Starting phenix.real_space_refine on Thu Mar 5 05:03:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7orl_13041/03_2026/7orl_13041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7orl_13041/03_2026/7orl_13041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7orl_13041/03_2026/7orl_13041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7orl_13041/03_2026/7orl_13041.map" model { file = "/net/cci-nas-00/data/ceres_data/7orl_13041/03_2026/7orl_13041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7orl_13041/03_2026/7orl_13041.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 51 5.49 5 Mg 1 5.21 5 S 116 5.16 5 C 11846 2.51 5 N 3157 2.21 5 O 3680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18852 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain breaks: 1 Chain: "A" Number of atoms: 17811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2183, 17811 Classifications: {'peptide': 2183} Link IDs: {'PTRANS': 72, 'TRANS': 2110} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 365 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "T" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 357 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna2p': 7, 'rna3p': 9} Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'GTG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 1, ' ZN': 1, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16753 SG CYS A2064 49.307 100.427 49.634 1.00118.87 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O POP A2302 " occ=0.74 ... (7 atoms not shown) pdb=" P2 POP A2302 " occ=0.74 Time building chain proxies: 4.49, per 1000 atoms: 0.24 Number of scatterers: 18852 At special positions: 0 Unit cell: (113.52, 118.68, 148.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 116 16.00 P 51 15.00 Mg 1 11.99 O 3680 8.00 N 3157 7.00 C 11846 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 813.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" NE2 HIS A2182 " pdb="ZN ZN A2303 " - pdb=" SG CYS A2064 " pdb="ZN ZN A2303 " - pdb=" NE2 HIS A2169 " 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4206 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 16 sheets defined 56.4% alpha, 9.7% beta 10 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.526A pdb=" N TYR A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 46 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 98 through 121 removed outlier: 3.949A pdb=" N SER A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.605A pdb=" N ALA A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 238 through 260 removed outlier: 4.642A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.878A pdb=" N LYS A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 475 through 489 removed outlier: 6.484A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 Processing helix chain 'A' and resid 502 through 521 removed outlier: 3.771A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 606 through 620 removed outlier: 4.321A pdb=" N LEU A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 639 removed outlier: 3.612A pdb=" N LEU A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 661 removed outlier: 3.834A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.068A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 680 through 700 removed outlier: 4.123A pdb=" N TYR A 698 " --> pdb=" O CYS A 694 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP A 699 " --> pdb=" O PHE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 704 Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 748 through 752 removed outlier: 3.775A pdb=" N ASN A 752 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 removed outlier: 4.231A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 814 removed outlier: 3.640A pdb=" N HIS A 814 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 875 through 879 removed outlier: 3.613A pdb=" N VAL A 879 " --> pdb=" O PRO A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.922A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 983 removed outlier: 3.631A pdb=" N ARG A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1020 removed outlier: 3.660A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1031 Processing helix chain 'A' and resid 1040 through 1048 Processing helix chain 'A' and resid 1071 through 1079 removed outlier: 3.753A pdb=" N TRP A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 Processing helix chain 'A' and resid 1106 through 1114 Processing helix chain 'A' and resid 1123 through 1129 Processing helix chain 'A' and resid 1148 through 1174 Processing helix chain 'A' and resid 1201 through 1220 removed outlier: 3.546A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1261 removed outlier: 3.797A pdb=" N LEU A1256 " --> pdb=" O TYR A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1285 Processing helix chain 'A' and resid 1288 through 1307 Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1330 through 1334 Processing helix chain 'A' and resid 1340 through 1347 Processing helix chain 'A' and resid 1350 through 1365 Processing helix chain 'A' and resid 1373 through 1380 removed outlier: 3.792A pdb=" N GLU A1380 " --> pdb=" O ASN A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1405 Processing helix chain 'A' and resid 1434 through 1441 Processing helix chain 'A' and resid 1441 through 1453 removed outlier: 3.876A pdb=" N SER A1445 " --> pdb=" O LEU A1441 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A1446 " --> pdb=" O TYR A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1467 removed outlier: 3.511A pdb=" N GLU A1459 " --> pdb=" O GLY A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1473 removed outlier: 4.299A pdb=" N VAL A1472 " --> pdb=" O PRO A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1488 Processing helix chain 'A' and resid 1489 through 1491 No H-bonds generated for 'chain 'A' and resid 1489 through 1491' Processing helix chain 'A' and resid 1493 through 1498 Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1550 through 1563 removed outlier: 3.702A pdb=" N ARG A1554 " --> pdb=" O THR A1550 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A1562 " --> pdb=" O ARG A1558 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A1563 " --> pdb=" O ASP A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1578 Processing helix chain 'A' and resid 1581 through 1593 Processing helix chain 'A' and resid 1613 through 1617 Processing helix chain 'A' and resid 1622 through 1632 Processing helix chain 'A' and resid 1644 through 1660 Processing helix chain 'A' and resid 1660 through 1677 removed outlier: 3.658A pdb=" N MET A1665 " --> pdb=" O LEU A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1702 Processing helix chain 'A' and resid 1717 through 1729 Processing helix chain 'A' and resid 1747 through 1753 removed outlier: 3.935A pdb=" N ILE A1752 " --> pdb=" O GLY A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1756 through 1779 Processing helix chain 'A' and resid 1780 through 1782 No H-bonds generated for 'chain 'A' and resid 1780 through 1782' Processing helix chain 'A' and resid 1783 through 1795 Processing helix chain 'A' and resid 1802 through 1812 Processing helix chain 'A' and resid 1815 through 1817 No H-bonds generated for 'chain 'A' and resid 1815 through 1817' Processing helix chain 'A' and resid 1818 through 1825 Processing helix chain 'A' and resid 1831 through 1839 Processing helix chain 'A' and resid 1840 through 1842 No H-bonds generated for 'chain 'A' and resid 1840 through 1842' Processing helix chain 'A' and resid 1894 through 1905 removed outlier: 3.732A pdb=" N ILE A1898 " --> pdb=" O GLU A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1944 through 1955 Processing helix chain 'A' and resid 1985 through 1991 removed outlier: 4.552A pdb=" N TYR A1989 " --> pdb=" O ARG A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2019 removed outlier: 3.823A pdb=" N LYS A2017 " --> pdb=" O HIS A2014 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2039 Processing helix chain 'A' and resid 2046 through 2052 Processing helix chain 'A' and resid 2054 through 2060 removed outlier: 3.515A pdb=" N PHE A2058 " --> pdb=" O ASN A2054 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A2060 " --> pdb=" O ILE A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2075 removed outlier: 3.586A pdb=" N LEU A2074 " --> pdb=" O ILE A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2109 through 2129 Processing helix chain 'A' and resid 2138 through 2155 Processing helix chain 'A' and resid 2160 through 2175 removed outlier: 4.117A pdb=" N ILE A2164 " --> pdb=" O TRP A2160 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2183 removed outlier: 3.802A pdb=" N HIS A2182 " --> pdb=" O ASP A2178 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A2183 " --> pdb=" O HIS A2179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2178 through 2183' Processing helix chain 'A' and resid 2200 through 2211 Processing helix chain 'A' and resid 2218 through 2237 removed outlier: 4.009A pdb=" N MET A2222 " --> pdb=" O PRO A2218 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A2224 " --> pdb=" O ASN A2220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.262A pdb=" N LEU A 88 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL A 127 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE A 90 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE A 129 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP A 92 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE A 131 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS A 94 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 removed outlier: 6.280A pdb=" N GLU A 293 " --> pdb=" O ILE A 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 388 removed outlier: 5.220A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 388 removed outlier: 5.220A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AA7, first strand: chain 'A' and resid 709 through 710 removed outlier: 6.717A pdb=" N ILE A 709 " --> pdb=" O TYR A2099 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N SER A2101 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A2096 " --> pdb=" O ILE A2090 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A2084 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA9, first