Starting phenix.real_space_refine on Sun Sep 13 00:00:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7orl_13041/09_2026/7orl_13041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7orl_13041/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7orl_13041/09_2026/7orl_13041.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7orl_13041/09_2026/7orl_13041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7orl_13041/09_2026/7orl_13041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7orl_13041/09_2026/7orl_13041.map" model { file = "/net/cci-nas-00/data/ceres_data/7orl_13041/09_2026/7orl_13041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7orl_13041/09_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): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: 4.68, per 1000 atoms: 0.25 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: 1.60 Conformation dependent library (CDL) restraints added in 804.4 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: 3.25 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: 6.18 Time building geometry restraints manager: 2.21 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 - 2.08: 25016 2.08 - 4.15: 1123 4.15 - 6.23: 134 6.23 - 8.30: 24 8.30 - 10.38: 3 Bond angle restraints: 26300 Sorted by residual: 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 angle pdb=" N HIS A2182 " pdb=" CA HIS A2182 " pdb=" C HIS A2182 " ideal model delta sigma weight residual 113.01 107.38 5.63 1.20e+00 6.94e-01 2.20e+01 ... (remaining 26295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.57: 11228 29.57 - 59.13: 415 59.13 - 88.70: 61 88.70 - 118.27: 0 118.27 - 147.83: 2 Dihedral angle restraints: 11706 sinusoidal: 5227 harmonic: 6479 Sorted by residual: dihedral pdb=" C4' U T 22 " pdb=" C3' U T 22 " pdb=" C2' U T 22 " pdb=" C1' U T 22 " ideal model delta sinusoidal sigma weight residual 36.35 -43.21 79.55 1 3.10e+00 1.04e-01 8.18e+02 dihedral pdb=" C4' C T 21 " pdb=" C3' C T 21 " pdb=" C2' C T 21 " pdb=" C1' C T 21 " ideal model delta sinusoidal sigma weight residual 36.34 -41.51 77.85 1 3.10e+00 1.04e-01 7.89e+02 dihedral pdb=" C4' A T 20 " pdb=" C3' A T 20 " pdb=" C2' A T 20 " pdb=" C1' A T 20 " ideal model delta sinusoidal sigma weight residual 36.34 -39.28 75.63 1 3.10e+00 1.04e-01 7.51e+02 ... (remaining 11703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2509 0.084 - 0.168: 310 0.168 - 0.252: 111 0.252 - 0.336: 28 0.336 - 0.420: 4 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=" C2' U T 22 " pdb=" C3' U T 22 " pdb=" O2' U T 22 " pdb=" C1' U T 22 " both_signs ideal model delta sigma weight residual False -2.79 -2.44 -0.35 2.00e-01 2.50e+01 2.98e+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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.870 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 26.850 Find NCS groups from input model: 0.120 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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= 0.381 Angle : 0.883 10.379 26300 Z= 0.579 Chirality : 0.070 0.420 2962 Planarity : 0.004 0.059 3157 Dihedral : 15.311 147.834 7500 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/Z covalent geometry : bond 0.00543 / 0.38 (19329) covalent geometry : angle 0.88319 / 0.58 (26300) hydrogen bonds : bond 0.16868 / 10.17 ( 945) hydrogen bonds : angle 5.97029 / 4.08 ( 2728) metal coordination : bond 0.08983 / 4.49 ( 3) Misc. bond : bond 0.06345 / 3.17 ( 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 : 0.877 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: 0.1384 time to fit residues: 50.0350 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 : 0.745 ------------------------------------------------------------------------------- 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... A 239 ASN A 319 ASN A 397 GLN A 932 GLN A 952 GLN A 985 ASN A1739 HIS A1842 HIS A1855 HIS A2046 ASN A2049 ASN A2179 HIS A2225 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.061195 restraints weight = 56620.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.063176 restraints weight = 28528.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064474 restraints weight = 18674.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065296 restraints weight = 14360.