 0.7473 (tp) cc_final: 0.7168 (tp) REVERT: A 2150 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7918 (mtmt) REVERT: A 2151 MET cc_start: 0.8364 (tmm) cc_final: 0.7792 (tpt) REVERT: B 743 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7237 (tpt) REVERT: B 774 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7824 (tm-30) REVERT: C 442 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.6800 (mp) REVERT: C 529 ARG cc_start: 0.8319 (mtt180) cc_final: 0.6986 (mtm180) REVERT: C 747 ARG cc_start: 0.8239 (ptp-110) cc_final: 0.7802 (ttp80) REVERT: C 1022 ASP cc_start: 0.6974 (m-30) cc_final: 0.6664 (m-30) REVERT: D 114 MET cc_start: 0.7673 (mmm) cc_final: 0.7437 (tpt) REVERT: D 399 TRP cc_start: 0.7838 (m-90) cc_final: 0.6952 (m-90) outliers start: 62 outliers final: 32 residues processed: 265 average time/residue: 0.1657 time to fit residues: 67.8879 Evaluate side-chains 245 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1234 GLU Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1464 GLU Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1594 LYS Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1843 MET Chi-restraints excluded: chain A residue 1940 LYS Chi-restraints excluded: chain A residue 1996 GLN Chi-restraints excluded: chain A residue 2006 MET Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain A residue 2150 LYS Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1162 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 341 CYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 1049 VAL Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain C residue 1115 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 287 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 294 optimal weight: 0.9990 chunk 300 optimal weight: 0.5980 chunk 235 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 857 GLN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 356 HIS D 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.075081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.051460 restraints weight = 65392.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.051594 restraints weight = 39429.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.051554 restraints weight = 40185.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.051897 restraints weight = 33966.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.052002 restraints weight = 30354.330| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25611 Z= 0.155 Angle : 0.499 7.475 34449 Z= 0.267 Chirality : 0.040 0.184 3768 Planarity : 0.003 0.043 4367 Dihedral : 4.517 36.915 3351 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.91 % Allowed : 12.60 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.42 (0.15), residues: 3063 helix: 1.84 (0.13), residues: 1669 sheet: -0.20 (0.39), residues: 169 loop : -0.07 (0.19), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 456 TYR 0.025 0.001 TYR C 963 PHE 0.018 0.001 PHE A1429 TRP 0.022 0.002 TRP C1044 HIS 0.010 0.001 HIS D 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (25592) covalent geometry : angle 0.49816 / 0.27 (34411) SS BOND : bond 0.00407 / 0.23 ( 19) SS BOND : angle 0.97271 / 0.55 ( 38) hydrogen bonds : bond 0.04594 / 2.97 ( 1322) hydrogen bonds : angle 4.27243 / 3.07 ( 3768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 TYR cc_start: 0.6127 (m-80) cc_final: 0.5854 (m-80) REVERT: A 53 MET cc_start: 0.7066 (mpp) cc_final: 0.6764 (mpp) REVERT: A 1017 GLU cc_start: 0.7654 (tt0) cc_final: 0.7395 (tt0) REVERT: A 1594 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8076 (ttmm) REVERT: A 1843 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7707 (mtt) REVERT: A 1919 MET cc_start: 0.8765 (ttp) cc_final: 0.8505 (ttp) REVERT: A 2006 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7622 (mpp) REVERT: A 2078 ILE cc_start: 0.7446 (tp) cc_final: 0.7141 (tp) REVERT: A 2150 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7899 (mtmt) REVERT: A 2151 MET cc_start: 0.8397 (tmm) cc_final: 0.7930 (tpp) REVERT: B 743 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7270 (tpt) REVERT: B 820 GLU cc_start: 0.7347 (mp0) cc_final: 0.7052 (mm-30) REVERT: C 529 ARG cc_start: 0.8234 (mtt180) cc_final: 0.6731 (mtm180) REVERT: C 747 ARG cc_start: 0.8227 (ptp-110) cc_final: 0.7781 (ttp80) REVERT: C 1002 MET cc_start: 0.6829 (tmm) cc_final: 0.6453 (tmm) REVERT: C 1022 ASP cc_start: 0.7093 (m-30) cc_final: 0.6781 (m-30) REVERT: D 110 TRP cc_start: 0.7316 (m100) cc_final: 0.6892 (m-10) REVERT: D 399 TRP cc_start: 0.7798 (m-90) cc_final: 0.7039 (m-90) REVERT: D 449 GLU cc_start: 0.7339 (tp30) cc_final: 0.7076 (tm-30) REVERT: D 487 SER cc_start: 0.8127 (t) cc_final: 0.7918 (m) outliers start: 54 outliers final: 28 residues processed: 258 average time/residue: 0.1813 time to fit residues: 72.9946 Evaluate side-chains 236 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1234 GLU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1464 GLU Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1594 LYS Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1843 MET Chi-restraints excluded: chain A residue 1940 LYS Chi-restraints excluded: chain A residue 2006 MET Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain A residue 2150 LYS Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1145 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 341 CYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1049 VAL Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 446 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 198 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 305 optimal weight: 7.9990 chunk 122 optimal weight: 0.2980 chunk 241 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 996 ASN A1996 GLN B 857 GLN C1034 ASN C1088 HIS C1123 ASN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN D 519 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.051742 restraints weight = 65172.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.051986 restraints weight = 39173.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.052258 restraints weight = 35593.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.052515 restraints weight = 31398.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.052446 restraints weight = 29933.995| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25611 Z= 0.137 Angle : 0.480 7.701 34449 Z= 0.256 Chirality : 0.040 0.183 3768 Planarity : 0.003 0.043 4367 Dihedral : 4.411 37.627 3351 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.12 % Allowed : 12.53 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.53 (0.15), residues: 3063 helix: 2.00 (0.13), residues: 1665 sheet: -0.40 (0.40), residues: 158 loop : -0.09 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 599 TYR 0.020 0.001 TYR C 963 PHE 0.018 0.001 PHE C1021 TRP 0.019 0.001 TRP C1044 HIS 0.004 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (25592) covalent geometry : angle 0.47914 / 0.26 (34411) SS BOND : bond 0.00263 / 0.13 ( 19) SS BOND : angle 0.85156 / 0.49 ( 38) hydrogen bonds : bond 0.04183 / 2.70 ( 1322) hydrogen bonds : angle 4.12091 / 2.96 ( 3768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 TYR cc_start: 0.6078 (m-80) cc_final: 0.5801 (m-80) REVERT: A 53 MET cc_start: 0.7072 (mpp) cc_final: 0.6815 (mpp) REVERT: A 1017 GLU cc_start: 0.7637 (tt0) cc_final: 0.7350 (tt0) REVERT: A 1199 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8140 (mtm-85) REVERT: A 1594 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7874 (ttmm) REVERT: A 1919 MET cc_start: 0.8760 (ttp) cc_final: 0.8496 (ttp) REVERT: A 1978 MET cc_start: 0.7667 (mmm) cc_final: 0.7446 (mmm) REVERT: A 2006 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7571 (mpp) REVERT: A 2078 ILE cc_start: 0.7310 (tp) cc_final: 0.6981 (tp) REVERT: A 2150 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7920 (mtmt) REVERT: A 2151 MET cc_start: 0.8435 (tmm) cc_final: 0.7970 (tpt) REVERT: A 2154 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6216 (pp-130) REVERT: B 743 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7243 (tpt) REVERT: B 967 ASP cc_start: 0.7713 (m-30) cc_final: 0.7175 (m-30) REVERT: C 442 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6660 (mt) REVERT: C 529 ARG cc_start: 0.8226 (mtt180) cc_final: 0.6717 (mtm180) REVERT: C 1002 MET cc_start: 0.6918 (tmm) cc_final: 0.6575 (tmm) REVERT: C 1123 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7657 (t0) REVERT: D 110 TRP cc_start: 0.7155 (m100) cc_final: 0.6890 (m-10) REVERT: D 399 TRP cc_start: 0.7750 (m-90) cc_final: 0.7134 (m-90) REVERT: D 449 GLU cc_start: 0.7303 (tp30) cc_final: 0.7052 (tm-30) outliers start: 60 outliers final: 36 residues processed: 266 average time/residue: 0.1745 time to fit residues: 72.1911 Evaluate side-chains 252 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1199 ARG Chi-restraints