Starting phenix.real_space_refine on Wed Mar 4 15:10:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nj0_12368/03_2026/7nj0_12368.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nj0_12368/03_2026/7nj0_12368.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 { model { file = "/net/cci-nas-00/data/ceres_data/7nj0_12368/03_2026/7nj0_12368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nj0_12368/03_2026/7nj0_12368.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nj0_12368/03_2026/7nj0_12368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nj0_12368/03_2026/7nj0_12368.map" } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 71 5.16 5 C 9167 2.51 5 N 2461 2.21 5 O 2628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14330 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9198 Classifications: {'peptide': 1188} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 65, 'TRANS': 1122} Chain breaks: 6 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2349 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2173 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain: "D" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 605 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ARG B 59 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 59 " occ=0.50 residue: pdb=" N GLN B 132 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN B 132 " occ=0.50 residue: pdb=" N TYR C 175 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR C 175 " occ=0.50 Time building chain proxies: 3.13, per 1000 atoms: 0.22 Number of scatterers: 14330 At special positions: 0 Unit cell: (91.52, 134.64, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 P 3 15.00 O 2628 8.00 N 2461 7.00 C 9167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 687 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 511.2 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 6 sheets defined 59.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 621 through 639 removed outlier: 3.599A pdb=" N HIS A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 removed outlier: 3.686A pdb=" N ALA A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 703 removed outlier: 4.381A pdb=" N GLN A 672 " --> pdb=" O GLN A 668 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 729 through 733 Processing helix chain 'A' and resid 736 through 759 removed outlier: 5.420A pdb=" N CYS A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 759 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.637A pdb=" N THR A 772 " --> pdb=" O CYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 807 removed outlier: 4.334A pdb=" N GLU A 794 " --> pdb=" O MET A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 826 Processing helix chain 'A' and resid 831 through 844 removed outlier: 3.750A pdb=" N HIS A 835 " --> pdb=" O TYR A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 872 Processing helix chain 'A' and resid 873 through 886 removed outlier: 3.657A pdb=" N GLY A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 892 removed outlier: 3.505A pdb=" N LYS A 892 " --> pdb=" O ALA A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 912 Processing helix chain 'A' and resid 920 through 930 Processing helix chain 'A' and resid 934 through 954 Processing helix chain 'A' and resid 975 through 999 removed outlier: 3.723A pdb=" N LYS A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.695A pdb=" N ALA A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1041 removed outlier: 3.924A pdb=" N LEU A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE A1030 " --> pdb=" O GLN A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1059 removed outlier: 3.714A pdb=" N LEU A1055 " --> pdb=" O LEU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 removed outlier: 3.942A pdb=" N VAL A1109 " --> pdb=" O LEU A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1174 Processing helix chain 'A' and resid 1178 through 1207 removed outlier: 3.761A pdb=" N ASP A1182 " --> pdb=" O ALA A1178 " (cutoff:3.500A) Proline residue: A1192 - end of helix removed outlier: 3.638A pdb=" N ALA A1204 " --> pdb=" O GLN A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1234 removed outlier: 4.077A pdb=" N ALA A1226 " --> pdb=" O ILE A1222 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A1233 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A1234 " --> pdb=" O LEU A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1257 removed outlier: 4.425A pdb=" N GLN A1248 " --> pdb=" O GLN A1244 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A1257 " --> pdb=" O PHE A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1278 Processing helix chain 'A' and resid 1286 through 1291 removed outlier: 3.704A pdb=" N SER A1290 " --> pdb=" O LEU A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1589 removed outlier: 3.999A pdb=" N ALA A1584 " --> pdb=" O SER A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1593 through 1608 removed outlier: 3.939A pdb=" N ALA A1598 " --> pdb=" O SER A1594 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS A1599 " --> pdb=" O GLY A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1622 removed outlier: 4.068A pdb=" N VAL A1620 " --> pdb=" O THR A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1645 removed outlier: 3.947A pdb=" N LEU A1632 " --> pdb=" O CYS A1628 