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.065811 restraints weight = 12205.653| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 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 = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19333 Z= 0.180 Angle : 0.765 19.996 26300 Z= 0.357 Chirality : 0.072 1.157 2962 Planarity : 0.004 0.053 3157 Dihedral : 11.207 143.837 2985 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 7.65 % Favored : 91.10 % 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: 1.00 (0.18), residues: 2169 helix: 1.89 (0.16), residues: 1104 sheet: 0.91 (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 A2120 TYR 0.021 0.001 TYR A 3 PHE 0.026 0.001 PHE A 344 TRP 0.014 0.001 TRP A2219 HIS 0.009 0.001 HIS A2179 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (19329) covalent geometry : angle 0.76505 / 0.36 (26300) hydrogen bonds : bond 0.04805 / 2.95 ( 945) hydrogen bonds : angle 4.66416 / 3.18 ( 2728) metal coordination : bond 0.00570 / 0.28 ( 3) Misc. bond : bond 0.00020 / 0.01 ( 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 203 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 20 CYS cc_start: 0.7763 (m) cc_final: 0.7545 (m) REVERT: A 31 MET cc_start: 0.8321 (ptp) cc_final: 0.7945 (ptm) REVERT: A 765 ASP cc_start: 0.8451 (t70) cc_final: 0.8204 (t0) REVERT: A 779 GLU cc_start: 0.8147 (tt0) cc_final: 0.7832 (tp30) REVERT: A 975 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7248 (mp0) REVERT: A 1014 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: A 1739 HIS cc_start: 0.7759 (m90) cc_final: 0.7327 (m-70) REVERT: A 1858 MET cc_start: 0.6955 (tpt) cc_final: 0.6697 (tpt) REVERT: A 2035 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7685 (mm-30) outliers start: 25 outliers final: 15 residues processed: 193 average time/residue: 0.1353 time to fit residues: 41.4956 Evaluate side-chains 170 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 1394 ILE Chi-restraints excluded: chain A residue 1477 ASP 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: 3.9990 chunk 197 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 0.0270 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 HIS A1621 HIS A1755 HIS A2134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.077770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.059978 restraints weight = 57373.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.061926 restraints weight = 28673.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.063216 restraints weight = 18731.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.064034 restraints weight = 14387.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.064535 restraints weight = 12209.440| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- 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 = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 19333 Z= 0.192 Angle : 0.665 13.566 26300 Z= 0.326 Chirality : 0.058 0.982 2962 Planarity : 0.004 0.052 3157 Dihedral : 11.455 178.775 2978 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.79 % Allowed : 9.24 % Favored : 88.97 % 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: 0.89 (0.18), residues: 2169 helix: 1.83 (0.16), residues: 1113 sheet: 0.88 (0.43), residues: 159 loop : -1.11 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1829 TYR 0.020 0.002 TYR A1576 PHE 0.017 0.002 PHE A 210 TRP 0.013 0.001 TRP A2219 HIS 0.039 0.001 HIS A2179 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (19329) covalent geometry : angle 0.66495 / 0.33 (26300) hydrogen bonds : bond 0.04303 / 2.65 ( 945) hydrogen bonds : angle 4.48055 / 3.05 ( 2728) metal coordination : bond 0.00387 / 0.19 ( 3) Misc. bond : bond 0.00006 / 0.00 ( 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 199 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8405 (ptp) cc_final: 0.8015 (ptm) REVERT: A 52 ASP cc_start: 0.8022 (m-30) cc_final: 0.7741 (m-30) REVERT: A 458 MET cc_start: 0.8829 (mmm) cc_final: 0.8598 (mmm) REVERT: A 765 ASP cc_start: 0.8452 (t70) cc_final: 0.8188 (t0) REVERT: A 779 GLU cc_start: 0.8196 (tt0) cc_final: 0.7787 (tp30) REVERT: A 1014 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: A 1371 ARG cc_start: 0.7498 (mmm160) cc_final: 0.7293 (mmm160) REVERT: A 1839 MET cc_start: 0.7918 (pmm) cc_final: 0.7711 (pmm) REVERT: A 1857 ASP cc_start: 0.8112 (t0) cc_final: 0.7900 (t0) REVERT: A 1858 MET cc_start: 0.6925 (tpt) cc_final: 0.6693 (tpt) REVERT: A 2035 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7775 (mm-30) outliers start: 36 outliers final: 20 residues processed: 186 average time/residue: 0.1259 time to fit residues: 38.4066 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 : 0.651 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 160 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN A1067 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1377 GLN A1693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.059564 restraints weight = 56979.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.061508 restraints weight = 28924.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.062771 restraints weight = 19164.