Starting phenix.real_space_refine on Mon Mar 18 09:24:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxk_30912/03_2024/7dxk_30912_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxk_30912/03_2024/7dxk_30912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxk_30912/03_2024/7dxk_30912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxk_30912/03_2024/7dxk_30912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxk_30912/03_2024/7dxk_30912_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxk_30912/03_2024/7dxk_30912_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 13129 2.51 5 N 3524 2.21 5 O 3709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ASP 736": "OD1" <-> "OD2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 827": "NH1" <-> "NH2" Residue "A ARG 853": "NH1" <-> "NH2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "A ASP 914": "OD1" <-> "OD2" Residue "A ASP 916": "OD1" <-> "OD2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 981": "NH1" <-> "NH2" Residue "A TYR 983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1257": "OE1" <-> "OE2" Residue "A GLU 1288": "OE1" <-> "OE2" Residue "A PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1544": "OD1" <-> "OD2" Residue "A GLU 1561": "OE1" <-> "OE2" Residue "A GLU 1565": "OE1" <-> "OE2" Residue "A ARG 1573": "NH1" <-> "NH2" Residue "A GLU 1594": "OE1" <-> "OE2" Residue "A GLU 1596": "OE1" <-> "OE2" Residue "A ARG 1604": "NH1" <-> "NH2" Residue "A ASP 1646": "OD1" <-> "OD2" Residue "A ARG 1677": "NH1" <-> "NH2" Residue "A ARG 1691": "NH1" <-> "NH2" Residue "A GLU 1694": "OE1" <-> "OE2" Residue "A TYR 1700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1709": "NH1" <-> "NH2" Residue "A ASP 1712": "OD1" <-> "OD2" Residue "A GLU 1733": "OE1" <-> "OE2" Residue "A ARG 1738": "NH1" <-> "NH2" Residue "A ARG 1789": "NH1" <-> "NH2" Residue "A ARG 1800": "NH1" <-> "NH2" Residue "A ASP 1802": "OD1" <-> "OD2" Residue "A PHE 1808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1817": "NH1" <-> "NH2" Residue "A ARG 1891": "NH1" <-> "NH2" Residue "A ASP 1934": "OD1" <-> "OD2" Residue "A ARG 1991": "NH1" <-> "NH2" Residue "A ARG 1998": "NH1" <-> "NH2" Residue "A ASP 2005": "OD1" <-> "OD2" Residue "A ARG 2011": "NH1" <-> "NH2" Residue "A GLU 2013": "OE1" <-> "OE2" Residue "A GLU 2030": "OE1" <-> "OE2" Residue "A ASP 2056": "OD1" <-> "OD2" Residue "A ARG 2059": "NH1" <-> "NH2" Residue "A GLU 2114": "OE1" <-> "OE2" Residue "A GLU 2135": "OE1" <-> "OE2" Residue "A PHE 2186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2203": "OD1" <-> "OD2" Residue "A TYR 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2389": "NH1" <-> "NH2" Residue "A ARG 2397": "NH1" <-> "NH2" Residue "A ARG 2406": "NH1" <-> "NH2" Residue "A ASP 2423": "OD1" <-> "OD2" Residue "A GLU 2430": "OE1" <-> "OE2" Residue "A GLU 2438": "OE1" <-> "OE2" Residue "A ARG 2457": "NH1" <-> "NH2" Residue "A ARG 2547": "NH1" <-> "NH2" Residue "A GLU 2553": "OE1" <-> "OE2" Residue "A GLU 2562": "OE1" <-> "OE2" Residue "A ASP 2574": "OD1" <-> "OD2" Residue "A ARG 2698": "NH1" <-> "NH2" Residue "A ASP 2705": "OD1" <-> "OD2" Residue "A GLU 2787": "OE1" <-> "OE2" Residue "A ASP 2804": "OD1" <-> "OD2" Residue "A GLU 2837": "OE1" <-> "OE2" Residue "A TYR 2871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2879": "OE1" <-> "OE2" Residue "A ASP 2901": "OD1" <-> "OD2" Residue "A ARG 2902": "NH1" <-> "NH2" Residue "A ARG 2910": "NH1" <-> "NH2" Residue "A GLU 2952": "OE1" <-> "OE2" Residue "A ASP 2959": "OD1" <-> "OD2" Residue "A ASP 2982": "OD1" <-> "OD2" Residue "A ASP 2988": "OD1" <-> "OD2" Residue "A TYR 3004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 343": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20491 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2353, 18458 Classifications: {'peptide': 2353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 106, 'TRANS': 2246} Chain breaks: 19 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2033 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 11.28, per 1000 atoms: 0.55 Number of scatterers: 20491 At special positions: 0 Unit cell: (139.05, 108, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 3709 8.00 N 3524 7.00 C 13129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.04 Simple disulfide: pdb=" SG CYS A 768 " - pdb=" SG CYS A 803 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 8.14 Conformation dependent library (CDL) restraints added in 4.0 seconds 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5014 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 91 through 108 Processing helix chain 'A' and resid 114 through 132 removed outlier: 3.527A pdb=" N SER A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.547A pdb=" N ARG A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 175 through 189 Processing helix chain 'A' and resid 190 through 193 removed outlier: 3.718A pdb=" N VAL A 193 " --> pdb=" O ALA A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 197 through 214 removed outlier: 3.707A pdb=" N TYR A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 236 Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 259 through 277 removed outlier: 3.629A pdb=" N ARG A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 304 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.821A pdb=" N LEU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.866A pdb=" N GLY A 398 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.710A pdb=" N HIS A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 