Starting phenix.real_space_refine on Fri Jul 3 19:31:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ojk_12954/07_2026/7ojk_12954.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ojk_12954/07_2026/7ojk_12954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ojk_12954/07_2026/7ojk_12954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ojk_12954/07_2026/7ojk_12954.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ojk_12954/07_2026/7ojk_12954.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ojk_12954/07_2026/7ojk_12954.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ojk_12954/07_2026/7ojk_12954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ojk_12954/07_2026/7ojk_12954.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 20 5.49 5 S 91 5.16 5 C 9691 2.51 5 N 2584 2.21 5 O 2929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15316 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 14866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1843, 14866 Classifications: {'peptide': 1843} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1780} Chain breaks: 12 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 193 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2531 SG CYS L 321 44.699 105.525 90.938 1.00135.50 S ATOM 2916 SG CYS L 366 42.614 104.378 93.658 1.00140.11 S Time building chain proxies: 3.45, per 1000 atoms: 0.23 Number of scatterers: 15316 At special positions: 0 Unit cell: (113.97, 126.15, 147.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 91 16.00 P 20 15.00 O 2929 8.00 N 2584 7.00 C 9691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 703.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 364 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 366 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 321 " 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 9 sheets defined 55.3% alpha, 3.7% beta 3 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'L' and resid 1 through 15 removed outlier: 3.578A pdb=" N MET L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 21 No H-bonds generated for 'chain 'L' and resid 19 through 21' Processing helix chain 'L' and resid 22 through 30 Processing helix chain 'L' and resid 34 through 59 Processing helix chain 'L' and resid 68 through 75 Processing helix chain 'L' and resid 112 through 131 removed outlier: 3.636A pdb=" N TYR L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 134 No H-bonds generated for 'chain 'L' and resid 132 through 134' Processing helix chain 'L' and resid 153 through 169 removed outlier: 3.726A pdb=" N THR L 163 " --> pdb=" O LYS L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 176 Processing helix chain 'L' and resid 179 through 188 removed outlier: 3.532A pdb=" N GLU L 188 " --> pdb=" O SER L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 206 Processing helix chain 'L' and resid 214 through 224 removed outlier: 3.864A pdb=" N ILE L 218 " --> pdb=" O TYR L 214 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 251 removed outlier: 4.140A pdb=" N LEU L 236 " --> pdb=" O HIS L 232 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN L 237 " --> pdb=" O GLU L 233 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS L 251 " --> pdb=" O ASN L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 284 through 293 removed outlier: 3.882A pdb=" N LYS L 293 " --> pdb=" O ILE L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 303 removed outlier: 3.534A pdb=" N TYR L 303 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 336 removed outlier: 3.628A pdb=" N LEU L 336 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 365 removed outlier: 3.738A pdb=" N PHE L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE L 353 " --> pdb=" O PHE L 349 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR L 362 " --> pdb=" O ILE L 358 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG L 363 " --> pdb=" O HIS L 359 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS L 364 " --> pdb=" O ASP L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 405 Processing helix chain 'L' and resid 412 through 433 Processing helix chain 'L' and resid 453 through 459 Processing helix chain 'L' and resid 491 through 506 removed outlier: 4.129A pdb=" N GLU L 495 " --> pdb=" O SER L 491 " (cutoff:3.500A) Processing helix chain 'L' and resid 507 through 509 No H-bonds generated for 'chain 'L' and resid 507 through 509' Processing helix chain 'L' and resid 522 through 527 removed outlier: 3.939A pdb=" N TYR L 526 " --> pdb=" O PRO L 523 " (cutoff:3.500A) Processing helix chain 'L' and resid 589 through 600 removed outlier: 3.816A pdb=" N TRP L 600 " --> pdb=" O THR L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 609 removed outlier: 6.017A pdb=" N GLU L 609 " --> pdb=" O GLU L 606 " (cutoff:3.500A) Processing helix chain 'L' and resid 610 through 628 removed outlier: 3.512A pdb=" N ILE L 614 " --> pdb=" O GLN L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 632 No H-bonds generated for 'chain 'L' and resid 630 through 632' Processing helix chain 'L' and resid 633 through 648 removed outlier: 3.845A pdb=" N LEU L 637 " --> pdb=" O SER L 633 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU L 640 " --> pdb=" O LEU L 636 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG L 641 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR L 642 " --> pdb=" O GLN L 638 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE L 643 " --> pdb=" O ASN L 639 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 660 Processing helix chain 'L' and resid 667 through 685 Processing helix chain 'L' and resid 691 through 704 removed outlier: 3.985A pdb=" N ARG L 695 " --> pdb=" O MET L 691 " (cutoff:3.500A) Processing helix chain 'L' and resid 716 through 729 removed outlier: 3.991A pdb=" N