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063554 restraints weight = 14877.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.064033 restraints weight = 12742.703| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19333 Z= 0.170 Angle : 0.628 12.769 26300 Z= 0.308 Chirality : 0.054 0.848 2962 Planarity : 0.003 0.050 3157 Dihedral : 11.309 179.131 2976 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.89 % Allowed : 10.54 % 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: 0.91 (0.18), residues: 2169 helix: 1.87 (0.16), residues: 1114 sheet: 0.84 (0.43), residues: 159 loop : -1.12 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2120 TYR 0.018 0.001 TYR A1576 PHE 0.036 0.001 PHE A 344 TRP 0.012 0.001 TRP A2219 HIS 0.012 0.001 HIS A1755 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (19329) covalent geometry : angle 0.62765 / 0.31 (26300) hydrogen bonds : bond 0.04063 / 2.50 ( 945) hydrogen bonds : angle 4.35863 / 2.97 ( 2728) metal coordination : bond 0.00261 / 0.13 ( 3) Misc. bond : bond 0.00005 / 0.00 ( 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 197 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8412 (ptp) cc_final: 0.8004 (ptm) REVERT: A 52 ASP cc_start: 0.8041 (m-30) cc_final: 0.7771 (m-30) REVERT: A 231 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: A 765 ASP cc_start: 0.8465 (t70) cc_final: 0.8200 (t0) REVERT: A 779 GLU cc_start: 0.8194 (tt0) cc_final: 0.7757 (tp30) REVERT: A 975 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7471 (mp0) REVERT: A 1014 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: A 2203 MET cc_start: 0.4016 (ttt) cc_final: 0.3234 (tmm) outliers start: 38 outliers final: 22 residues processed: 183 average time/residue: 0.1213 time to fit residues: 36.3201 Evaluate side-chains 172 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 156 ILE 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 588 ILE 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 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 1852 THR 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: 7.9990 chunk 128 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 139 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1739 HIS A2054 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.060792 restraints weight = 56615.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.062766 restraints weight = 28446.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064016 restraints weight = 18678.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064830 restraints weight = 14445.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.065322 restraints weight = 12326.139| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19333 Z= 0.121 Angle : 0.586 11.969 26300 Z= 0.288 Chirality : 0.051 0.705 2962 Planarity : 0.003 0.048 3157 Dihedral : 11.117 177.808 2976 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.49 % Allowed : 11.48 % 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: 0.97 (0.18), residues: 2169 helix: 1.93 (0.16), residues: 1116 sheet: 0.73 (0.43), residues: 165 loop : -1.10 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2120 TYR 0.014 0.001 TYR A1576 PHE 0.016 0.001 PHE A1768 TRP 0.009 0.001 TRP A2219 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (19329) covalent geometry : angle 0.58573 / 0.29 (26300) hydrogen bonds : bond 0.03664 / 2.25 ( 945) hydrogen bonds : angle 4.19492 / 2.84 ( 2728) metal coordination : bond 0.00126 / 0.06 ( 3) Misc. bond : bond 0.00027 / 0.01 ( 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 196 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8402 (ptp) cc_final: 0.7984 (ptm) REVERT: A 231 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7521 (m-80) REVERT: A 765 ASP cc_start: 0.8460 (t70) cc_final: 0.8210 (t0) REVERT: A 975 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7477 (mp0) REVERT: A 1214 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7736 (mm-30) REVERT: A 1839 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7523 (pmm) REVERT: A 2203 MET cc_start: 0.4166 (ttt) cc_final: 0.3274 (tmm) outliers start: 30 outliers final: 20 residues processed: 183 average time/residue: 0.1213 time to fit residues: 36.4401 Evaluate side-chains 174 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 588 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 964 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 1714 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1839 MET 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: 0.9990 chunk 178 optimal weight: 0.0070 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 148 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.061785 restraints weight = 56595.