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS A1637 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A1643 " --> pdb=" O GLN A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1678 Processing helix chain 'A' and resid 1687 through 1701 removed outlier: 4.329A pdb=" N GLU A1691 " --> pdb=" O PHE A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1746 No H-bonds generated for 'chain 'A' and resid 1744 through 1746' Processing helix chain 'A' and resid 1749 through 1768 Processing helix chain 'A' and resid 1772 through 1797 removed outlier: 3.612A pdb=" N GLU A1795 " --> pdb=" O ILE A1791 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1806 removed outlier: 3.773A pdb=" N LYS A1803 " --> pdb=" O GLY A1800 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY A1804 " --> pdb=" O CYS A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1828 removed outlier: 4.098A pdb=" N LEU A1825 " --> pdb=" O ARG A1821 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A1826 " --> pdb=" O LEU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1843 removed outlier: 3.871A pdb=" N LEU A1839 " --> pdb=" O ASP A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1850 through 1862 removed outlier: 4.104A pdb=" N CYS A1862 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing helix chain 'A' and resid 1869 through 1880 removed outlier: 4.602A pdb=" N GLU A1875 " --> pdb=" O GLU A1871 " (cutoff:3.500A) Processing helix chain 'A' and resid 1898 through 1902 removed outlier: 3.929A pdb=" N LYS A1901 " --> pdb=" O ASP A1898 " (cutoff:3.500A) Processing helix chain 'A' and resid 1903 through 1907 removed outlier: 3.741A pdb=" N SER A1906 " --> pdb=" O PRO A1903 " (cutoff:3.500A) Processing helix chain 'A' and resid 1921 through 1933 removed outlier: 3.917A pdb=" N LEU A1925 " --> pdb=" O PHE A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1941 Processing helix chain 'A' and resid 1958 through 1972 removed outlier: 3.723A pdb=" N GLU A1962 " --> pdb=" O LEU A1958 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A1964 " --> pdb=" O SER A1960 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ALA A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN A1968 " --> pdb=" O GLN A1964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 1994 Processing helix chain 'A' and resid 2012 through 2018 removed outlier: 3.634A pdb=" N LEU A2018 " --> pdb=" O ALA A2014 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2052 removed outlier: 4.360A pdb=" N LYS A2048 " --> pdb=" O GLY A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2084 removed outlier: 3.976A pdb=" N LEU A2081 " --> pdb=" O LEU A2077 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A2082 " --> pdb=" O GLN A2078 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY A2084 " --> pdb=" O TRP A2080 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2096 removed outlier: 3.877A pdb=" N TYR A2092 " --> pdb=" O PRO A2088 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 101 through 122 Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.702A pdb=" N ARG B 170 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 184 through 199 removed outlier: 3.661A pdb=" N SER B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.609A pdb=" N LEU B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 283 through 288 removed outlier: 6.126A pdb=" N TYR B 286 " --> pdb=" O ASN B 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 3.517A pdb=" N TYR C 175 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 217 Processing helix chain 'C' and resid 219 through 235 removed outlier: 3.668A pdb=" N MET C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 259 Processing helix chain 'C' and resid 265 through 273 removed outlier: 4.253A pdb=" N PHE C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 293 removed outlier: 3.752A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 removed outlier: 3.714A pdb=" N PHE C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 333 removed outlier: 3.790A pdb=" N MET C 331 " --> pdb=" O MET C 327 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 356 removed outlier: 3.512A pdb=" N LEU C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 370 Processing helix chain 'C' and resid 376 through 392 Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 420 through 430 removed outlier: 4.230A pdb=" N VAL C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 removed outlier: 3.893A pdb=" N LYS D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 47 Processing sheet with id=AA1, first strand: chain 'A' and resid 1739 through 1742 removed outlier: 4.065A pdb=" N THR A1724 " --> pdb=" O ALA A1714 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A1707 " --> pdb=" O HIS A1890 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A1892 " --> pdb=" O THR A1707 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A1916 " --> pdb=" O LEU A1891 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1976 through 1977 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 13 removed outlier: 7.339A pdb=" N ILE B 7 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ARG B 22 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS B 9 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS B 20 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLY B 11 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 18 " --> pdb=" O GLY B 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 16 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 68 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU B 81 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU B 66 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA5, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA6, first strand: chain 'D' and resid 7 through 8 730 hydrogen bonds defined for protein. 