excluded: chain A residue 1234 GLU Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1464 GLU Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1594 LYS Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1940 LYS Chi-restraints excluded: chain A residue 2006 MET Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain A residue 2150 LYS Chi-restraints excluded: chain A residue 2154 MET Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1145 MET Chi-restraints excluded: chain B residue 1162 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 341 CYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 849 TYR Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 1049 VAL Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain C residue 1074 VAL Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain C residue 1123 ASN Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 446 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 191 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 278 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 857 GLN C 999 GLN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.051387 restraints weight = 65374.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.051858 restraints weight = 39024.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.052083 restraints weight = 34687.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.052333 restraints weight = 32846.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.052299 restraints weight = 28119.051| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25611 Z= 0.158 Angle : 0.490 9.707 34449 Z= 0.261 Chirality : 0.040 0.184 3768 Planarity : 0.003 0.043 4367 Dihedral : 4.420 38.685 3351 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.95 % Allowed : 13.13 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.53 (0.15), residues: 3063 helix: 2.04 (0.13), residues: 1665 sheet: -0.48 (0.40), residues: 158 loop : -0.15 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 599 TYR 0.019 0.001 TYR C 963 PHE 0.016 0.001 PHE A1717 TRP 0.018 0.001 TRP C1044 HIS 0.004 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (25592) covalent geometry : angle 0.48920 / 0.26 (34411) SS BOND : bond 0.00281 / 0.13 ( 19) SS BOND : angle 0.86679 / 0.50 ( 38) hydrogen bonds : bond 0.04199 / 2.71 ( 1322) hydrogen bonds : angle 4.07548 / 2.92 ( 3768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 212 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 TYR cc_start: 0.6074 (m-80) cc_final: 0.5772 (m-80) REVERT: A 53 MET cc_start: 0.7163 (mpp) cc_final: 0.6900 (mpp) REVERT: A 1017 GLU cc_start: 0.7664 (tt0) cc_final: 0.7368 (tt0) REVERT: A 1199 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8107 (mtm-85) REVERT: A 1843 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7596 (mtt) REVERT: A 1919 MET cc_start: 0.8753 (ttp) cc_final: 0.8494 (ttp) REVERT: A 2006 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7552 (mpp) REVERT: A 2078 ILE cc_start: 0.7276 (tp) cc_final: 0.6922 (tp) REVERT: A 2150 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7941 (mtmt) REVERT: A 2151 MET cc_start: 0.8444 (tmm) cc_final: 0.7986 (tpt) REVERT: A 2154 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6174 (pp-130) REVERT: B 743 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7241 (tpt) REVERT: C 442 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6649 (mt) REVERT: C 529 ARG cc_start: 0.8263 (mtt180) cc_final: 0.6625 (mtm180) REVERT: C 962 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8098 (m) REVERT: C 1002 MET cc_start: 0.6879 (tmm) cc_final: 0.6488 (tmm) REVERT: C 1114 ILE cc_start: 0.8199 (pt) cc_final: 0.7859 (mm) REVERT: D 110 TRP cc_start: 0.7204 (m100) cc_final: 0.6895 (m100) REVERT: D 399 TRP cc_start: 0.7774 (m-90) cc_final: 0.7185 (m-90) outliers start: 55 outliers final: 35 residues processed: 250 average time/residue: 0.1819 time to fit residues: 69.9827 Evaluate side-chains 248 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1199 ARG Chi-restraints excluded: chain A residue 1234 GLU Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1464 GLU Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1801 MET Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1843 MET Chi-restraints excluded: chain A residue 1940 LYS Chi-restraints excluded: chain A residue 2006 MET Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain A residue 2150 LYS Chi-restraints