LYS L 722 " --> pdb=" O THR L 718 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS L 723 " --> pdb=" O ASP L 719 " (cutoff:3.500A) Processing helix chain 'L' and resid 729 through 734 removed outlier: 4.314A pdb=" N GLU L 733 " --> pdb=" O GLU L 729 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE L 734 " --> pdb=" O PRO L 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 729 through 734' Processing helix chain 'L' and resid 746 through 761 removed outlier: 3.678A pdb=" N LEU L 750 " --> pdb=" O THR L 746 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU L 761 " --> pdb=" O ALA L 757 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 793 Processing helix chain 'L' and resid 798 through 803 Processing helix chain 'L' and resid 842 through 861 removed outlier: 3.651A pdb=" N LEU L 846 " --> pdb=" O ASP L 842 " (cutoff:3.500A) Processing helix chain 'L' and resid 862 through 865 Processing helix chain 'L' and resid 870 through 884 Processing helix chain 'L' and resid 897 through 905 Processing helix chain 'L' and resid 908 through 925 removed outlier: 3.607A pdb=" N ASP L 912 " --> pdb=" O SER L 908 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU L 916 " --> pdb=" O ASP L 912 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR L 925 " --> pdb=" O ILE L 921 " (cutoff:3.500A) Processing helix chain 'L' and resid 943 through 949 Processing helix chain 'L' and resid 952 through 964 removed outlier: 4.100A pdb=" N ILE L 956 " --> pdb=" O ASN L 952 " (cutoff:3.500A) Processing helix chain 'L' and resid 977 through 991 removed outlier: 3.953A pdb=" N TYR L 981 " --> pdb=" O PRO L 977 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU L 982 " --> pdb=" O GLY L 978 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN L 991 " --> pdb=" O ALA L 987 " (cutoff:3.500A) Processing helix chain 'L' and resid 991 through 999 Processing helix chain 'L' and resid 1014 through 1024 removed outlier: 3.821A pdb=" N PHE L1022 " --> pdb=" O THR L1018 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP L1023 " --> pdb=" O ARG L1019 " (cutoff:3.500A) Processing helix chain 'L' and resid 1025 through 1038 Processing helix chain 'L' and resid 1059 through 1067 removed outlier: 3.841A pdb=" N LEU L1063 " --> pdb=" O ASP L1059 " (cutoff:3.500A) Processing helix chain 'L' and resid 1075 through 1084 removed outlier: 3.553A pdb=" N LEU L1079 " --> pdb=" O ASN L1075 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS L1081 " --> pdb=" O GLU L1077 " (cutoff:3.500A) Processing helix chain 'L' and resid 1092 through 1096 removed outlier: 3.532A pdb=" N LEU L1096 " --> pdb=" O LEU L1093 " (cutoff:3.500A) Processing helix chain 'L' and resid 1137 through 1156 removed outlier: 3.940A pdb=" N LEU L1146 " --> pdb=" O MET L1142 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) Processing helix chain 'L' and resid 1168 through 1180 Processing helix chain 'L' and resid 1199 through 1209 removed outlier: 3.613A pdb=" N PHE L1203 " --> pdb=" O CYS L1199 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN L1209 " --> pdb=" O ALA L1205 " (cutoff:3.500A) Processing helix chain 'L' and resid 1218 through 1235 Processing helix chain 'L' and resid 1242 through 1259 removed outlier: 3.698A pdb=" N VAL L1246 " --> pdb=" O PRO L1242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU L1258 " --> pdb=" O ILE L1254 " (cutoff:3.500A) Processing helix chain 'L' and resid 1267 through 1278 removed outlier: 3.814A pdb=" N ASP L1271 " --> pdb=" O SER L1267 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN L1276 " --> pdb=" O PHE L1272 " (cutoff:3.500A) Processing helix chain 'L' and resid 1297 through 1320 Processing helix chain 'L' and resid 1338 through 1345 removed outlier: 3.787A pdb=" N MET L1345 " --> pdb=" O LEU L1341 " (cutoff:3.500A) Processing helix chain 'L' and resid 1348 through 1366 Processing helix chain 'L' and resid 1396 through 1406 removed outlier: 3.774A pdb=" N PHE L1400 " --> pdb=" O LEU L1396 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS L1406 " --> pdb=" O ALA L1402 " (cutoff:3.500A) Processing helix chain 'L' and resid 1414 through 1429 removed outlier: 4.396A pdb=" N GLU L1418 " --> pdb=" O HIS L1414 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA L1429 " --> pdb=" O ASP L1425 " (cutoff:3.500A) Processing helix chain 'L' and resid 1433 through 1450 removed outlier: 3.704A pdb=" N CYS L1437 " --> pdb=" O PRO L1433 " (cutoff:3.500A) Processing helix chain 'L' and resid 1466 through 1471 removed outlier: 4.080A pdb=" N VAL L1470 " --> pdb=" O VAL L1466 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP L1471 " --> pdb=" O ARG L1467 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1466 through 1471' Processing helix chain 'L' and resid 1475 through 1486 Processing helix chain 'L' and resid 1489 through 1506 removed outlier: 3.531A pdb=" N ILE L1493 " --> pdb=" O ALA L1489 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER L1495 " --> pdb=" O GLY L1491 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR L1506 " --> pdb=" O ASN L1502 " (cutoff:3.500A) Processing helix chain 'L' and resid 1524 through 1534 Processing helix chain 'L' and resid 1613 through 1624 removed outlier: 3.934A pdb=" N LEU L1624 " --> pdb=" O LEU L1620 " (cutoff:3.500A) Processing helix chain 'L' and resid 1639 through 1649 removed outlier: 4.191A pdb=" N ILE L1649 " --> pdb=" O LEU L1645 " (cutoff:3.500A) Processing helix chain 'L' and resid 1667 through 1671 Processing helix chain 'L' and resid 1684 through 1699 Processing helix chain 'L' and resid 1700 through 1705 removed outlier: 3.500A pdb=" N VAL L1703 " --> pdb=" O GLY L1700 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU L1704 " --> pdb=" O ALA L1701 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY L1705 " --> pdb=" O TRP L1702 