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.063775 restraints weight = 28345.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.065055 restraints weight = 18566.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065883 restraints weight = 14326.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.066384 restraints weight = 12184.337| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 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 = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 19333 Z= 0.102 Angle : 0.561 11.407 26300 Z= 0.276 Chirality : 0.049 0.631 2962 Planarity : 0.003 0.047 3157 Dihedral : 10.920 177.038 2976 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.19 % Allowed : 11.98 % Favored : 86.83 % 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: 2.02 (0.16), residues: 1118 sheet: 0.72 (0.42), residues: 166 loop : -1.05 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2120 TYR 0.012 0.001 TYR A1402 PHE 0.015 0.001 PHE A 210 TRP 0.009 0.001 TRP A2219 HIS 0.003 0.000 HIS A1944 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (19329) covalent geometry : angle 0.56134 / 0.28 (26300) hydrogen bonds : bond 0.03338 / 2.04 ( 945) hydrogen bonds : angle 4.04438 / 2.75 ( 2728) metal coordination : bond 0.00333 / 0.17 ( 3) Misc. bond : bond 0.00041 / 0.02 ( 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 194 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8406 (ptp) cc_final: 0.7990 (ptm) REVERT: A 231 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: A 765 ASP cc_start: 0.8433 (t70) cc_final: 0.8180 (t0) REVERT: A 975 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7460 (mp0) REVERT: A 1839 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7341 (pmm) REVERT: A 2035 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7638 (mm-30) outliers start: 24 outliers final: 15 residues processed: 184 average time/residue: 0.1236 time to fit residues: 37.1051 Evaluate side-chains 174 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 565 HIS Chi-restraints excluded: chain A residue 588 ILE 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 1839 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 171 optimal weight: 0.0170 chunk 41 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.0060 chunk 125 optimal weight: 0.9980 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.062115 restraints weight = 56759.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.064097 restraints weight = 28704.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.065438 restraints weight = 18763.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.066234 restraints weight = 14348.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066729 restraints weight = 12261.323| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 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 = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19333 Z= 0.100 Angle : 0.557 12.790 26300 Z= 0.272 Chirality : 0.049 0.779 2962 Planarity : 0.003 0.047 3157 Dihedral : 10.778 176.544 2976 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.39 % Allowed : 12.72 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 2169 helix: 2.13 (0.16), residues: 1110 sheet: 0.59 (0.42), residues: 165 loop : -0.92 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1371 TYR 0.014 0.001 TYR A1402 PHE 0.015 0.001 PHE A 948 TRP 0.008 0.001 TRP A2219 HIS 0.003 0.001 HIS A1944 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (19329) covalent geometry : angle 0.55707 / 0.27 (26300) hydrogen bonds : bond 0.03242 / 1.98 ( 945) hydrogen bonds : angle 3.97249 / 2.70 ( 2728) metal coordination : bond 0.00109 / 0.05 ( 3) Misc. bond : bond 0.00041 / 0.02 ( 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 191 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8409 (ptp) cc_final: 0.8036 (ptm) REVERT: A 231 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: A 350 MET cc_start: 0.8377 (mtt) cc_final: 0.8044 (mtt) REVERT: A 765 ASP cc_start: 0.8435 (t70) cc_final: 0.8184 (t0) REVERT: A 975 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7474 (mp0) REVERT: A 1415 MET cc_start: 0.6485 (mmm) cc_final: 0.6174 (mtp) REVERT: A 1839 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7320 (pmm) REVERT: A 2035 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7651 (mm-30) outliers start: 28 outliers final: 19 residues processed: 179 average time/residue: 0.1236 time to fit residues: 36.2253 Evaluate side-chains 178 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 565 HIS 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 1350 GLU 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 1714 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 1852 THR 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: 8.9990 chunk 171 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 165 optimal weight: 5.9990 chunk 91 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1225 ASN ** 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 = 0.3361 r_free = 0.3361 target = 0.079793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.061833 restraints weight = 57186.