strand: chain 'A' and resid 842 through 846 Processing sheet with id=AB1, first strand: chain 'A' and resid 959 through 963 removed outlier: 6.289A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1236 through 1238 removed outlier: 3.572A pdb=" N LEU A1241 " --> pdb=" O PHE A1238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1606 through 1608 removed outlier: 3.525A pdb=" N PHE A1709 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1800 through 1801 Processing sheet with id=AB5, first strand: chain 'A' and resid 1844 through 1849 removed outlier: 6.754A pdb=" N ASN A1862 " --> pdb=" O ASN A1848 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A1871 " --> pdb=" O CYS A1887 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU A1877 " --> pdb=" O LEU A1881 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A1881 " --> pdb=" O GLU A1877 " (cutoff:3.500A) removed outlier: 12.578A pdb=" N LYS A1880 " --> pdb=" O THR A1966 " (cutoff:3.500A) removed outlier: 10.722A pdb=" N VAL A1968 " --> pdb=" O LYS A1880 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N THR A1882 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A1970 " --> pdb=" O THR A1882 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A1966 " --> pdb=" O TYR A1929 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A1929 " --> pdb=" O THR A1966 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1927 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL A1970 " --> pdb=" O TYR A1925 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR A1925 " --> pdb=" O VAL A1970 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1999 through 2000 Processing sheet with id=AB7, first strand: chain 'A' and resid 2027 through 2028 935 hydrogen bonds defined for protein. 2676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 4.80 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3327 1.33 - 1.45: 5068 1.45 - 1.57: 10646 1.57 - 1.69: 96 1.69 - 1.82: 192 Bond restraints: 19329 Sorted by residual: bond pdb=" C5B GTG P 101 " pdb=" C6B GTG P 101 " ideal model delta sigma weight residual 1.424 1.328 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C5A GTG P 101 " pdb=" C6A GTG P 101 " ideal model delta sigma weight residual 1.427 1.335 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" N LEU A1593 " pdb=" CA LEU A1593 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.10e-02 8.26e+03 1.58e+01 bond pdb=" C PRO A1288 " pdb=" O PRO A1288 " ideal model delta sigma weight residual 1.246 1.213 0.032 8.50e-03 1.38e+04 1.46e+01 bond pdb=" O5D GTG P 101 " pdb=" PA GTG P 101 " ideal model delta sigma weight residual 1.653 1.586 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 19324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 26122 3.89 - 7.79: 168 7.79 - 11.68: 9 11.68 - 15.58: 0 15.58 - 19.47: 1 Bond angle restraints: 26300 Sorted by residual: angle pdb=" P1 POP A2302 " pdb=" O POP A2302 " pdb=" P2 POP A2302 " ideal model delta sigma weight residual 139.66 120.19 19.47 3.00e+00 1.11e-01 4.21e+01 angle pdb=" N PRO A2218 " pdb=" CA PRO A2218 " pdb=" C PRO A2218 " ideal model delta sigma weight residual 113.84 105.74 8.10 1.30e+00 5.92e-01 3.89e+01 angle pdb=" C ILE A1577 " pdb=" N ILE A1578 " pdb=" CA ILE A1578 " ideal model delta sigma weight residual 123.08 117.80 5.28 1.01e+00 9.80e-01 2.73e+01 angle pdb=" N CYS A2064 " pdb=" CA CYS A2064 " pdb=" C CYS A2064 " ideal model delta sigma weight residual 111.07 116.54 -5.47 1.07e+00 8.73e-01 2.61e+01 angle pdb=" C TYR A1740 " pdb=" CA TYR A1740 " pdb=" CB TYR A1740 " ideal model delta sigma weight residual 110.26 117.42 -7.16 1.50e+00 4.44e-01 2.28e+01 ... (remaining 26295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 11541 35.09 - 70.19: 284 70.19 - 105.28: 29 105.28 - 140.38: 1 140.38 - 175.47: 3 Dihedral angle restraints: 11858 sinusoidal: 5379 harmonic: 6479 Sorted by residual: dihedral pdb=" O4' U P 9 " pdb=" C1' U P 9 " pdb=" N1 U P 9 " pdb=" C2 U P 9 " ideal model delta sinusoidal sigma weight residual 232.00 56.53 175.47 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U P 7 " pdb=" C1' U P 7 " pdb=" N1 U P 7 " pdb=" C2 U P 7 " ideal model delta sinusoidal sigma weight residual 232.00 58.73 173.27 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" C TYR A1364 " pdb=" N TYR A1364 " pdb=" CA TYR A1364 " pdb=" CB TYR A1364 " ideal model delta harmonic sigma weight residual -122.60 -135.25 12.65 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 11855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2573 0.084 - 0.168: 318 0.168 - 0.252: 59 0.252 - 0.336: 10 0.336 - 0.420: 2 Chirality restraints: 2962 Sorted by residual: chirality pdb=" CA TYR A1364 " pdb=" N TYR A1364 " pdb=" C TYR A1364 " pdb=" CB TYR A1364 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA TYR A1576 " pdb=" N TYR A1576 " pdb=" C TYR A1576 " pdb=" CB TYR A1576 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA ILE A1500 " pdb=" N ILE A1500 " pdb=" C ILE A1500 " pdb=" CB ILE A1500 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2959 not shown) Planarity restraints: 3157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1593 