2115 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4667 1.34 - 1.46: 3153 1.46 - 1.59: 6705 1.59 - 1.71: 7 1.71 - 1.83: 104 Bond restraints: 14636 Sorted by residual: bond pdb=" OG1 TPO B 161 " pdb=" P TPO B 161 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" O2P TPO B 161 " pdb=" P TPO B 161 " ideal model delta sigma weight residual 1.528 1.606 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O3P TPO B 161 " pdb=" P TPO B 161 " ideal model delta sigma weight residual 1.528 1.605 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O3 PO4 D 101 " pdb=" P PO4 D 101 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.21e+00 bond pdb=" O4 PO4 D 101 " pdb=" P PO4 D 101 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.41e+00 ... (remaining 14631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 19610 2.33 - 4.67: 232 4.67 - 7.00: 30 7.00 - 9.34: 6 9.34 - 11.67: 1 Bond angle restraints: 19879 Sorted by residual: angle pdb=" C LEU A1129 " pdb=" CA LEU A1129 " pdb=" CB LEU A1129 " ideal model delta sigma weight residual 115.89 109.58 6.31 1.32e+00 5.74e-01 2.28e+01 angle pdb=" N GLY A1814 " pdb=" CA GLY A1814 " pdb=" C GLY A1814 " ideal model delta sigma weight residual 112.34 120.35 -8.01 2.04e+00 2.40e-01 1.54e+01 angle pdb=" CB TPO B 161 " pdb=" OG1 TPO B 161 " pdb=" P TPO B 161 " ideal model delta sigma weight residual 119.31 107.64 11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C CYS C 167 " pdb=" N SER C 168 " pdb=" CA SER C 168 " ideal model delta sigma weight residual 121.54 128.08 -6.54 1.91e+00 2.74e-01 1.17e+01 angle pdb=" CA GLY A1744 " pdb=" C GLY A1744 " pdb=" O GLY A1744 " ideal model delta sigma weight residual 120.75 117.40 3.35 1.03e+00 9.43e-01 1.06e+01 ... (remaining 19874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 8029 16.97 - 33.93: 728 33.93 - 50.90: 106 50.90 - 67.87: 23 67.87 - 84.83: 10 Dihedral angle restraints: 8896 sinusoidal: 3579 harmonic: 5317 Sorted by residual: dihedral pdb=" CA GLY A 955 " pdb=" C GLY A 955 " pdb=" N SER A 956 " pdb=" CA SER A 956 " ideal model delta harmonic sigma weight residual 180.00 -150.39 -29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA ILE B 155 " pdb=" C ILE B 155 " pdb=" N PRO B 156 " pdb=" CA PRO B 156 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ILE A2050 " pdb=" C ILE A2050 " pdb=" N MET A2051 " pdb=" CA MET A2051 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 8893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1286 0.028 - 0.057: 675 0.057 - 0.085: 218 0.085 - 0.114: 88 0.114 - 0.142: 18 Chirality restraints: 2285 Sorted by residual: chirality pdb=" CB ILE B 10 " pdb=" CA ILE B 10 " pdb=" CG1 ILE B 10 " pdb=" CG2 ILE B 10 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ASP A1050 " pdb=" N ASP A1050 " pdb=" C ASP A1050 " pdb=" CB ASP A1050 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA PRO A1919 " pdb=" N PRO A1919 " pdb=" C PRO A1919 " pdb=" CB PRO A1919 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 2282 not shown) Planarity restraints: 2526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 183 " -0.050 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO B 184 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 184 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 184 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A2113 " -0.010 2.00e-02 2.50e+03 1.40e-02 3.95e+00 pdb=" CG TYR A2113 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A2113 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A2113 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A2113 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A2113 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A2113 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A2113 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 155 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B 156 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " -0.026 5.00e-02 4.00e+02 ... (remaining 2523 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1177 2.74 - 3.28: 14544 3.28 - 3.82: 22418 3.82 - 4.36: 26600 4.36 - 4.90: 46508 Nonbonded interactions: 111247 Sorted by model distance: nonbonded pdb=" O MET C 327 " pdb=" OG1 THR C 330 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASN A1236 " pdb=" NE2 GLN A1717 " model vdw 2.209 3.120 nonbonded pdb=" OD1 ASP B 101 " pdb=" OG SER B 103 " model vdw 2.233 3.040 nonbonded pdb=" OG SER A1625 " pdb=" OG SER A1920 " model vdw 2.242 3.040 nonbonded pdb=" NH2 ARG A1586 " pdb=" O HIS A1686 " model vdw 2.263 3.120 ... (remaining 111242 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.005 0.115 14637 Z= 0.204 Angle : 0.661 11.669 19881 Z= 0.352 Chirality : 0.040 0.142 2285 Planarity : 0.005 0.074 2526 Dihedral : 13.213 84.834 5443 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.18), residues: 1792 helix: -1.10 (0.15), residues: 985 sheet: -2.54 (0.45), residues: 99 loop : -2.82 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 800 TYR 0.033 0.001 TYR A2113 PHE 0.016 0.001 PHE A1100 TRP 0.024 0.002 TRP B 244 HIS 0.004 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00451 (14636) covalent geometry : angle 0.66052 (19879) SS BOND : bond 0.00075 ( 1) SS BOND : angle 2.84157 ( 2) hydrogen bonds : bond 0.13890 ( 730) hydrogen bonds : angle 5.62055 ( 2115) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.555 Fit side-chains REVERT: A 700 ASP cc_start: 0.8097 (t0) cc_final: 0.7826 (m-30) REVERT: A 762 GLN cc_start: 0.5885 (mt0) cc_final: 0.5501 (pt0) REVERT: A 948 SER cc_start: 0.8182 (m) cc_final: 0.7917 (t) REVERT: A 1817 GLN cc_start: 0.6600 (tp40) cc_final: 0.6224 (pt0) REVERT: A 1840 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7440 (tppt) REVERT: A 1920 SER cc_start: 0.8573 (m) cc_final: 0.8285 (t) REVERT: A 1990 GLU cc_start: 0.6359 (mt-10) cc_final: 0.6081 (mt-10) REVERT: A 1994 LYS cc_start: 0.7432 (mtmm) cc_final: 0.7206 (mmtp) REVERT: A 2074 GLU cc_start: 0.8648 (tp30) cc_final: 0.8115 (tp30) REVERT: B 8 GLU cc_start: 0.7068 (pt0) cc_final: 0.6396 (pm20) REVERT: B 34 LYS cc_start: 0.7725 (tttp) cc_final: 0.7155 (tmtt) REVERT: B 77 TYR cc_start: 0.7048 (m-80) cc_final: 0.6781 (m-80) REVERT: B 136 ILE cc_start: 0.9107 (pt) cc_final: 0.8679 (mt) REVERT: B 269 ILE cc_start: 0.8023 (mm) cc_final: 0.7802 (mt) REVERT: C 328 GLU cc_start: 0.8115 (tp30) cc_final: 0.7528 (tp30) REVERT: D 23 MET cc_start: 0.7702 (mtp) cc_final: 0.7328 (mtm) REVERT: D 45 ASN cc_start: 0.6692 (t0) cc_final: 0.6378 (m-40) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.1306 time to fit residues: 56.4367 Evaluate side-chains 170 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A 749 GLN A 771 GLN A 821 GLN A 871 HIS A1200 GLN A1674 GLN ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 132 GLN C 367 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.160786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138774 restraints weight = 19474.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140688 restraints weight = 14166.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141429 restraints weight = 12325.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.141896 restraints weight = 10152.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142141 restraints weight = 9969.978| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14637 Z= 0.143 Angle : 0.627 8.501 19881 Z= 0.309 Chirality : 0.039 0.135 2285 Planarity : 0.005 0.065 2526 Dihedral : 4.979 58.938 1960 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.53 % Allowed : 10.58 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.20), residues: 1792 helix: 0.18 (0.16), residues: 1005 sheet: -1.99 (0.50), residues: 97 loop : -2.28 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 805 TYR 0.016 0.001 TYR A2113 PHE 0.014 0.001 PHE A1100 TRP 0.019 0.001 TRP D 54 HIS 0.008 0.001 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00328 (14636) covalent geometry : angle 0.62605 (19879) SS BOND : bond 0.01365 ( 1) SS BOND : angle 3.83784 ( 2) hydrogen bonds : bond 0.04263 ( 730) hydrogen bonds : angle 4.31351 ( 2115) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.560 Fit side-chains REVERT: A 948 SER cc_start: 0.8203 (m) cc_final: 0.7920 (t) REVERT: A 997 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7512 (t-90) REVERT: A 1817 GLN cc_start: 0.6697 (tp40) cc_final: 0.6473 (pt0) REVERT: A 1933 TYR cc_start: 0.6393 (m-80) cc_final: 0.5929 (m-10) REVERT: A 2074 GLU cc_start: 0.8447 (tp30) cc_final: 0.7985 (tp30) REVERT: B 8 GLU cc_start: 0.6709 (pt0) cc_final: 0.6398 (pm20) REVERT: B 136 ILE cc_start: 0.9108 (pt) cc_final: 0.8734 (mt) REVERT: D 23 MET cc_start: 0.7741 (mtp) cc_final: 0.7343 (mtm) REVERT: D 42 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7839 (mt-10) outliers start: 24 outliers final: 16 residues processed: 222 average time/residue: 0.1103 time to fit residues: 37.5888 Evaluate side-chains 185 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 11 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 173 optimal weight: 0.0570 chunk 110 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1761 GLN A1874 ASN B 60 HIS B 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134711 restraints weight = 18951.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136800 restraints weight = 13728.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138121 restraints weight = 10931.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139292 restraints weight = 9336.