excluded: chain A residue 2154 MET Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1145 MET Chi-restraints excluded: chain B residue 1162 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 341 CYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 1049 VAL Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain C residue 1074 VAL Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 446 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 278 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 256 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1713 ASN B 857 GLN ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1123 ASN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.051298 restraints weight = 65560.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.051389 restraints weight = 38281.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.051571 restraints weight = 34312.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.051742 restraints weight = 31493.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.051793 restraints weight = 29251.651| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25611 Z= 0.163 Angle : 0.491 8.643 34449 Z= 0.262 Chirality : 0.040 0.181 3768 Planarity : 0.003 0.044 4367 Dihedral : 4.421 39.403 3351 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.12 % Allowed : 12.85 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.15), residues: 3063 helix: 2.08 (0.13), residues: 1659 sheet: -0.42 (0.39), residues: 158 loop : -0.18 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 599 TYR 0.018 0.001 TYR C 963 PHE 0.023 0.001 PHE A1429 TRP 0.020 0.001 TRP C1044 HIS 0.005 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (25592) covalent geometry : angle 0.49026 / 0.26 (34411) SS BOND : bond 0.00287 / 0.13 ( 19) SS BOND : angle 0.84108 / 0.49 ( 38) hydrogen bonds : bond 0.04201 / 2.71 ( 1322) hydrogen bonds : angle 4.05093 / 2.90 ( 3768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7252 (mpp) cc_final: 0.6944 (mpp) REVERT: A 1017 GLU cc_start: 0.7687 (tt0) cc_final: 0.7379 (tt0) REVERT: A 1199 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8059 (mtm-85) REVERT: A 1843 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7640 (mtt) REVERT: A 1919 MET cc_start: 0.8755 (ttp) cc_final: 0.8503 (ttp) REVERT: A 2006 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7518 (mpp) REVERT: A 2078 ILE cc_start: 0.7255 (tp) cc_final: 0.6908 (tp) REVERT: A 2141 LYS cc_start: 0.8457 (tptt) cc_final: 0.8209 (tptt) REVERT: A 2150 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7984 (mtmt) REVERT: A 2151 MET cc_start: 0.8429 (tmm) cc_final: 0.7968 (tpt) REVERT: A 2154 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6156 (pp-130) REVERT: B 743 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7267 (tpt) REVERT: B 967 ASP cc_start: 0.7615 (m-30) cc_final: 0.7401 (m-30) REVERT: B 1079 MET cc_start: 0.7958 (mtp) cc_final: 0.7605 (mtp) REVERT: C 442 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6533 (mt) REVERT: C 529 ARG cc_start: 0.8262 (mtt180) cc_final: 0.6707 (mtm180) REVERT: C 962 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8160 (m) REVERT: C 1114 ILE cc_start: 0.8209 (pt) cc_final: 0.7929 (mm) REVERT: C 1123 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7641 (t0) REVERT: D 110 TRP cc_start: 0.7253 (m100) cc_final: 0.6885 (m100) REVERT: D 399 TRP cc_start: 0.7728 (m-90) cc_final: 0.7072 (m-90) outliers start: 60 outliers final: 38 residues processed: 252 average time/residue: 0.1844 time to fit residues: 71.7780 Evaluate side-chains 252 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1199 ARG Chi-restraints excluded: chain A residue 1234 GLU Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1464 GLU Chi-restraints excluded: chain A residue 1594 LYS Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1801 MET Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1843 MET Chi-restraints excluded: chain A residue 1940 LYS Chi-restraints excluded: chain A residue 2006 MET Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain A residue 2150 LYS Chi-restraints excluded: chain A residue 2154 MET Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1145 MET Chi-restraints excluded: chain B residue 1162 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 341 CYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 1049 VAL Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain C residue 1074 VAL Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain C residue 1123 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 226 optimal weight: 0.5980 chunk 280 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 270 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 173 optimal weight: 0.0570 chunk 81 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 857 GLN C 999 GLN ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.075175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.052176 restraints weight = 65072.