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1700 through 1705' Processing helix chain 'L' and resid 1740 through 1751 Processing helix chain 'L' and resid 1751 through 1757 removed outlier: 3.691A pdb=" N LYS L1757 " --> pdb=" O SER L1753 " (cutoff:3.500A) Processing helix chain 'L' and resid 1759 through 1764 Processing helix chain 'L' and resid 1777 through 1790 Processing helix chain 'L' and resid 1835 through 1852 removed outlier: 3.830A pdb=" N TYR L1850 " --> pdb=" O TYR L1846 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL L1851 " --> pdb=" O PHE L1847 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG L1852 " --> pdb=" O GLU L1848 " (cutoff:3.500A) Processing helix chain 'L' and resid 1878 through 1884 removed outlier: 3.834A pdb=" N LEU L1882 " --> pdb=" O LEU L1879 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY L1883 " --> pdb=" O GLN L1880 " (cutoff:3.500A) Proline residue: L1884 - end of helix Processing helix chain 'L' and resid 1885 through 1892 removed outlier: 3.632A pdb=" N VAL L1889 " --> pdb=" O PHE L1885 " (cutoff:3.500A) Processing helix chain 'L' and resid 1893 through 1896 Processing helix chain 'L' and resid 1902 through 1906 removed outlier: 3.661A pdb=" N LEU L1906 " --> pdb=" O LYS L1903 " (cutoff:3.500A) Processing helix chain 'L' and resid 2102 through 2114 Processing helix chain 'L' and resid 2118 through 2134 Processing helix chain 'L' and resid 2144 through 2152 Processing helix chain 'L' and resid 2155 through 2165 removed outlier: 3.838A pdb=" N VAL L2159 " --> pdb=" O ASN L2155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 91 through 94 removed outlier: 3.676A pdb=" N LEU L 100 " --> pdb=" O ILE L 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 258 through 260 removed outlier: 3.788A pdb=" N TYR L 651 " --> pdb=" O ILE L1376 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE L1376 " --> pdb=" O TYR L 651 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET L1189 " --> pdb=" O GLN L1333 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN L1333 " --> pdb=" O MET L1189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP L1325 " --> pdb=" O LEU L1336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 375 through 376 removed outlier: 3.679A pdb=" N PHE L 375 " --> pdb=" O VAL L 383 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL L 383 " --> pdb=" O PHE L 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 536 through 540 Processing sheet with id=AA5, first strand: chain 'L' and resid 826 through 829 Processing sheet with id=AA6, first strand: chain 'L' and resid 1120 through 1125 Processing sheet with id=AA7, first strand: chain 'L' and resid 1653 through 1655 removed outlier: 3.564A pdb=" N TRP L1664 " --> pdb=" O SER L1546 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER L1546 " --> pdb=" O TRP L1664 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 1724 through 1726 removed outlier: 4.063A pdb=" N VAL L1810 " --> pdb=" O PHE L1724 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 1854 through 1855 removed outlier: 3.805A pdb=" N PHE L1854 " --> pdb=" O VAL L2082 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS L2092 " --> pdb=" O GLU L2089 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 1.85 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: 4753 1.34 - 1.46: 2456 1.46 - 1.58: 8271 1.58 - 1.70: 39 1.70 - 1.81: 139 Bond restraints: 15658 Sorted by residual: bond pdb=" CA ARG L 342 " pdb=" C ARG L 342 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.34e-02 5.57e+03 2.03e+00 bond pdb=" C SER L 296 " pdb=" N PRO L 297 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.35e+00 bond pdb=" CA THR L 710 " pdb=" CB THR L 710 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.93e-02 2.68e+03 8.72e-01 bond pdb=" CA ARG L 342 " pdb=" CB ARG L 342 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.53e-01 bond pdb=" N ARG L 342 " pdb=" CA ARG L 342 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.57e-01 ... (remaining 15653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 20970 2.35 - 4.70: 223 4.70 - 7.04: 27 7.04 - 9.39: 4 9.39 - 11.74: 2 Bond angle restraints: 21226 Sorted by residual: angle pdb=" C THR L 341 " pdb=" N ARG L 342 " pdb=" CA ARG L 342 " ideal model delta sigma weight residual 121.54 132.71 -11.17 1.91e+00 2.74e-01 3.42e+01 angle pdb=" N ARG L 342 " pdb=" CA ARG L 342 " pdb=" CB ARG L 342 " ideal model delta sigma weight residual 110.49 104.01 6.48 1.69e+00 3.50e-01 1.47e+01 angle pdb=" CA ARG L 342 " pdb=" CB ARG L 342 " pdb=" CG ARG L 342 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" C MET L1189 " pdb=" N ASP L1190 " pdb=" CA ASP L1190 " ideal model delta sigma weight residual 122.45 129.11 -6.66 1.78e+00 3.16e-01 1.40e+01 angle pdb=" N ARG L 342 " pdb=" CA ARG L 342 " pdb=" C ARG L 342 " ideal model delta sigma weight residual 110.80 118.58 -7.78 2.13e+00 2.20e-01 1.33e+01 ... (remaining 21221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.21: 8828 22.21 - 44.42: 577 44.42 - 66.63: 43 66.63 - 88.84: 20 88.84 - 111.04: 2 Dihedral angle restraints: 9470 sinusoidal: 4042 harmonic: 5428 Sorted by residual: dihedral pdb=" CA PHE L 581 " pdb=" C PHE L 581 " pdb=" N PRO L 582 " pdb=" CA PRO L 582 " ideal model delta harmonic sigma weight residual -180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA TYR L1663 " pdb=" C TYR L1663 " pdb=" N TRP L1664 " pdb=" CA TRP L1664 " ideal model delta harmonic sigma weight residual -180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ARG L 210 " pdb=" C ARG L 210 " pdb=" N SER L 211 " pdb=" CA SER L 211 " ideal model delta harmonic sigma weight residual 180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 9467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1696 0.036 - 0.073: 521 0.073 - 0.109: 145 