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.063828 restraints weight = 28679.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065129 restraints weight = 18759.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.065940 restraints weight = 14430.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066442 restraints weight = 12294.383| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 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 = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19333 Z= 0.107 Angle : 0.556 12.091 26300 Z= 0.272 Chirality : 0.048 0.708 2962 Planarity : 0.003 0.045 3157 Dihedral : 10.675 177.228 2976 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.44 % Allowed : 12.77 % 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: 1.27 (0.19), residues: 2169 helix: 2.20 (0.16), residues: 1110 sheet: 0.60 (0.42), residues: 166 loop : -0.89 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1371 TYR 0.013 0.001 TYR A1402 PHE 0.017 0.001 PHE A 210 TRP 0.010 0.001 TRP A2219 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (19329) covalent geometry : angle 0.55556 / 0.27 (26300) hydrogen bonds : bond 0.03237 / 1.99 ( 945) hydrogen bonds : angle 3.94578 / 2.69 ( 2728) metal coordination : bond 0.00108 / 0.05 ( 3) Misc. bond : bond 0.00028 / 0.01 ( 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 194 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8401 (ptp) cc_final: 0.8027 (ptm) REVERT: A 231 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: A 765 ASP cc_start: 0.8454 (t70) cc_final: 0.8186 (t0) REVERT: A 975 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7468 (mp0) REVERT: A 1415 MET cc_start: 0.6527 (mmm) cc_final: 0.6210 (mtp) REVERT: A 1563 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8038 (mm) REVERT: A 1839 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7275 (pmm) REVERT: A 2035 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 2180 MET cc_start: 0.7568 (tpt) cc_final: 0.7340 (tpt) REVERT: A 2224 GLU cc_start: 0.8385 (tp30) cc_final: 0.7669 (pt0) outliers start: 29 outliers final: 18 residues processed: 183 average time/residue: 0.1259 time to fit residues: 37.5323 Evaluate side-chains 179 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 1350 GLU 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 1839 MET Chi-restraints excluded: chain A residue 1852 THR 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: 1.9990 chunk 79 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.078864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.060871 restraints weight = 56793.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.062854 restraints weight = 28579.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.064130 restraints weight = 18756.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.064919 restraints weight = 14457.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065402 restraints weight = 12351.350| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19333 Z= 0.147 Angle : 0.588 11.786 26300 Z= 0.288 Chirality : 0.049 0.714 2962 Planarity : 0.003 0.046 3157 Dihedral : 10.677 177.920 2976 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.24 % Allowed : 13.42 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 2169 helix: 2.16 (0.16), residues: 1118 sheet: 0.51 (0.42), residues: 165 loop : -0.97 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1371 TYR 0.016 0.001 TYR A1402 PHE 0.017 0.001 PHE A 344 TRP 0.013 0.001 TRP A2219 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (19329) covalent geometry : angle 0.58780 / 0.29 (26300) hydrogen bonds : bond 0.03514 / 2.16 ( 945) hydrogen bonds : angle 4.01871 / 2.74 ( 2728) metal coordination : bond 0.00099 / 0.05 ( 3) Misc. bond : bond 0.00008 / 0.00 ( 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 183 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8394 (ptp) cc_final: 0.8032 (ptm) REVERT: A 231 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: A 350 MET cc_start: 0.8384 (mtt) cc_final: 0.8068 (mtt) REVERT: A 765 ASP cc_start: 0.8461 (t70) cc_final: 0.8202 (t0) REVERT: A 975 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7493 (mp0) REVERT: A 1415 MET cc_start: 0.6598 (mmm) cc_final: 0.6328 (mtp) REVERT: A 1563 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 1839 