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.051644 restraints weight = 41439.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.051861 restraints weight = 43288.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.052143 restraints weight = 36063.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.052176 restraints weight = 32349.603| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25611 Z= 0.140 Angle : 0.483 8.366 34449 Z= 0.258 Chirality : 0.040 0.182 3768 Planarity : 0.003 0.044 4367 Dihedral : 4.338 38.238 3349 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.12 % Allowed : 12.85 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.15), residues: 3063 helix: 2.11 (0.13), residues: 1663 sheet: -0.41 (0.39), residues: 158 loop : -0.19 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 599 TYR 0.027 0.001 TYR A 41 PHE 0.023 0.001 PHE C1021 TRP 0.018 0.001 TRP C1044 HIS 0.004 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (25592) covalent geometry : angle 0.48226 / 0.26 (34411) SS BOND : bond 0.00260 / 0.12 ( 19) SS BOND : angle 0.79280 / 0.46 ( 38) hydrogen bonds : bond 0.04007 / 2.59 ( 1322) hydrogen bonds : angle 4.00461 / 2.87 ( 3768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7193 (mpp) cc_final: 0.6989 (mpp) REVERT: A 1017 GLU cc_start: 0.7665 (tt0) cc_final: 0.7357 (tt0) REVERT: A 1199 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8049 (mtm-85) REVERT: A 1672 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7970 (mtm-85) REVERT: A 1843 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7585 (mtt) REVERT: A 1919 MET cc_start: 0.8743 (ttp) cc_final: 0.8495 (ttp) REVERT: A 2006 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7432 (mpp) REVERT: A 2078 ILE cc_start: 0.7153 (tp) cc_final: 0.6807 (tp) REVERT: A 2141 LYS cc_start: 0.8436 (tptt) cc_final: 0.8187 (tptt) REVERT: A 2150 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7988 (mtmt) REVERT: A 2151 MET cc_start: 0.8463 (tmm) cc_final: 0.7973 (tpt) REVERT: A 2154 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6184 (pp-130) REVERT: B 743 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7262 (tpt) REVERT: C 442 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6491 (mt) REVERT: C 529 ARG cc_start: 0.8248 (mtt180) cc_final: 0.6710 (mtm180) REVERT: C 962 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8164 (m) REVERT: C 1114 ILE cc_start: 0.8243 (pt) cc_final: 0.7974 (mm) REVERT: D 110 TRP cc_start: 0.7171 (m100) cc_final: 0.6901 (m100) REVERT: D 190 MET cc_start: 0.6678 (tpt) cc_final: 0.6196 (tpp) REVERT: D 399 TRP cc_start: 0.7714 (m-90) cc_final: 0.7227 (m-90) outliers start: 60 outliers final: 42 residues processed: 251 average time/residue: 0.1887 time to fit residues: 72.8800 Evaluate side-chains 259 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 924 TYR Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1199 ARG Chi-restraints excluded: chain A residue 1234 GLU Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1464 GLU Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1594 LYS Chi-restraints excluded: chain A residue 1601 ILE Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1801 MET Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1843 MET Chi-restraints excluded: chain A residue 1940 LYS Chi-restraints excluded: chain A residue 2006 MET Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain A residue 2150 LYS Chi-restraints excluded: chain A residue 2154 MET Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1145 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 341 CYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 1049 VAL Chi-restraints excluded: chain C residue 1058 SER Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain C residue 1074 VAL Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 88 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 204 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 857 GLN ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1123 ASN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 519 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.051429 restraints weight = 65230.