0.109 - 0.146: 37 0.146 - 0.182: 4 Chirality restraints: 2403 Sorted by residual: chirality pdb=" CA ILE L1376 " pdb=" N ILE L1376 " pdb=" C ILE L1376 " pdb=" CB ILE L1376 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CA ARG L 343 " pdb=" N ARG L 343 " pdb=" C ARG L 343 " pdb=" CB ARG L 343 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB ILE L2144 " pdb=" CA ILE L2144 " pdb=" CG1 ILE L2144 " pdb=" CG2 ILE L2144 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 2400 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER L 616 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C SER L 616 " 0.050 2.00e-02 2.50e+03 pdb=" O SER L 616 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU L 617 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 620 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C MET L 620 " 0.048 2.00e-02 2.50e+03 pdb=" O MET L 620 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE L 621 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L1016 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.36e+00 pdb=" C VAL L1016 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL L1016 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA L1017 " 0.016 2.00e-02 2.50e+03 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 704 2.72 - 3.26: 16229 3.26 - 3.81: 23034 3.81 - 4.35: 27761 4.35 - 4.90: 45356 Nonbonded interactions: 113084 Sorted by model distance: nonbonded pdb=" OD2 ASP L2143 " pdb=" OG SER L2146 " model vdw 2.174 3.040 nonbonded pdb=" OG SER L 384 " pdb=" OE1 GLU L 386 " model vdw 2.182 3.040 nonbonded pdb=" OD1 ASP L 350 " pdb=" OG SER L 377 " model vdw 2.184 3.040 nonbonded pdb=" O LEU L 385 " pdb=" OG1 THR L 388 " model vdw 2.184 3.040 nonbonded pdb=" OH TYR L1476 " pdb=" NH2 ARG L1480 " model vdw 2.187 3.120 ... (remaining 113079 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: 9.180 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.840 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.002 0.027 15661 Z= 0.112 Angle : 0.614 11.741 21226 Z= 0.328 Chirality : 0.040 0.182 2403 Planarity : 0.005 0.053 2618 Dihedral : 14.158 111.045 5942 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.24 % Favored : 84.53 % Rotamer: Outliers : 0.06 % Allowed : 1.72 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.16), residues: 1817 helix: -1.57 (0.15), residues: 921 sheet: -3.65 (0.44), residues: 90 loop : -4.24 (0.17), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 860 TYR 0.013 0.001 TYR L1476 PHE 0.032 0.001 PHE L1458 TRP 0.015 0.002 TRP L1233 HIS 0.008 0.001 HIS L1819 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (15658) covalent geometry : angle 0.61383 / 0.33 (21226) hydrogen bonds : bond 0.13093 / 8.62 ( 665) hydrogen bonds : angle 6.14446 / 4.35 ( 1891) metal coordination : bond 0.00192 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 393 GLU cc_start: 0.8657 (tt0) cc_final: 0.8445 (tp30) REVERT: L 394 LYS cc_start: 0.9263 (tppt) cc_final: 0.8984 (tppt) REVERT: L 442 TYR cc_start: 0.7880 (m-80) cc_final: 0.7632 (m-10) REVERT: L 483 MET cc_start: 0.9032 (mmt) cc_final: 0.8771 (mmm) REVERT: L 692 MET cc_start: 0.7848 (mmm) cc_final: 0.7629 (tpp) REVERT: L 753 MET cc_start: 0.8850 (tpp) cc_final: 0.8583 (tpp) REVERT: L 956 ILE cc_start: 0.9657 (mt) cc_final: 0.9449 (mp) REVERT: L 1060 MET cc_start: 0.7631 (mmm) cc_final: 0.7343 (mmm) REVERT: L 1077 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8102 (mt-10) REVERT: L 1842 MET cc_start: 0.9058 (mmp) cc_final: 0.8720 (mmm) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.1659 time to fit residues: 47.3033 Evaluate side-chains 121 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 76 HIS ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 ASN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1208 GLN L1435 HIS L1438 ASN L1461 ASN ** L1844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.081590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.057617 restraints weight = 63894.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.059548 restraints weight = 35991.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.060050 restraints weight = 20330.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060211 restraints weight = 18521.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.060244 restraints weight = 16834.463| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15661 Z= 0.139 Angle : 0.653 11.399 21226 Z= 0.329 Chirality : 0.040 0.162 2403 Planarity : 0.004 0.082 2618 Dihedral : 7.175 109.581 2238 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.24 % Favored : 89.71 % Rotamer: Outliers : 0.89 % Allowed : 8.90 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.19), residues: 1817 helix: -0.05 (0.17), residues: 927 sheet: -2.99 (0.44), residues: 102 loop : -3.53 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 71 TYR 0.013 0.001 TYR L1187 PHE 0.027 0.002 PHE L1885 TRP 0.025 0.002 TRP L2088 HIS 0.011 0.001 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15658) covalent geometry : angle 0.65322 / 0.33 (21226) hydrogen bonds : bond 0.04304 / 2.93 ( 665) hydrogen bonds : angle 4.50377 / 3.09 ( 1891) metal coordination : bond 0.00289 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 393 GLU cc_start: 0.8899 (tt0) cc_final: 0.8584 (tp30) REVERT: L 394 LYS cc_start: 0.9341 (tppt) cc_final: 0.9053 (tppt) REVERT: L 442 TYR cc_start: 0.8140 (m-80) cc_final: 0.7861 (m-10) REVERT: L 483 MET cc_start: 0.8982 (mmt) cc_final: 0.8597 (mmm) REVERT: L 684 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8758 (mm) REVERT: L 753 MET cc_start: 0.8953 (tpp) cc_final: 0.8615 (tpp) REVERT: L 971 PHE cc_start: 0.8148 (t80) cc_final: 0.7900 (t80) REVERT: L 1032 SER cc_start: 0.9504 (m) cc_final: 0.9166 (p) REVERT: L 1077 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8133 (mt-10) REVERT: L 1885 PHE cc_start: 0.8244 (t80) cc_final: 0.7969 (t80) REVERT: L 1901 MET cc_start: 0.5643 (mmm) cc_final: 0.5186 (mmp) outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 0.1469 time to fit residues: 30.6268 Evaluate side-chains 114 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 684 LEU Chi-restraints excluded: chain L residue 833 THR Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 401 GLN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1028 GLN L1407 ASN L1742 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.079203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054976 restraints weight = 64480.