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C LEU A1593 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU A1593 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A1594 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1655 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C PHE A1655 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE A1655 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A1656 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1571 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C GLN A1571 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN A1571 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A1572 " -0.014 2.00e-02 2.50e+03 ... (remaining 3154 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 391 2.69 - 3.24: 18719 3.24 - 3.79: 30541 3.79 - 4.35: 41443 4.35 - 4.90: 66298 Nonbonded interactions: 157392 Sorted by model distance: nonbonded pdb=" OD1 ASP A1188 " pdb="MG MG A2301 " model vdw 2.134 2.170 nonbonded pdb=" O ILE A2118 " pdb=" OG1 THR A2122 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR A2109 " pdb=" OD1 ASN A2112 " model vdw 2.271 3.040 nonbonded pdb=" OD2 ASP A1776 " pdb=" OG SER A1998 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2303 " model vdw 2.312 2.230 ... (remaining 157387 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=0.74 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: 6.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 23.520 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.006 0.120 19333 Z= 0.382 Angle : 0.859 19.473 26300 Z= 0.577 Chirality : 0.059 0.420 2962 Planarity : 0.004 0.059 3157 Dihedral : 15.483 175.469 7652 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 0.94 % Allowed : 2.19 % Favored : 96.87 % Cbeta Deviations : 0.10 % 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 (0.18), residues: 2169 helix: 1.79 (0.16), residues: 1088 sheet: 1.08 (0.42), residues: 169 loop : -0.95 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1829 TYR 0.019 0.001 TYR A1364 PHE 0.022 0.001 PHE A2207 TRP 0.020 0.001 TRP A2219 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00543 (19329) covalent geometry : angle 0.85886 (26300) hydrogen bonds : bond 0.16868 ( 945) hydrogen bonds : angle 5.97029 ( 2728) metal coordination : bond 0.08983 ( 3) Misc. bond : bond 0.06345 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 CYS cc_start: 0.7754 (m) cc_final: 0.7480 (m) REVERT: A 58 ILE cc_start: 0.9156 (mt) cc_final: 0.8786 (mt) REVERT: A 765 ASP cc_start: 0.8377 (t70) cc_final: 0.8151 (t0) REVERT: A 779 GLU cc_start: 0.8150 (tt0) cc_final: 0.7880 (tp30) REVERT: A 995 ASP cc_start: 0.7844 (p0) cc_final: 0.7568 (p0) REVERT: A 1501 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: A 1613 PHE cc_start: 0.8121 (t80) cc_final: 0.7624 (t80) REVERT: A 2035 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7471 (mm-30) outliers start: 19 outliers final: 4 residues processed: 229 average time/residue: 0.1360 time to fit residues: 48.4674 Evaluate side-chains 164 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 1501 GLN Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1829 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 319 ASN A 397 GLN A 932 GLN A 952 GLN A 985 ASN A1621 HIS A1739 HIS A1842 HIS A1855 HIS A2046 ASN A2049 ASN A2179 HIS A2225 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.078816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.060899 restraints weight = 56598.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.062891 restraints weight = 28480.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.064175 restraints weight = 18653.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.065011 restraints weight = 14334.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065451 restraints weight = 12145.968| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19333 Z= 0.162 Angle : 0.548 6.513 26300 Z= 0.297 Chirality : 0.041 0.169 2962 Planarity : 0.004 0.053 3157 Dihedral : 13.611 175.848 3137 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.29 % Allowed : 7.85 % Favored : 90.85 % 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: 0.99 (0.18), residues: 2169 helix: 1.88 (0.16), residues: 1104 sheet: 0.89 (0.41), residues: 171 loop : -0.99 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1784 TYR 0.022 0.001 TYR A 3 PHE 0.029 0.001 PHE A 344 TRP 0.013 0.001 TRP A2219 HIS 0.008 0.001 HIS A2179 Details of bonding type rmsd covalent geometry : bond 0.00360 (19329) covalent geometry : angle 0.54779 (26300) hydrogen bonds : bond 0.04655 ( 945) hydrogen bonds : angle 4.63679 ( 2728) metal coordination : bond 0.00466 ( 3) Misc. bond : bond 0.00078 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 CYS cc_start: 0.7734 (m) cc_final: 0.7517 (m) REVERT: A 31 MET cc_start: 0.8369 (ptp) cc_final: 0.8008 (ptm) REVERT: A 765 ASP cc_start: 0.8442 (t70) cc_final: 0.8198 (t0) REVERT: A 779 GLU cc_start: 0.8154 (tt0) cc_final: 0.7824 (tp30) REVERT: A 975 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7247 (mp0) REVERT: A 1014 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: A 1739 HIS cc_start: 0.7756 (m90) cc_final: 0.7324 (m-70) REVERT: A 1858 MET cc_start: 0.6947 (tpt) cc_final: 0.6711 (tpt) REVERT: A 2035 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7685 (mm-30) outliers start: 26 outliers final: 15 residues processed: 192 average time/residue: 0.1322 time to fit residues: 39.9390 Evaluate side-chains 171 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1521 PHE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 2070 ILE Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2179 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 211 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 97 optimal weight: 0.0270 chunk 112 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A1620 HIS A1755 HIS A2134 ASN A2179 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.060153 restraints weight = 57233.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.062086 restraints weight = 28602.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.063373 restraints weight = 18771.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064170 restraints weight = 14410.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064577 restraints weight = 12288.485| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19333 Z= 0.163 Angle : 0.522 5.862 26300 Z= 0.283 Chirality : 0.041 0.153 2962 Planarity : 0.003 0.051 3157 Dihedral : 13.504 176.915 3130 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.74 % Allowed : 9.24 % Favored : 89.02 % 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: 0.92 (0.18), residues: 2169 helix: 1.85 (0.16), residues: 1114 sheet: 0.91 (0.43), residues: 159 loop : -1.07 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2120 TYR 0.019 0.001 TYR A1576 PHE 0.016 0.001 PHE A2184 TRP 0.011 0.001 TRP A2219 HIS 0.024 0.001 HIS A2179 Details of bonding type rmsd covalent geometry : bond 0.00365 (19329) covalent geometry : angle 0.52152 (26300) hydrogen bonds : bond 0.04195 ( 945) hydrogen bonds : angle 4.45205 ( 2728) metal coordination : bond 0.00351 ( 3) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8396 (ptp) cc_final: 0.8012 (ptm) REVERT: A 52 ASP cc_start: 0.8039 (m-30) cc_final: 0.7761 (m-30) REVERT: A 765 ASP cc_start: 0.8429 (t70) cc_final: 0.8183 (t0) REVERT: A 779 GLU cc_start: 0.8157 (tt0) cc_final: 0.7778 (tp30) REVERT: A 975 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7347 (mp0) REVERT: A 1014 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: A 1858 MET cc_start: 0.6889 (tpt) cc_final: 0.6676 (tpt) REVERT: A 2035 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7765 (mm-30) outliers start: 35 outliers final: 20 residues processed: 181 average time/residue: 0.1186 time to fit residues: 34.9847 Evaluate side-chains 174 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1755 HIS Chi-restraints excluded: chain A residue 1852 THR Chi-restraints excluded: chain A residue 1868 TYR Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2207 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 28 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 168 optimal weight: 0.0060 chunk 180 optimal weight: 0.0010 overall best weight: 0.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 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 = 0.3342 r_free = 0.3342 target = 0.078916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.061059 restraints weight = 56501.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063030 restraints weight = 28328.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064304 restraints weight = 18593.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065101 restraints weight = 14322.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.065603 restraints weight = 12214.748| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19333 Z= 0.109 Angle : 0.485 7.315 26300 Z= 0.262 Chirality : 0.039 0.154 2962 Planarity : 0.003 0.049 3157 Dihedral : 13.377 176.531 3128 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.39 % Allowed : 10.54 % Favored : 88.07 % 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: 1.08 (0.18), residues: 2169 helix: 2.00 (0.16), residues: 1102 sheet: 0.92 (0.43), residues: 159 loop : -0.97 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2120 TYR 0.022 0.001 TYR A 3 PHE 0.016 0.001 PHE A 307 TRP 0.009 0.001 TRP A2219 HIS 0.010 0.001 HIS A1755 Details of bonding type rmsd covalent geometry : bond 0.00233 (19329) covalent geometry : angle 0.48453 (26300) hydrogen bonds : bond 0.03753 ( 945) hydrogen bonds : angle 4.25052 ( 2728) metal coordination : bond 0.00019 ( 3) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8398 (ptp) cc_final: 0.8007 (ptm) REVERT: A 231 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: A 765 ASP cc_start: 0.8428 (t70) cc_final: 0.8185 (t0) REVERT: A 975 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7442 (mp0) REVERT: A 1014 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: A 2035 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7736 (mm-30) REVERT: A 2203 MET cc_start: 0.3921 (ttt) cc_final: 0.3108 (tmm) outliers start: 28 outliers final: 17 residues processed: 186 average time/residue: 0.1205 time to fit residues: 36.3529 Evaluate side-chains 169 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 2041 ASP Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2207 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 37 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 173 optimal weight: 2.9990 chunk 150 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 chunk 210 optimal weight: 0.5980 chunk 189 optimal weight: 4.