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.051318 restraints weight = 38627.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.051201 restraints weight = 41980.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.051562 restraints weight = 36421.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.051611 restraints weight = 32193.149| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25611 Z= 0.175 Angle : 0.503 8.198 34449 Z= 0.267 Chirality : 0.041 0.180 3768 Planarity : 0.003 0.043 4367 Dihedral : 4.386 39.568 3348 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.09 % Allowed : 13.10 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.53 (0.15), residues: 3063 helix: 2.09 (0.13), residues: 1662 sheet: -0.44 (0.40), residues: 158 loop : -0.22 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 599 TYR 0.022 0.001 TYR A 41 PHE 0.018 0.001 PHE C1021 TRP 0.019 0.001 TRP C1044 HIS 0.005 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (25592) covalent geometry : angle 0.50227 / 0.27 (34411) SS BOND : bond 0.00291 / 0.13 ( 19) SS BOND : angle 0.81832 / 0.48 ( 38) hydrogen bonds : bond 0.04202 / 2.71 ( 1322) hydrogen bonds : angle 4.04732 / 2.90 ( 3768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 214 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7271 (mpp) cc_final: 0.7058 (mpp) REVERT: A 1017 GLU cc_start: 0.7713 (tt0) cc_final: 0.7405 (tt0) REVERT: A 1199 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8128 (mtm-85) REVERT: A 1672 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.7977 (mtm-85) REVERT: A 1843 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7693 (mtt) REVERT: A 1919 MET cc_start: 0.8740 (ttp) cc_final: 0.8483 (ttp) REVERT: A 2006 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7407 (mpp) REVERT: A 2078 ILE cc_start: 0.7178 (tp) cc_final: 0.6837 (tp) REVERT: A 2117 TRP cc_start: 0.7565 (t-100) cc_final: 0.6423 (t-100) REVERT: A 2141 LYS cc_start: 0.8447 (tptt) cc_final: 0.8173 (tptt) REVERT: A 2150 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7715 (mtmt) REVERT: A 2151 MET cc_start: 0.8451 (tmm) cc_final: 0.7929 (tpt) REVERT: B 743 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7283 (tpt) REVERT: C 442 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6520 (mt) REVERT: C 529 ARG cc_start: 0.8258 (mtt180) cc_final: 0.6674 (mtm180) REVERT: C 747 ARG cc_start: 0.8053 (ptm160) cc_final: 0.7640 (ttp80) REVERT: C 962 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8168 (m) REVERT: C 1114 ILE cc_start: 0.8232 (pt) cc_final: 0.7993 (mm) REVERT: D 110 TRP cc_start: 0.7308 (m100) cc_final: 0.7000 (m100) REVERT: D 190 MET cc_start: 0.6609 (tpt) cc_final: 0.6145 (tpp) REVERT: D 399 TRP cc_start: 0.7711 (m-90) cc_final: 0.7129 (m-90) REVERT: D 496 MET cc_start: 0.4235 (tpp) cc_final: 0.3984 (tpp) outliers start: 59 outliers final: 40 residues processed: 255 average time/residue: 0.1849 time to fit residues: 72.8609 Evaluate side-chains 254 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1199 ARG Chi-restraints excluded: chain A residue 1234 GLU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1464 GLU Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1594 LYS Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1801 MET Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1843 MET Chi-restraints excluded: chain A residue 1940 LYS Chi-restraints excluded: chain A residue 2006 MET Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain A residue 2150 LYS Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1145 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 341 CYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 1049 VAL Chi-restraints excluded: chain C residue 1058 SER Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain C residue 1074 VAL Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 189 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 214 optimal weight: 0.0670 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 234 optimal weight: 0.4980 chunk 293 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1590 GLN B 857 GLN C 999 GLN D 123 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.075615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.052230 restraints weight = 65478.