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056292 restraints weight = 38800.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.056950 restraints weight = 24154.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.057291 restraints weight = 19467.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.057293 restraints weight = 17804.383| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15661 Z= 0.202 Angle : 0.659 11.995 21226 Z= 0.335 Chirality : 0.041 0.182 2403 Planarity : 0.004 0.052 2618 Dihedral : 7.203 110.399 2238 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 1.96 % Allowed : 11.51 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.19), residues: 1817 helix: 0.25 (0.17), residues: 934 sheet: -2.66 (0.46), residues: 102 loop : -3.29 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L2084 TYR 0.015 0.002 TYR L1026 PHE 0.020 0.002 PHE L1058 TRP 0.012 0.002 TRP L1233 HIS 0.009 0.001 HIS L1819 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (15658) covalent geometry : angle 0.65945 / 0.34 (21226) hydrogen bonds : bond 0.04567 / 3.17 ( 665) hydrogen bonds : angle 4.48878 / 3.06 ( 1891) metal coordination : bond 0.00373 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.8941 (ppp) cc_final: 0.8536 (tmm) REVERT: L 154 ASP cc_start: 0.8794 (m-30) cc_final: 0.8309 (m-30) REVERT: L 393 GLU cc_start: 0.8904 (tt0) cc_final: 0.8599 (tp30) REVERT: L 394 LYS cc_start: 0.9333 (tppt) cc_final: 0.9069 (tppt) REVERT: L 483 MET cc_start: 0.8900 (mmt) cc_final: 0.8671 (mmm) REVERT: L 684 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8856 (mm) REVERT: L 753 MET cc_start: 0.8990 (tpp) cc_final: 0.8645 (tpp) REVERT: L 1060 MET cc_start: 0.8176 (mmm) cc_final: 0.7907 (mmp) REVERT: L 1077 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8018 (mt-10) REVERT: L 1770 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6924 (tmtt) REVERT: L 1871 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7176 (t) REVERT: L 1885 PHE cc_start: 0.8409 (t80) cc_final: 0.8118 (t80) outliers start: 33 outliers final: 16 residues processed: 138 average time/residue: 0.1226 time to fit residues: 25.8848 Evaluate side-chains 115 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 684 LEU Chi-restraints excluded: chain L residue 833 THR Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Chi-restraints excluded: chain L residue 1513 PHE Chi-restraints excluded: chain L residue 1693 LEU Chi-restraints excluded: chain L residue 1697 ILE Chi-restraints excluded: chain L residue 1770 LYS Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2109 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 179 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 139 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 56 ASN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.080659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056466 restraints weight = 63843.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.058591 restraints weight = 35713.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.058857 restraints weight = 19946.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.059119 restraints weight = 18302.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.059071 restraints weight = 16515.362| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15661 Z= 0.120 Angle : 0.589 12.980 21226 Z= 0.296 Chirality : 0.038 0.162 2403 Planarity : 0.003 0.046 2618 Dihedral : 6.891 110.614 2238 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 1.54 % Allowed : 13.46 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.20), residues: 1817 helix: 0.64 (0.17), residues: 939 sheet: -2.27 (0.48), residues: 102 loop : -3.12 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L1899 TYR 0.014 0.001 TYR L 91 PHE 0.026 0.001 PHE L 954 TRP 0.008 0.001 TRP L1547 HIS 0.006 0.001 HIS L1819 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15658) covalent geometry : angle 0.58851 / 0.30 (21226) hydrogen bonds : bond 0.03653 / 2.50 ( 665) hydrogen bonds : angle 4.12947 / 2.81 ( 1891) metal coordination : bond 0.00259 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8422 (mm) REVERT: L 154 ASP cc_start: 0.8760 (m-30) cc_final: 0.8249 (m-30) REVERT: L 167 LEU cc_start: 0.9214 (mm) cc_final: 0.8992 (pp) REVERT: L 393 GLU cc_start: 0.8910 (tt0) cc_final: 0.8589 (tp30) REVERT: L 394 LYS cc_start: 0.9356 (tppt) cc_final: 0.9063 (tppt) REVERT: L 442 TYR cc_start: 0.8228 (m-80) cc_final: 0.7990 (m-10) REVERT: L 483 MET cc_start: 0.8826 (mmt) cc_final: 0.8485 (mmm) REVERT: L 753 MET cc_start: 0.8996 (tpp) cc_final: 0.8681 (tpp) REVERT: L 1060 MET cc_start: 0.8184 (mmm) cc_final: 0.7716 (mmp) REVERT: L 1077 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8013 (mt-10) REVERT: L 1770 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7187 (tmtt) REVERT: L 1871 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7335 (t) REVERT: L 1885 PHE cc_start: 0.8426 (t80) cc_final: 0.8177 (t80) REVERT: L 1901 MET cc_start: 0.5632 (mmm) cc_final: 0.5346 (mmp) outliers start: 26 outliers final: 12 residues processed: 131 average time/residue: 0.1336 time to fit residues: 25.7500 Evaluate side-chains 115 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Chi-restraints excluded: chain L residue 1513 PHE Chi-restraints excluded: chain L residue 1693 LEU Chi-restraints excluded: chain L residue 1770 LYS Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2109 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 0.0470 chunk 101 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.080978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.057369 restraints weight = 63871.