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1280 GLN A1377 GLN A1693 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.062045 restraints weight = 56600.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064017 restraints weight = 28499.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065310 restraints weight = 18784.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.066127 restraints weight = 14479.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.066574 restraints weight = 12331.573| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19333 Z= 0.094 Angle : 0.466 6.181 26300 Z= 0.252 Chirality : 0.039 0.134 2962 Planarity : 0.003 0.047 3157 Dihedral : 13.265 176.505 3128 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 1.59 % Allowed : 10.83 % Favored : 87.57 % 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: 1.15 (0.18), residues: 2169 helix: 2.06 (0.16), residues: 1110 sheet: 0.72 (0.42), residues: 165 loop : -0.93 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1371 TYR 0.013 0.001 TYR A1576 PHE 0.035 0.001 PHE A 344 TRP 0.006 0.001 TRP A2219 HIS 0.003 0.001 HIS A1944 Details of bonding type rmsd covalent geometry : bond 0.00195 (19329) covalent geometry : angle 0.46610 (26300) hydrogen bonds : bond 0.03372 ( 945) hydrogen bonds : angle 4.07592 ( 2728) metal coordination : bond 0.00103 ( 3) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7030 (mmp) cc_final: 0.6820 (mmp) REVERT: A 31 MET cc_start: 0.8387 (ptp) cc_final: 0.8000 (ptm) REVERT: A 231 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: A 627 MET cc_start: 0.8348 (tpt) cc_final: 0.8137 (tpp) REVERT: A 765 ASP cc_start: 0.8403 (t70) cc_final: 0.8171 (t0) REVERT: A 975 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7444 (mp0) REVERT: A 2203 MET cc_start: 0.4069 (ttt) cc_final: 0.3387 (tmm) REVERT: A 2224 GLU cc_start: 0.8383 (tp30) cc_final: 0.8056 (tp30) outliers start: 32 outliers final: 17 residues processed: 190 average time/residue: 0.1266 time to fit residues: 39.4044 Evaluate side-chains 172 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 2041 ASP Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2207 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 73 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 54 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 0.0270 chunk 148 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 chunk 10 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A1067 GLN A1739 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.062499 restraints weight = 56498.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.064487 restraints weight = 28351.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065802 restraints weight = 18531.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066607 restraints weight = 14212.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.067127 restraints weight = 12096.318| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19333 Z= 0.092 Angle : 0.466 7.635 26300 Z= 0.249 Chirality : 0.039 0.147 2962 Planarity : 0.003 0.045 3157 Dihedral : 13.201 176.693 3128 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.29 % Allowed : 11.68 % Favored : 87.03 % 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: 1.15 (0.18), residues: 2169 helix: 2.09 (0.16), residues: 1118 sheet: 0.60 (0.41), residues: 165 loop : -0.99 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1901 TYR 0.013 0.001 TYR A1576 PHE 0.014 0.001 PHE A2184 TRP 0.008 0.001 TRP A2219 HIS 0.003 0.000 HIS A1944 Details of bonding type rmsd covalent geometry : bond 0.00195 (19329) covalent geometry : angle 0.46623 (26300) hydrogen bonds : bond 0.03224 ( 945) hydrogen bonds : angle 4.00853 ( 2728) metal coordination : bond 0.00218 ( 3) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6954 (mmp) cc_final: 0.6735 (mmp) REVERT: A 31 MET cc_start: 0.8388 (ptp) cc_final: 0.8003 (ptm) REVERT: A 231 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: A 765 ASP cc_start: 0.8414 (t70) cc_final: 0.8166 (t0) REVERT: A 975 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7441 (mp0) REVERT: A 1415 MET cc_start: 0.6478 (mmm) cc_final: 0.6181 (mtp) REVERT: A 2203 MET cc_start: 0.3991 (ttt) cc_final: 0.3115 (tmm) REVERT: A 2224 GLU cc_start: 0.8391 (tp30) cc_final: 0.8052 (tp30) outliers start: 26 outliers final: 15 residues processed: 186 average time/residue: 0.1246 time to fit residues: 37.5354 Evaluate side-chains 171 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 171 optimal weight: 0.0470 chunk 41 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 215 optimal weight: 0.1980 chunk 7 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.062452 restraints weight = 56622.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.064438 restraints weight = 28433.