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.052050 restraints weight = 41723.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.052366 restraints weight = 38345.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.052674 restraints weight = 32936.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.052725 restraints weight = 29585.173| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25611 Z= 0.115 Angle : 0.473 8.505 34449 Z= 0.252 Chirality : 0.039 0.182 3768 Planarity : 0.003 0.043 4367 Dihedral : 4.276 36.645 3348 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.73 % Allowed : 13.35 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.61 (0.16), residues: 3063 helix: 2.16 (0.13), residues: 1667 sheet: -0.42 (0.40), residues: 158 loop : -0.20 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 599 TYR 0.020 0.001 TYR A 41 PHE 0.017 0.001 PHE C1021 TRP 0.017 0.001 TRP C 499 HIS 0.003 0.001 HIS D 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (25592) covalent geometry : angle 0.47304 / 0.25 (34411) SS BOND : bond 0.00235 / 0.11 ( 19) SS BOND : angle 0.76267 / 0.45 ( 38) hydrogen bonds : bond 0.03801 / 2.45 ( 1322) hydrogen bonds : angle 3.96035 / 2.83 ( 3768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.7700 (tt0) cc_final: 0.7420 (tt0) REVERT: A 1199 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8114 (mtm-85) REVERT: A 1672 ARG cc_start: 0.8295 (ttp-110) cc_final: 0.7987 (mtm-85) REVERT: A 1843 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7536 (mtt) REVERT: A 1919 MET cc_start: 0.8735 (ttp) cc_final: 0.8478 (ttp) REVERT: A 2006 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7415 (mpp) REVERT: A 2078 ILE cc_start: 0.7120 (tp) cc_final: 0.6774 (tp) REVERT: A 2141 LYS cc_start: 0.8426 (tptt) cc_final: 0.8154 (tptt) REVERT: A 2151 MET cc_start: 0.8387 (tmm) cc_final: 0.7838 (tpt) REVERT: B 743 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7241 (tpt) REVERT: C 442 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6480 (mt) REVERT: C 529 ARG cc_start: 0.8228 (mtt180) cc_final: 0.6696 (mtm180) REVERT: C 747 ARG cc_start: 0.7999 (ptm160) cc_final: 0.7591 (ttp80) REVERT: C 962 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8170 (m) REVERT: C 1114 ILE cc_start: 0.8211 (pt) cc_final: 0.7950 (mm) REVERT: D 110 TRP cc_start: 0.7277 (m100) cc_final: 0.6999 (m-10) REVERT: D 190 MET cc_start: 0.6615 (tpt) cc_final: 0.6171 (tpp) REVERT: D 399 TRP cc_start: 0.7644 (m-90) cc_final: 0.7100 (m-90) REVERT: D 496 MET cc_start: 0.4305 (tpp) cc_final: 0.4040 (tpp) outliers start: 49 outliers final: 34 residues processed: 255 average time/residue: 0.1836 time to fit residues: 71.5137 Evaluate side-chains 255 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1199 ARG Chi-restraints excluded: chain A residue 1234 GLU Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1464 GLU Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1801 MET Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1843 MET Chi-restraints excluded: chain A residue 1940 LYS Chi-restraints excluded: chain A residue 2006 MET Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1145 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 341 CYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 1049 VAL Chi-restraints excluded: chain C residue 1058 SER Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain C residue 1074 VAL Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 288 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 259 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 213 optimal weight: 0.2980 chunk 128 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 857 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.075454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.052409 restraints weight = 65428.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.051973 restraints weight = 45896.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.052318 restraints weight = 41167.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.052564 restraints weight = 34625.