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.058478 restraints weight = 36428.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059468 restraints weight = 22936.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059402 restraints weight = 19486.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.059521 restraints weight = 17144.965| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15661 Z= 0.112 Angle : 0.567 12.185 21226 Z= 0.286 Chirality : 0.038 0.174 2403 Planarity : 0.003 0.046 2618 Dihedral : 6.656 111.285 2238 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 1.72 % Allowed : 13.64 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.20), residues: 1817 helix: 0.80 (0.17), residues: 948 sheet: -2.27 (0.46), residues: 109 loop : -2.97 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 920 TYR 0.012 0.001 TYR L 91 PHE 0.014 0.001 PHE L 292 TRP 0.008 0.001 TRP L 155 HIS 0.005 0.001 HIS L1819 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15658) covalent geometry : angle 0.56720 / 0.29 (21226) hydrogen bonds : bond 0.03482 / 2.39 ( 665) hydrogen bonds : angle 3.98886 / 2.72 ( 1891) metal coordination : bond 0.00243 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8303 (mm) REVERT: L 154 ASP cc_start: 0.8823 (m-30) cc_final: 0.8243 (m-30) REVERT: L 393 GLU cc_start: 0.8854 (tt0) cc_final: 0.8564 (tp30) REVERT: L 394 LYS cc_start: 0.9315 (tppt) cc_final: 0.9025 (tppt) REVERT: L 442 TYR cc_start: 0.8154 (m-80) cc_final: 0.7923 (m-10) REVERT: L 483 MET cc_start: 0.8805 (mmt) cc_final: 0.8512 (mmt) REVERT: L 753 MET cc_start: 0.8901 (tpp) cc_final: 0.8627 (tpp) REVERT: L 1030 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: L 1060 MET cc_start: 0.8152 (mmm) cc_final: 0.7675 (mmp) REVERT: L 1077 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7935 (mt-10) REVERT: L 1699 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8729 (mt) REVERT: L 1770 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6963 (tmtt) REVERT: L 1871 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7241 (t) REVERT: L 1885 PHE cc_start: 0.8389 (t80) cc_final: 0.8176 (t80) REVERT: L 1901 MET cc_start: 0.6115 (mmm) cc_final: 0.5494 (mmp) outliers start: 29 outliers final: 14 residues processed: 138 average time/residue: 0.1220 time to fit residues: 25.5550 Evaluate side-chains 118 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1030 PHE Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1770 LYS Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 GLN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.056200 restraints weight = 63862.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057866 restraints weight = 33198.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058935 restraints weight = 22089.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059604 restraints weight = 17107.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059963 restraints weight = 14657.601| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15661 Z= 0.112 Angle : 0.569 13.995 21226 Z= 0.284 Chirality : 0.038 0.172 2403 Planarity : 0.003 0.047 2618 Dihedral : 6.543 111.757 2238 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 1.96 % Allowed : 14.41 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.20), residues: 1817 helix: 0.89 (0.17), residues: 951 sheet: -2.09 (0.47), residues: 109 loop : -2.92 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 716 TYR 0.008 0.001 TYR L 91 PHE 0.017 0.001 PHE L 421 TRP 0.010 0.001 TRP L 155 HIS 0.004 0.001 HIS L1819 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (15658) covalent geometry : angle 0.56874 / 0.28 (21226) hydrogen bonds : bond 0.03404 / 2.33 ( 665) hydrogen bonds : angle 3.95010 / 2.70 ( 1891) metal coordination : bond 0.00089 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8307 (mm) REVERT: L 154 ASP cc_start: 0.8809 (m-30) cc_final: 0.8158 (m-30) REVERT: L 393 GLU cc_start: 0.8882 (tt0) cc_final: 0.8565 (tp30) REVERT: L 394 LYS cc_start: 0.9318 (tppt) cc_final: 0.9018 (tppt) REVERT: L 420 MET cc_start: 0.8446 (tmm) cc_final: 0.8242 (tmm) REVERT: L 483 MET cc_start: 0.8779 (mmt) cc_final: 0.8441 (mmm) REVERT: L 753 MET cc_start: 0.9057 (tpp) cc_final: 0.8809 (tpp) REVERT: L 1030 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: L 1060 MET cc_start: 0.8211 (mmm) cc_final: 0.7780 (tpp) REVERT: L 1077 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7905 (mt-10) REVERT: L 1699 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8670 (mt) REVERT: L 1770 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7155 (tmtt) REVERT: L 1885 PHE cc_start: 0.8497 (t80) cc_final: 0.8223 (t80) REVERT: L 1901 MET cc_start: 0.6155 (mmm) cc_final: 0.5424 (mmp) outliers start: 33 outliers final: 21 residues processed: 131 average time/residue: 0.1101 time to fit residues: 22.4532 Evaluate side-chains 120 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1030 PHE Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Chi-restraints excluded: chain L residue 1693 LEU Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1770 LYS Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2118 LEU Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 116 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.080287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.056586 restraints weight = 63919.