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.065754 restraints weight = 18551.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066588 restraints weight = 14200.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.067085 restraints weight = 12032.577| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19333 Z= 0.094 Angle : 0.462 6.758 26300 Z= 0.246 Chirality : 0.039 0.160 2962 Planarity : 0.003 0.044 3157 Dihedral : 13.166 176.880 3128 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.29 % Allowed : 12.28 % Favored : 86.43 % 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 (0.19), residues: 2169 helix: 2.16 (0.16), residues: 1119 sheet: 0.52 (0.41), residues: 165 loop : -0.96 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 63 TYR 0.013 0.001 TYR A1576 PHE 0.024 0.001 PHE A 344 TRP 0.007 0.001 TRP A2219 HIS 0.003 0.000 HIS A1944 Details of bonding type rmsd covalent geometry : bond 0.00202 (19329) covalent geometry : angle 0.46156 (26300) hydrogen bonds : bond 0.03215 ( 945) hydrogen bonds : angle 3.96071 ( 2728) metal coordination : bond 0.00134 ( 3) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8402 (ptp) cc_final: 0.8028 (ptm) REVERT: A 231 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: A 765 ASP cc_start: 0.8403 (t70) cc_final: 0.8159 (t0) REVERT: A 975 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7430 (mp0) REVERT: A 1415 MET cc_start: 0.6521 (mmm) cc_final: 0.6223 (mtp) REVERT: A 2224 GLU cc_start: 0.8374 (tp30) cc_final: 0.7650 (pt0) outliers start: 26 outliers final: 17 residues processed: 179 average time/residue: 0.1287 time to fit residues: 37.5776 Evaluate side-chains 170 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1714 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2207 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 85 optimal weight: 7.9990 chunk 171 optimal weight: 0.5980 chunk 116 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 91 optimal weight: 0.1980 chunk 104 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2054 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.061210 restraints weight = 56907.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.063161 restraints weight = 28443.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064461 restraints weight = 18629.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065272 restraints weight = 14319.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.065760 restraints weight = 12169.151| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19333 Z= 0.128 Angle : 0.490 8.984 26300 Z= 0.260 Chirality : 0.040 0.172 2962 Planarity : 0.003 0.044 3157 Dihedral : 13.184 177.363 3128 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 0.99 % Allowed : 12.97 % Favored : 86.03 % 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: 1.22 (0.19), residues: 2169 helix: 2.18 (0.16), residues: 1117 sheet: 0.48 (0.41), residues: 165 loop : -0.97 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 63 TYR 0.016 0.001 TYR A1402 PHE 0.014 0.001 PHE A1768 TRP 0.011 0.001 TRP A2219 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00289 (19329) covalent geometry : angle 0.48970 (26300) hydrogen bonds : bond 0.03440 ( 945) hydrogen bonds : angle 4.03239 ( 2728) metal coordination : bond 0.00124 ( 3) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8392 (ptp) cc_final: 0.8023 (ptm) REVERT: A 231 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: A 765 ASP cc_start: 0.8421 (t70) cc_final: 0.8166 (t0) REVERT: A 975 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7457 (mp0) REVERT: A 1415 MET cc_start: 0.6602 (mmm) cc_final: 0.6333 (mtp) REVERT: A 1563 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8028 (mm) REVERT: A 2180 MET cc_start: 0.7607 (tpt) cc_final: 0.7362 (tpt) REVERT: A 2224 GLU cc_start: 0.8387 (tp30) cc_final: 0.7648 (pt0) outliers start: 20 outliers final: 16 residues processed: 174 average time/residue: 0.1172 time to fit residues: 33.3189 Evaluate side-chains 173 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2207 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 57 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 168 optimal weight: 0.3980 chunk 204 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1739 HIS ** 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 = 0.3352 r_free = 0.3352 target = 0.079355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.061463 restraints weight = 56566.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.063446 restraints weight = 28518.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064732 restraints weight = 18673.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.065535 restraints weight = 14361.