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.052569 restraints weight = 32919.685| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25611 Z= 0.129 Angle : 0.488 8.719 34449 Z= 0.257 Chirality : 0.039 0.181 3768 Planarity : 0.003 0.061 4367 Dihedral : 4.264 36.543 3348 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.49 % Allowed : 13.66 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.64 (0.16), residues: 3063 helix: 2.21 (0.13), residues: 1659 sheet: -0.38 (0.40), residues: 158 loop : -0.22 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 599 TYR 0.020 0.001 TYR A 41 PHE 0.017 0.001 PHE C1021 TRP 0.017 0.001 TRP C1044 HIS 0.004 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (25592) covalent geometry : angle 0.48756 / 0.26 (34411) SS BOND : bond 0.00246 / 0.11 ( 19) SS BOND : angle 0.75213 / 0.44 ( 38) hydrogen bonds : bond 0.03852 / 2.48 ( 1322) hydrogen bonds : angle 3.94316 / 2.82 ( 3768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.7668 (tt0) cc_final: 0.7366 (tt0) REVERT: A 1199 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8116 (mtm-85) REVERT: A 1672 ARG cc_start: 0.8269 (ttp-110) cc_final: 0.7977 (mtm-85) REVERT: A 1843 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7576 (mtt) REVERT: A 1919 MET cc_start: 0.8731 (ttp) cc_final: 0.8475 (ttp) REVERT: A 2006 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7421 (mpp) REVERT: A 2078 ILE cc_start: 0.7079 (tp) cc_final: 0.6734 (tp) REVERT: A 2141 LYS cc_start: 0.8426 (tptt) cc_final: 0.8175 (tptt) REVERT: A 2151 MET cc_start: 0.8401 (tmm) cc_final: 0.7888 (tpt) REVERT: B 743 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7244 (tpt) REVERT: C 442 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6502 (mt) REVERT: C 529 ARG cc_start: 0.8255 (mtt180) cc_final: 0.6704 (mtm180) REVERT: C 599 ARG cc_start: 0.7178 (mmm160) cc_final: 0.6758 (mmm-85) REVERT: C 747 ARG cc_start: 0.8034 (ptm160) cc_final: 0.7617 (ttp80) REVERT: C 962 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8168 (m) REVERT: C 1114 ILE cc_start: 0.8253 (pt) cc_final: 0.7985 (mm) REVERT: D 190 MET cc_start: 0.6742 (tpt) cc_final: 0.6279 (tpp) REVERT: D 399 TRP cc_start: 0.7677 (m-90) cc_final: 0.7211 (m-90) REVERT: D 496 MET cc_start: 0.4444 (tpp) cc_final: 0.4174 (tpp) outliers start: 42 outliers final: 34 residues processed: 251 average time/residue: 0.1876 time to fit residues: 72.3225 Evaluate side-chains 248 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1199 ARG Chi-restraints excluded: chain A residue 1234 GLU Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1464 GLU Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1843 MET Chi-restraints excluded: chain A residue 1940 LYS Chi-restraints excluded: chain A residue 2006 MET Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1145 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 341 CYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 1049 VAL Chi-restraints excluded: chain C residue 1058 SER Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain C residue 1074 VAL Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 152 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 286 optimal weight: 0.0980 chunk 195 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 857 GLN C 794 ASN C 999 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.051045 restraints weight = 65399.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.050694 restraints weight = 45271.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.051009 restraints weight = 39173.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.051263 restraints weight = 35575.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.051259 restraints weight = 32706.300| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25611 Z= 0.207 Angle : 0.533 8.723 34449 Z= 0.281 Chirality : 0.042 0.180 3768 Planarity : 0.004 0.060 4367 Dihedral : 4.452 40.345 3348 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.84 % Allowed : 13.52 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.47 (0.16), residues: 3063 helix: 2.06 (0.13), residues: 1668 sheet: -0.45 (0.40), residues: 158 loop : -0.30 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 599 TYR 0.023 0.001 TYR A 41 PHE 0.021 0.001 PHE A1717 TRP 0.032 0.002 TRP D 110 HIS 0.006 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (25592) covalent geometry : angle 0.53267 / 0.28 (34411) SS BOND : bond 0.00328 / 0.14 ( 19) SS BOND : angle 0.89185 / 0.53 ( 38) hydrogen bonds : bond 0.04386 / 2.82 ( 1322) hydrogen bonds : angle 4.06808 / 2.91 ( 3768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3992.43 seconds wall clock time: 70 minutes 25.39 seconds (4225.39 seconds total)