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.057658 restraints weight = 36131.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.058624 restraints weight = 22621.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.058619 restraints weight = 18916.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058674 restraints weight = 16781.044| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15661 Z= 0.139 Angle : 0.577 11.189 21226 Z= 0.293 Chirality : 0.038 0.153 2403 Planarity : 0.003 0.047 2618 Dihedral : 6.582 112.619 2238 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 1.72 % Allowed : 15.30 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.20), residues: 1817 helix: 0.86 (0.17), residues: 947 sheet: -1.95 (0.48), residues: 109 loop : -2.91 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L1480 TYR 0.009 0.001 TYR L1187 PHE 0.033 0.001 PHE L 954 TRP 0.010 0.001 TRP L 155 HIS 0.004 0.001 HIS L1406 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15658) covalent geometry : angle 0.57719 / 0.29 (21226) hydrogen bonds : bond 0.03668 / 2.54 ( 665) hydrogen bonds : angle 4.04024 / 2.77 ( 1891) metal coordination : bond 0.00276 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8399 (mm) REVERT: L 154 ASP cc_start: 0.8841 (m-30) cc_final: 0.8196 (m-30) REVERT: L 393 GLU cc_start: 0.9048 (tt0) cc_final: 0.8675 (tp30) REVERT: L 394 LYS cc_start: 0.9363 (tppt) cc_final: 0.9097 (tppt) REVERT: L 483 MET cc_start: 0.8818 (mmt) cc_final: 0.8428 (mmm) REVERT: L 753 MET cc_start: 0.9062 (tpp) cc_final: 0.8805 (tpp) REVERT: L 856 GLU cc_start: 0.8716 (tt0) cc_final: 0.8500 (tt0) REVERT: L 1060 MET cc_start: 0.8200 (mmm) cc_final: 0.7881 (tpp) REVERT: L 1077 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7875 (mt-10) REVERT: L 1092 MET cc_start: 0.8156 (tpt) cc_final: 0.7272 (mtm) REVERT: L 1699 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8655 (mt) REVERT: L 1770 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7170 (tmtt) REVERT: L 1885 PHE cc_start: 0.8522 (t80) cc_final: 0.8296 (t80) REVERT: L 1901 MET cc_start: 0.6290 (mmm) cc_final: 0.5522 (mmp) REVERT: L 2137 MET cc_start: 0.0763 (ptp) cc_final: 0.0509 (ptp) outliers start: 29 outliers final: 19 residues processed: 127 average time/residue: 0.1211 time to fit residues: 23.8393 Evaluate side-chains 114 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1770 LYS Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 1864 PHE Chi-restraints excluded: chain L residue 2118 LEU Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 17 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 183 optimal weight: 0.1980 chunk 158 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 63 ASN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.081464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056689 restraints weight = 64100.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058364 restraints weight = 33660.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.059430 restraints weight = 22449.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.060089 restraints weight = 17459.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.060452 restraints weight = 15006.073| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15661 Z= 0.105 Angle : 0.566 12.525 21226 Z= 0.285 Chirality : 0.037 0.156 2403 Planarity : 0.003 0.046 2618 Dihedral : 6.442 112.513 2238 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 1.54 % Allowed : 15.60 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.20), residues: 1817 helix: 0.97 (0.17), residues: 951 sheet: -1.84 (0.49), residues: 109 loop : -2.82 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 144 TYR 0.007 0.001 TYR L 214 PHE 0.025 0.001 PHE L 481 TRP 0.017 0.001 TRP L2088 HIS 0.003 0.001 HIS L 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (15658) covalent geometry : angle 0.56634 / 0.29 (21226) hydrogen bonds : bond 0.03260 / 2.22 ( 665) hydrogen bonds : angle 3.87296 / 2.66 ( 1891) metal coordination : bond 0.00233 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8367 (mm) REVERT: L 154 ASP cc_start: 0.8744 (m-30) cc_final: 0.8079 (m-30) REVERT: L 393 GLU cc_start: 0.8734 (tt0) cc_final: 0.8480 (tp30) REVERT: L 394 LYS cc_start: 0.9253 (tppt) cc_final: 0.9023 (tppt) REVERT: L 420 MET cc_start: 0.8875 (tmm) cc_final: 0.8627 (tmm) REVERT: L 483 MET cc_start: 0.8727 (mmt) cc_final: 0.8499 (mmm) REVERT: L 753 MET cc_start: 0.8861 (tpp) cc_final: 0.8650 (tpp) REVERT: L 1060 MET cc_start: 0.8167 (mmm) cc_final: 0.7782 (tpp) REVERT: L 1077 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7804 (mt-10) REVERT: L 1092 MET cc_start: 0.8143 (tpt) cc_final: 0.7414 (mtt) REVERT: L 1885 PHE cc_start: 0.8470 (t80) cc_final: 0.8250 (t80) REVERT: L 1901 MET cc_start: 0.6290 (mmm) cc_final: 0.5566 (mmp) outliers start: 26 outliers final: 19 residues processed: 126 average time/residue: 0.1206 time to fit residues: 23.3066 Evaluate side-chains 114 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2118 LEU Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 102 optimal weight: 0.1980 chunk 172 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 45 optimal weight: 0.0470 chunk 142 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.081704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057103 restraints weight = 63358.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058760 restraints weight = 33401.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059823 restraints weight = 22383.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.060409 restraints weight = 17397.