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139886 restraints weight = 8285.285| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14637 Z= 0.119 Angle : 0.557 8.905 19881 Z= 0.274 Chirality : 0.038 0.131 2285 Planarity : 0.004 0.067 2526 Dihedral : 4.673 57.739 1960 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 2.61 % Allowed : 10.90 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.21), residues: 1792 helix: 0.82 (0.17), residues: 1002 sheet: -1.11 (0.54), residues: 94 loop : -1.96 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 805 TYR 0.015 0.001 TYR C 368 PHE 0.014 0.001 PHE A1100 TRP 0.013 0.001 TRP B 228 HIS 0.005 0.001 HIS A 809 Details of bonding type rmsd covalent geometry : bond 0.00279 (14636) covalent geometry : angle 0.55662 (19879) SS BOND : bond 0.00648 ( 1) SS BOND : angle 1.59911 ( 2) hydrogen bonds : bond 0.03700 ( 730) hydrogen bonds : angle 3.92288 ( 2115) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.400 Fit side-chains REVERT: A 948 SER cc_start: 0.8212 (m) cc_final: 0.7943 (t) REVERT: A 997 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7575 (t-90) REVERT: A 1840 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7590 (ttmt) REVERT: A 1933 TYR cc_start: 0.6263 (OUTLIER) cc_final: 0.5898 (m-10) REVERT: A 2074 GLU cc_start: 0.8426 (tp30) cc_final: 0.7926 (tp30) REVERT: B 136 ILE cc_start: 0.9114 (pt) cc_final: 0.8792 (mt) REVERT: D 23 MET cc_start: 0.7600 (mtp) cc_final: 0.7370 (mtm) outliers start: 41 outliers final: 21 residues processed: 208 average time/residue: 0.1077 time to fit residues: 34.5391 Evaluate side-chains 178 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1920 SER Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 163 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 122 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A 771 GLN A1761 GLN A1823 GLN A1827 GLN B 132 GLN C 235 GLN D 45 ASN D 52 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135716 restraints weight = 18968.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.138275 restraints weight = 13668.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138926 restraints weight = 10600.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139658 restraints weight = 9209.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140063 restraints weight = 8377.042| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14637 Z= 0.116 Angle : 0.547 8.960 19881 Z= 0.269 Chirality : 0.038 0.130 2285 Planarity : 0.004 0.068 2526 Dihedral : 4.512 57.647 1960 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.64 % Rotamer: Outliers : 2.61 % Allowed : 13.13 % Favored : 84.26 % 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: -0.14 (0.21), residues: 1792 helix: 1.11 (0.17), residues: 1004 sheet: -1.31 (0.53), residues: 98 loop : -1.73 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1821 TYR 0.014 0.001 TYR A 685 PHE 0.014 0.001 PHE A1100 TRP 0.015 0.001 TRP D 54 HIS 0.004 0.001 HIS A 809 Details of bonding type rmsd covalent geometry : bond 0.00271 (14636) covalent geometry : angle 0.54707 (19879) SS BOND : bond 0.00443 ( 1) SS BOND : angle 0.77295 ( 2) hydrogen bonds : bond 0.03470 ( 730) hydrogen bonds : angle 3.76567 ( 2115) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.535 Fit side-chains REVERT: A 948 SER cc_start: 0.8197 (m) cc_final: 0.7909 (t) REVERT: A 997 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7589 (t-90) REVERT: A 1823 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7090 (tp-100) REVERT: A 1840 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7739 (tppt) REVERT: A 1933 TYR cc_start: 0.6270 (OUTLIER) cc_final: 0.5900 (m-10) REVERT: A 2074 GLU cc_start: 0.8458 (tp30) cc_final: 0.7961 (tp30) REVERT: B 136 ILE cc_start: 0.9132 (pt) cc_final: 0.8764 (mt) REVERT: D 23 MET cc_start: 0.7694 (mtp) cc_final: 0.7401 (mtm) REVERT: D 70 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6873 (ttm170) outliers start: 41 outliers final: 26 residues processed: 200 average time/residue: 0.1064 time to fit residues: 32.4601 Evaluate side-chains 186 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1823 GLN Chi-restraints excluded: chain A residue 1920 SER Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 131 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 110 optimal weight: 0.0670 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 128 optimal weight: 0.0570 chunk 14 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.157602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135889 restraints weight = 18913.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137953 restraints weight = 13622.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139401 restraints weight = 10824.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140476 restraints weight = 9161.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141115 restraints weight = 8156.284| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14637 Z= 0.112 Angle : 0.538 8.335 19881 Z= 0.263 Chirality : 0.038 0.137 2285 Planarity : 0.004 0.066 2526 Dihedral : 4.413 57.514 1960 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 2.61 % Allowed : 13.38 % Favored : 84.00 % 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: 0.07 (0.21), residues: 1792 helix: 1.26 (0.17), residues: 1005 sheet: -0.79 (0.58), residues: 88 loop : -1.69 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1868 TYR 0.009 0.001 TYR A 685 PHE 0.012 0.001 PHE A1100 TRP 0.011 0.001 TRP D 54 HIS 0.004 0.001 HIS A 809 Details of bonding type rmsd covalent geometry : bond 0.00261 (14636) covalent geometry : angle 0.53768 (19879) SS BOND : bond 0.00229 ( 1) SS BOND : angle 1.12975 ( 2) hydrogen bonds : bond 0.03369 ( 730) hydrogen bonds : angle 3.67191 ( 2115) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.494 Fit side-chains REVERT: A 783 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: A 948 SER cc_start: 0.8220 (m) cc_final: 0.7929 (t) REVERT: A 997 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7579 (t-90) REVERT: A 1382 ARG cc_start: 0.6426 (ptt180) cc_final: 0.6071 (ptp90) REVERT: A 1933 TYR cc_start: 0.6265 (OUTLIER) cc_final: 0.5911 (m-10) REVERT: A 2074 GLU cc_start: 0.8440 (tp30) cc_final: 0.7922 (tp30) REVERT: B 51 GLU cc_start: 0.6489 (tt0) cc_final: 0.5839 (pt0) REVERT: B 70 LEU cc_start: 0.7591 (mt) cc_final: 0.7382 (tp) REVERT: B 136 ILE cc_start: 0.9101 (pt) cc_final: 0.8736 (mt) REVERT: C 277 TYR cc_start: 0.8378 (m-80) cc_final: 0.8096 (m-80) REVERT: D 23 MET cc_start: 0.7620 (mtp) cc_final: 0.7365 (mtm) REVERT: D 70 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.6874 (ttm170) outliers start: 41 outliers final: 28 residues processed: 193 average time/residue: 0.1074 time to fit residues: 31.8677 Evaluate side-chains 192 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1920 SER Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 26 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 128 optimal weight: 0.0670 chunk 121 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A1827 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133317 restraints weight = 18922.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135398 restraints weight = 13816.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136871 restraints weight = 11026.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.137706 restraints weight = 9375.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138562 restraints weight = 8409.723| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14637 Z= 0.144 Angle : 0.563 7.405 19881 Z= 0.275 Chirality : 0.039 0.143 2285 Planarity : 0.004 0.069 2526 Dihedral : 4.473 56.481 1960 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.97 % Rotamer: Outliers : 2.68 % Allowed : 14.09 % Favored : 83.24 % 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: 0.11 (0.21), residues: 1792 helix: 1.26 (0.17), residues: 1011 sheet: -1.29 (0.55), residues: 88 loop : -1.55 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1868 TYR 0.014 0.001 TYR A 685 PHE 0.012 0.001 PHE A1100 TRP 0.013 0.001 TRP A1272 HIS 0.005 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00351 (14636) covalent geometry : angle 0.56294 (19879) SS BOND : bond 0.00268 ( 1) SS BOND : angle 1.32378 ( 2) hydrogen bonds : bond 0.03694 ( 730) hydrogen bonds : angle 3.72106 ( 2115) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.522 Fit side-chains REVERT: A 783 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: A 948 SER cc_start: 0.8265 (m) cc_final: 0.7964 (t) REVERT: A 997 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7559 (t-90) REVERT: A 1382 ARG cc_start: 0.6462 (ptt180) cc_final: 0.6120 (ptp90) REVERT: A 1727 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8337 (mp) REVERT: A 1842 MET cc_start: 0.8719 (mmm) cc_final: 0.8474 (mmp) REVERT: A 1899 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8643 (mt) REVERT: A 1933 TYR cc_start: 0.6304 (OUTLIER) cc_final: 0.5947 (m-10) REVERT: A 2074 GLU cc_start: 0.8401 (tp30) cc_final: 0.7907 (tp30) REVERT: B 51 GLU cc_start: 0.6503 (tt0) cc_final: 0.5861 (pt0) REVERT: B 136 ILE cc_start: 0.9086 (pt) cc_final: 0.8703 (mt) REVERT: C 277 TYR cc_start: 0.8382 (m-80) cc_final: 0.8036 (m-80) REVERT: D 23 MET cc_start: 0.7605 (mtp) cc_final: 0.7340 (mtm) REVERT: D 70 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6918 (ttm170) outliers start: 42 outliers final: 30 residues processed: 193 average time/residue: 0.1084 time to fit residues: 32.3187 Evaluate side-chains 191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 1906 SER Chi-restraints excluded: chain A residue 1920 SER Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 164 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A1761 GLN D 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137971 restraints weight = 19429.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140846 restraints weight = 12939.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142832 restraints weight = 9772.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144086 restraints weight = 8043.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145060 restraints weight = 7008.405| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14637 Z= 0.115 Angle : 0.535 7.044 19881 Z= 0.263 Chirality : 0.038 0.131 2285 Planarity : 0.004 0.064 2526 Dihedral : 4.388 56.939 1960 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 2.42 % Allowed : 14.66 % Favored : 82.92 % 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: 0.30 (0.21), residues: 1792 helix: 1.41 (0.17), residues: 1012 sheet: -0.79 (0.56), residues: 94 loop : -1.52 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1868 TYR 0.010 0.001 TYR A 685 PHE 0.011 0.001 PHE A1100 TRP 0.014 0.001 TRP D 54 HIS 0.003 0.001 HIS A 809 Details of bonding type rmsd covalent geometry : bond 0.00273 (14636) covalent geometry : angle 0.53504 (19879) SS BOND : bond 0.00205 ( 1) SS BOND : angle 1.25146 ( 2) hydrogen bonds : bond 0.03358 ( 730) hydrogen bonds : angle 3.63232 ( 2115) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.583 Fit side-chains REVERT: A 783 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: A 948 SER cc_start: 0.8229 (m) cc_final: 0.7915 (t) REVERT: A 997 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7513 (t-90) REVERT: A 1382 ARG cc_start: 0.6425 (ptt180) cc_final: 0.6073 (ptp90) REVERT: A 1842 MET cc_start: 0.8734 (mmm) cc_final: 0.8502 (mmp) REVERT: A 1899 