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.066053 restraints weight = 12213.937| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19333 Z= 0.112 Angle : 0.489 8.335 26300 Z= 0.258 Chirality : 0.039 0.158 2962 Planarity : 0.003 0.045 3157 Dihedral : 13.165 176.977 3128 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 1.04 % Allowed : 13.17 % Favored : 85.79 % 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 (0.19), residues: 2169 helix: 2.19 (0.16), residues: 1117 sheet: 0.41 (0.41), residues: 165 loop : -0.97 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 63 TYR 0.013 0.001 TYR A1402 PHE 0.018 0.001 PHE A 210 TRP 0.011 0.001 TRP A2219 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00250 (19329) covalent geometry : angle 0.48866 (26300) hydrogen bonds : bond 0.03355 ( 945) hydrogen bonds : angle 3.97349 ( 2728) metal coordination : bond 0.00134 ( 3) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8407 (ptp) cc_final: 0.8036 (ptm) REVERT: A 231 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: A 765 ASP cc_start: 0.8425 (t70) cc_final: 0.8169 (t0) REVERT: A 975 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7461 (mp0) REVERT: A 1415 MET cc_start: 0.6604 (mmm) cc_final: 0.6323 (mtp) REVERT: A 1563 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8017 (mm) REVERT: A 1745 LEU cc_start: 0.9032 (tt) cc_final: 0.8830 (tp) REVERT: A 2180 MET cc_start: 0.7615 (tpt) cc_final: 0.7383 (tpt) REVERT: A 2224 GLU cc_start: 0.8401 (tp30) cc_final: 0.7651 (pt0) outliers start: 21 outliers final: 17 residues processed: 174 average time/residue: 0.1183 time to fit residues: 33.7043 Evaluate side-chains 172 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2207 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 120 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 0.2980 chunk 200 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1739 HIS ** 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 = 0.3356 r_free = 0.3356 target = 0.079537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.061760 restraints weight = 56624.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.063739 restraints weight = 28384.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065037 restraints weight = 18550.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065843 restraints weight = 14217.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066332 restraints weight = 12078.831| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19333 Z= 0.105 Angle : 0.496 10.098 26300 Z= 0.260 Chirality : 0.039 0.158 2962 Planarity : 0.003 0.044 3157 Dihedral : 13.143 176.913 3128 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.08 % Rotamer: Outliers : 0.89 % Allowed : 13.57 % Favored : 85.54 % 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: 1.21 (0.19), residues: 2169 helix: 2.20 (0.16), residues: 1117 sheet: 0.35 (0.41), residues: 165 loop : -0.98 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 63 TYR 0.013 0.001 TYR A1402 PHE 0.015 0.001 PHE A 210 TRP 0.010 0.001 TRP A2219 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00232 (19329) covalent geometry : angle 0.49558 (26300) hydrogen bonds : bond 0.03288 ( 945) hydrogen bonds : angle 3.94468 ( 2728) metal coordination : bond 0.00118 ( 3) Misc. bond : bond 0.00020 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8399 (ptp) cc_final: 0.8024 (ptm) REVERT: A 231 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: A 765 ASP cc_start: 0.8422 (t70) cc_final: 0.8171 (t0) REVERT: A 975 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7450 (mp0) REVERT: A 1415 MET cc_start: 0.6591 (mmm) cc_final: 0.6306 (mtp) REVERT: A 1563 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8033 (mm) REVERT: A 2224 GLU cc_start: 0.8401 (tp30) cc_final: 0.7651 (pt0) outliers start: 18 outliers final: 15 residues processed: 168 average time/residue: 0.1207 time to fit residues: 33.2947 Evaluate side-chains 171 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2207 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 138 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 101 optimal weight: 0.1980 chunk 87 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1914 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.061425 restraints weight = 56911.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.063398 restraints weight = 28502.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064692 restraints weight = 18612.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.065484 restraints weight = 14295.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.065999 restraints weight = 12158.727| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19333 Z= 0.114 Angle : 0.496 9.861 26300 Z= 0.261 Chirality : 0.039 0.154 2962 Planarity : 0.003 0.044 3157 Dihedral : 13.128 177.111 3128 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 0.99 % Allowed : 13.52 % Favored : 85.49 % 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: 1.28 (0.19), residues: 2169 helix: 2.26 (0.16), residues: 1109 sheet: 0.34 (0.41), residues: 165 loop : -0.90 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 63 TYR 0.014 0.001 TYR A1402 PHE 0.019 0.001 PHE A 210 TRP 0.011 0.001 TRP A2219 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00257 (19329) covalent geometry : angle 0.49639 (26300) hydrogen bonds : bond 0.03335 ( 945) hydrogen bonds : angle 3.94424 ( 2728) metal coordination : bond 0.00140 ( 3) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2972.42 seconds wall clock time: 53 minutes 27.46 seconds (3207.46 seconds total)