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.060866 restraints weight = 15059.746| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 15661 Z= 0.104 Angle : 0.574 12.498 21226 Z= 0.288 Chirality : 0.037 0.155 2403 Planarity : 0.003 0.045 2618 Dihedral : 6.376 112.361 2238 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.59 % Favored : 91.36 % Rotamer: Outliers : 1.48 % Allowed : 16.07 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.20), residues: 1817 helix: 1.04 (0.17), residues: 952 sheet: -1.65 (0.49), residues: 109 loop : -2.75 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 144 TYR 0.014 0.001 TYR L 442 PHE 0.045 0.001 PHE L 954 TRP 0.014 0.001 TRP L2088 HIS 0.003 0.000 HIS L1869 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (15658) covalent geometry : angle 0.57352 / 0.29 (21226) hydrogen bonds : bond 0.03197 / 2.18 ( 665) hydrogen bonds : angle 3.83517 / 2.64 ( 1891) metal coordination : bond 0.00202 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8131 (mm) REVERT: L 154 ASP cc_start: 0.8738 (m-30) cc_final: 0.8076 (m-30) REVERT: L 393 GLU cc_start: 0.8711 (tt0) cc_final: 0.8454 (tp30) REVERT: L 394 LYS cc_start: 0.9261 (tppt) cc_final: 0.9026 (tppt) REVERT: L 421 PHE cc_start: 0.8218 (m-10) cc_final: 0.7867 (m-80) REVERT: L 446 MET cc_start: 0.8513 (mmm) cc_final: 0.8301 (mmp) REVERT: L 483 MET cc_start: 0.8760 (mmt) cc_final: 0.8280 (mmm) REVERT: L 753 MET cc_start: 0.8848 (tpp) cc_final: 0.8645 (tpp) REVERT: L 1060 MET cc_start: 0.8189 (mmm) cc_final: 0.7778 (tpp) REVERT: L 1077 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7880 (mt-10) REVERT: L 1092 MET cc_start: 0.8115 (tpt) cc_final: 0.7505 (mtt) REVERT: L 1901 MET cc_start: 0.6226 (mmm) cc_final: 0.5525 (mmp) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.1205 time to fit residues: 23.5504 Evaluate side-chains 115 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2118 LEU Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 145 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 148 optimal weight: 0.0040 chunk 175 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.081875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.057181 restraints weight = 63727.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.058848 restraints weight = 33538.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059932 restraints weight = 22451.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.060595 restraints weight = 17408.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.060991 restraints weight = 14944.802| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15661 Z= 0.106 Angle : 0.591 13.035 21226 Z= 0.295 Chirality : 0.038 0.279 2403 Planarity : 0.004 0.048 2618 Dihedral : 6.364 112.282 2238 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.04 % Favored : 91.91 % Rotamer: Outliers : 1.19 % Allowed : 16.31 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1817 helix: 1.11 (0.17), residues: 951 sheet: -1.52 (0.49), residues: 109 loop : -2.71 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 342 TYR 0.020 0.001 TYR L 442 PHE 0.065 0.001 PHE L1885 TRP 0.010 0.001 TRP L2088 HIS 0.003 0.001 HIS L 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15658) covalent geometry : angle 0.59082 / 0.30 (21226) hydrogen bonds : bond 0.03241 / 2.22 ( 665) hydrogen bonds : angle 3.86108 / 2.68 ( 1891) metal coordination : bond 0.00185 / 0.09 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8162 (mm) REVERT: L 154 ASP cc_start: 0.8743 (m-30) cc_final: 0.8113 (m-30) REVERT: L 393 GLU cc_start: 0.8740 (tt0) cc_final: 0.8463 (tp30) REVERT: L 394 LYS cc_start: 0.9272 (tppt) cc_final: 0.9033 (tppt) REVERT: L 420 MET cc_start: 0.8663 (tmm) cc_final: 0.8430 (tmm) REVERT: L 483 MET cc_start: 0.8755 (mmt) cc_final: 0.8279 (mmm) REVERT: L 1060 MET cc_start: 0.8178 (mmm) cc_final: 0.7726 (tpp) REVERT: L 1077 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7878 (mt-10) REVERT: L 1092 MET cc_start: 0.8095 (tpt) cc_final: 0.7502 (mtt) REVERT: L 1530 CYS cc_start: 0.8263 (m) cc_final: 0.8044 (m) REVERT: L 1699 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8689 (mt) REVERT: L 1901 MET cc_start: 0.6095 (mmm) cc_final: 0.5485 (mmp) outliers start: 20 outliers final: 17 residues processed: 117 average time/residue: 0.1191 time to fit residues: 22.0476 Evaluate side-chains 117 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2118 LEU Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 chunk 120 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 GLN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.081695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056918 restraints weight = 63311.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.058572 restraints weight = 33605.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.059621 restraints weight = 22597.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.060286 restraints weight = 17681.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.060716 restraints weight = 15137.780| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15661 Z= 0.114 Angle : 0.595 12.932 21226 Z= 0.298 Chirality : 0.038 0.243 2403 Planarity : 0.004 0.058 2618 Dihedral : 6.340 112.328 2238 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 1.30 % Allowed : 16.13 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1817 helix: 1.09 (0.17), residues: 953 sheet: -1.43 (0.49), residues: 109 loop : -2.71 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 337 TYR 0.008 0.001 TYR L1187 PHE 0.062 0.002 PHE L1885 TRP 0.008 0.001 TRP L1194 HIS 0.003 0.001 HIS L 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (15658) covalent geometry : angle 0.59503 / 0.30 (21226) hydrogen bonds : bond 0.03310 / 2.26 ( 665) hydrogen bonds : angle 3.87955 / 2.69 ( 1891) metal coordination : bond 0.00194 / 0.10 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2767.10 seconds wall clock time: 48 minutes 53.16 seconds (2933.16 seconds total)