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8657 (mt) REVERT: A 1933 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5929 (m-10) REVERT: A 2074 GLU cc_start: 0.8427 (tp30) cc_final: 0.7922 (tp30) REVERT: B 51 GLU cc_start: 0.6491 (tt0) cc_final: 0.5846 (pt0) REVERT: B 136 ILE cc_start: 0.9098 (pt) cc_final: 0.8695 (mt) REVERT: C 277 TYR cc_start: 0.8383 (m-80) cc_final: 0.7956 (m-80) REVERT: D 23 MET cc_start: 0.7647 (mtp) cc_final: 0.7360 (mtm) REVERT: D 70 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6811 (ttm170) outliers start: 38 outliers final: 28 residues processed: 188 average time/residue: 0.1070 time to fit residues: 30.9477 Evaluate side-chains 186 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 1920 SER Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 64 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 174 optimal weight: 0.0040 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 123 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A1207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.158561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137057 restraints weight = 18807.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139040 restraints weight = 14060.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139771 restraints weight = 11569.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141057 restraints weight = 9734.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141309 restraints weight = 8461.044| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14637 Z= 0.108 Angle : 0.525 6.736 19881 Z= 0.258 Chirality : 0.037 0.137 2285 Planarity : 0.004 0.071 2526 Dihedral : 4.320 57.513 1960 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.87 % Rotamer: Outliers : 2.42 % Allowed : 14.60 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1792 helix: 1.54 (0.17), residues: 1011 sheet: -0.65 (0.57), residues: 84 loop : -1.41 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1868 TYR 0.010 0.001 TYR A 685 PHE 0.011 0.001 PHE A1100 TRP 0.016 0.001 TRP D 54 HIS 0.003 0.001 HIS A 809 Details of bonding type rmsd covalent geometry : bond 0.00255 (14636) covalent geometry : angle 0.52507 (19879) SS BOND : bond 0.00201 ( 1) SS BOND : angle 1.21387 ( 2) hydrogen bonds : bond 0.03188 ( 730) hydrogen bonds : angle 3.58165 ( 2115) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.516 Fit side-chains REVERT: A 783 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: A 948 SER cc_start: 0.8180 (m) cc_final: 0.7947 (t) REVERT: A 997 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7617 (t-90) REVERT: A 1382 ARG cc_start: 0.6428 (ptt180) cc_final: 0.6087 (ptp90) REVERT: A 1727 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 1823 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7151 (tm-30) REVERT: A 1842 MET cc_start: 0.8739 (mmm) cc_final: 0.8502 (mmp) REVERT: A 1899 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8640 (mt) REVERT: A 1933 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5947 (m-10) REVERT: A 2074 GLU cc_start: 0.8413 (tp30) cc_final: 0.7904 (tp30) REVERT: B 51 GLU cc_start: 0.6505 (tt0) cc_final: 0.5810 (pt0) REVERT: B 136 ILE cc_start: 0.9098 (pt) cc_final: 0.8656 (mt) REVERT: C 277 TYR cc_start: 0.8350 (m-80) cc_final: 0.7912 (m-80) REVERT: D 23 MET cc_start: 0.7659 (mtp) cc_final: 0.7290 (mtm) REVERT: D 70 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6783 (ttm170) outliers start: 38 outliers final: 30 residues processed: 185 average time/residue: 0.1077 time to fit residues: 30.8133 Evaluate side-chains 186 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 1920 SER Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 145 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** 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 = 0.3820 r_free = 0.3820 target = 0.156979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135563 restraints weight = 18867.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137232 restraints weight = 13791.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138218 restraints weight = 10974.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139309 restraints weight = 9491.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139519 restraints weight = 8490.934| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14637 Z= 0.123 Angle : 0.538 6.605 19881 Z= 0.264 Chirality : 0.038 0.141 2285 Planarity : 0.004 0.066 2526 Dihedral : 4.326 57.160 1960 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.25 % Favored : 94.64 % Rotamer: Outliers : 2.49 % Allowed : 14.72 % Favored : 82.79 % 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: 0.51 (0.21), residues: 1792 helix: 1.55 (0.17), residues: 1012 sheet: -0.81 (0.56), residues: 94 loop : -1.37 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1868 TYR 0.014 0.001 TYR A 685 PHE 0.011 0.001 PHE A1100 TRP 0.016 0.001 TRP D 54 HIS 0.004 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00297 (14636) covalent geometry : angle 0.53739 (19879) SS BOND : bond 0.00215 ( 1) SS BOND : angle 1.29871 ( 2) hydrogen bonds : bond 0.03348 ( 730) hydrogen bonds : angle 3.60760 ( 2115) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.533 Fit side-chains REVERT: A 783 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: A 948 SER cc_start: 0.8198 (m) cc_final: 0.7973 (t) REVERT: A 997 HIS cc_start: 0.8160 (OUTLIER) cc_final: 0.7602 (t-90) REVERT: A 1382 ARG cc_start: 0.6400 (ptt180) cc_final: 0.6123 (ptp90) REVERT: A 1727 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8318 (mp) REVERT: A 1823 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7149 (tm-30) REVERT: A 1899 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8637 (mt) REVERT: A 1933 TYR cc_start: 0.6287 (OUTLIER) cc_final: 0.5977 (m-10) REVERT: A 2074 GLU cc_start: 0.8391 (tp30) cc_final: 0.7887 (tp30) REVERT: B 51 GLU cc_start: 0.6484 (tt0) cc_final: 0.5817 (pt0) REVERT: B 136 ILE cc_start: 0.8920 (pt) cc_final: 0.8528 (mt) REVERT: C 277 TYR cc_start: 0.8350 (m-80) cc_final: 0.7892 (m-80) REVERT: C 367 HIS cc_start: 0.7669 (t70) cc_final: 0.7469 (t-170) REVERT: D 23 MET cc_start: 0.7592 (mtp) cc_final: 0.7315 (mtm) REVERT: D 70 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6832 (ttm170) outliers start: 39 outliers final: 31 residues processed: 183 average time/residue: 0.1113 time to fit residues: 31.3169 Evaluate side-chains 195 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 1920 SER Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 138 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1717 GLN C 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140897 restraints weight = 18865.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140488 restraints weight = 21424.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141510 restraints weight = 19924.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141948 restraints weight = 14969.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142210 restraints weight = 13462.320| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14637 Z= 0.119 Angle : 0.534 6.570 19881 Z= 0.262 Chirality : 0.038 0.135 2285 Planarity : 0.004 0.065 2526 Dihedral : 4.312 57.179 1960 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.19 % Favored : 94.70 % Rotamer: Outliers : 2.36 % Allowed : 14.79 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1792 helix: 1.58 (0.17), residues: 1012 sheet: -1.14 (0.52), residues: 104 loop : -1.29 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.014 0.001 TYR A 685 PHE 0.011 0.001 PHE A1100 TRP 0.017 0.001 TRP D 54 HIS 0.003 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00287 (14636) covalent geometry : angle 0.53368 (19879) SS BOND : bond 0.00191 ( 1) SS BOND : angle 1.28217 ( 2) hydrogen bonds : bond 0.03309 ( 730) hydrogen bonds : angle 3.58966 ( 2115) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.608 Fit side-chains REVERT: A 783 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: A 948 SER cc_start: 0.8249 (m) cc_final: 0.8039 (t) REVERT: A 997 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7531 (t-90) REVERT: A 1727 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8401 (mp) REVERT: A 1823 GLN cc_start: 0.7424 (tm-30) cc_final: 0.7022 (tm-30) REVERT: A 1899 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8622 (mt) REVERT: A 1933 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.5946 (m-10) REVERT: A 2074 GLU cc_start: 0.8335 (tp30) cc_final: 0.7850 (tp30) REVERT: B 51 GLU cc_start: 0.6381 (tt0) cc_final: 0.5783 (pt0) REVERT: C 277 TYR cc_start: 0.8302 (m-80) cc_final: 0.7858 (m-80) REVERT: C 367 HIS cc_start: 0.7535 (t70) cc_final: 0.7321 (t-170) REVERT: D 70 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7025 (ttm170) outliers start: 37 outliers final: 30 residues processed: 179 average time/residue: 0.1133 time to fit residues: 31.0662 Evaluate side-chains 187 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 1920 SER Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 142 optimal weight: 0.0770 chunk 134 optimal weight: 3.9990 chunk 66 optimal weight: 0.0050 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** 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 = 0.3836 r_free = 0.3836 target = 0.158449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141288 restraints weight = 18816.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140755 restraints weight = 21364.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141969 restraints weight = 19543.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142323 restraints weight = 15096.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143646 restraints weight = 13236.908| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14637 Z= 0.106 Angle : 0.526 6.591 19881 Z= 0.259 Chirality : 0.037 0.133 2285 Planarity : 0.004 0.063 2526 Dihedral : 4.249 57.839 1960 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.63 % Favored : 95.26 % Rotamer: Outliers : 2.23 % Allowed : 15.23 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.21), residues: 1792 helix: 1.65 (0.17), residues: 1013 sheet: -0.70 (0.55), residues: 94 loop : -1.33 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 699 TYR 0.013 0.001 TYR A 685 PHE 0.011 0.001 PHE A1100 TRP 0.018 0.001 TRP D 54 HIS 0.003 0.001 HIS A 809 Details of bonding type rmsd covalent geometry : bond 0.00250 (14636) covalent geometry : angle 0.52587 (19879) SS BOND : bond 0.00174 ( 1) SS BOND : angle 1.22718 ( 2) hydrogen bonds : bond 0.03113 ( 730) hydrogen bonds : angle 3.53896 ( 2115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2105.68 seconds wall clock time: 37 minutes 14.37 seconds (2234.37 seconds total)