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7342 (pmm) REVERT: A 2224 GLU cc_start: 0.8379 (tp30) cc_final: 0.7672 (pt0) outliers start: 25 outliers final: 20 residues processed: 173 average time/residue: 0.1288 time to fit residues: 36.2950 Evaluate side-chains 178 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 156 ILE 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 1200 MET Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1521 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 1839 MET Chi-restraints excluded: chain A residue 1852 THR 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: 10.0000 chunk 209 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1181 ASN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2091 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.077836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.059682 restraints weight = 56921.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.061606 restraints weight = 28822.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.062865 restraints weight = 19105.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.063645 restraints weight = 14826.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064098 restraints weight = 12706.556| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19333 Z= 0.184 Angle : 0.615 11.476 26300 Z= 0.303 Chirality : 0.049 0.708 2962 Planarity : 0.003 0.046 3157 Dihedral : 10.711 179.123 2976 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.14 % Allowed : 13.47 % Favored : 85.39 % 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: 1.12 (0.19), residues: 2169 helix: 2.08 (0.16), residues: 1118 sheet: 0.42 (0.42), residues: 168 loop : -0.99 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1371 TYR 0.018 0.001 TYR A1402 PHE 0.020 0.001 PHE A 210 TRP 0.017 0.001 TRP A2219 HIS 0.004 0.001 HIS A1591 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (19329) covalent geometry : angle 0.61469 / 0.30 (26300) hydrogen bonds : bond 0.03820 / 2.35 ( 945) hydrogen bonds : angle 4.13007 / 2.82 ( 2728) metal coordination : bond 0.00234 / 0.12 ( 3) Misc. bond : bond 0.00001 / 0.00 ( 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 181 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8421 (ptp) cc_final: 0.8036 (ptm) REVERT: A 231 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: A 765 ASP cc_start: 0.8497 (t70) cc_final: 0.8222 (t0) REVERT: A 975 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7498 (mp0) REVERT: A 1415 MET cc_start: 0.6700 (mmm) cc_final: 0.6444 (mtp) REVERT: A 1563 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8061 (mm) REVERT: A 1839 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7509 (pmm) outliers start: 23 outliers final: 18 residues processed: 172 average time/residue: 0.1277 time to fit residues: 36.0179 Evaluate side-chains 172 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 156 ILE 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 1350 GLU 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 1839 MET Chi-restraints excluded: chain A residue 1852 THR 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: 0.8980 chunk 18 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3315 r_free = 0.3315 target = 0.077567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.059426 restraints weight = 57081.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.061361 restraints weight = 28880.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.062625 restraints weight = 19048.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.063407 restraints weight = 14737.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.063899 restraints weight = 12605.915| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2497 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= 0.186 Angle : 0.623 10.906 26300 Z= 0.307 Chirality : 0.049 0.679 2962 Planarity : 0.003 0.046 3157 Dihedral : 10.633 179.220 2976 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.09 % Allowed : 13.67 % Favored : 85.24 % 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: 1.03 (0.19), residues: 2169 helix: 2.02 (0.16), residues: 1119 sheet: 0.42 (0.42), residues: 169 loop : -1.06 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1371 TYR 0.018 0.001 TYR A1402 PHE 0.020 0.001 PHE A 344 TRP 0.017 0.001 TRP A2219 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (19329) covalent geometry : angle 0.62273 / 0.31 (26300) hydrogen bonds : bond 0.03880 / 2.39 ( 945) hydrogen bonds : angle 4.15848 / 2.84 ( 2728) metal coordination : bond 0.00186 / 0.09 ( 3) Misc. bond : bond 0.00005 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3129.44 seconds wall clock time: 55 minutes 13.79 seconds (3313.79 seconds total)