722 Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 748 through 752 removed outlier: 3.550A pdb=" N TYR A 752 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 779 Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 799 through 802 Processing helix chain 'A' and resid 803 through 812 removed outlier: 3.716A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 834 removed outlier: 3.582A pdb=" N CYS A 819 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N MET A 831 " --> pdb=" O ARG A 827 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 851 Processing helix chain 'A' and resid 857 through 868 removed outlier: 3.783A pdb=" N ARG A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 872 through 883 removed outlier: 3.716A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 905 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.711A pdb=" N ASP A 914 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 931 Processing helix chain 'A' and resid 944 through 958 removed outlier: 3.560A pdb=" N ALA A 948 " --> pdb=" O ASP A 944 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1011 Processing helix chain 'A' and resid 1015 through 1032 removed outlier: 4.133A pdb=" N PHE A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A1024 " --> pdb=" O GLY A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1071 removed outlier: 4.054A pdb=" N ILE A1066 " --> pdb=" O MET A1062 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1096 through 1101 removed outlier: 3.801A pdb=" N SER A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1130 through 1153 removed outlier: 3.871A pdb=" N VAL A1134 " --> pdb=" O LEU A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1249 removed outlier: 3.712A pdb=" N LEU A1235 " --> pdb=" O SER A1231 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A1249 " --> pdb=" O ASN A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1274 Processing helix chain 'A' and resid 1275 through 1277 No H-bonds generated for 'chain 'A' and resid 1275 through 1277' Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1285 through 1296 removed outlier: 3.591A pdb=" N ILE A1289 " --> pdb=" O CYS A1285 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A1295 " --> pdb=" O GLY A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1315 removed outlier: 3.563A pdb=" N THR A1305 " --> pdb=" O PRO A1301 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A1306 " --> pdb=" O MET A1302 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N CYS A1307 " --> pdb=" O MET A1303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A1308 " --> pdb=" O ALA A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1370 Processing helix chain 'A' and resid 1421 through 1435 Processing helix chain 'A' and resid 1437 through 1454 removed outlier: 3.702A pdb=" N GLN A1441 " --> pdb=" O CYS A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1462 removed outlier: 3.802A pdb=" N LEU A1461 " --> pdb=" O TYR A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1480 Processing helix chain 'A' and resid 1489 through 1501 Processing helix chain 'A' and resid 1512 through 1526 removed outlier: 3.851A pdb=" N ILE A1516 " --> pdb=" O GLY A1512 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A1526 " --> pdb=" O GLY A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1544 Proline residue: A1540 - end of helix Processing helix chain 'A' and resid 1558 through 1574 removed outlier: 3.842A pdb=" N LEU A1574 " --> pdb=" O MET A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1595 removed outlier: 3.694A pdb=" N LYS A1593 " --> pdb=" O GLN A1589 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A1594 " --> pdb=" O GLN A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1616 Proline residue: A1612 - end of helix Processing helix chain 'A' and resid 1623 through 1637 Processing helix chain 'A' and resid 1645 through 1651 Processing helix chain 'A' and resid 1661 through 1682 removed outlier: 3.528A pdb=" N VAL A1665 " --> pdb=" O SER A1661 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A1678 " --> pdb=" O ALA A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1695 removed outlier: 3.740A pdb=" N VAL A1688 " --> pdb=" O THR A1684 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1695 " --> pdb=" O ARG A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1713 Processing helix chain 'A' and resid 1731 through 1753 removed outlier: 4.093A pdb=" N THR A1753 " --> pdb=" O GLU A1749 " (cutoff:3.500A) Processing helix chain 'A' and resid 1761 through 1785 Processing helix chain 'A' and resid 1788 through 1800 removed outlier: 3.943A pdb=" N THR A1792 " --> pdb=" O PHE A1788 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A1800 " --> pdb=" O THR A1796 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1822 Processing helix chain 'A' and resid 1826 through 1839 Processing helix chain 'A' and resid 1843 through 1852 Processing helix chain 'A' and resid 1885 through 1905 Processing helix chain 'A' and resid 1910 through 1919 Processing helix chain 'A' and resid 1920 through 1925 Processing helix chain 'A' and resid 1929 through 1940 Processing helix chain 'A' and resid 1943 through 1956 Processing helix chain 'A' and resid 1962 through 1973 Processing helix chain 'A' and resid 1977 through 1979 No H-bonds generated for 'chain 'A' and resid 1977 through 1979' Processing helix chain 'A' and resid 1980 through 1991 Processing helix chain 'A' and resid 1997 through 2018 removed outlier: 3.807A pdb=" N ALA A2018 " --> pdb=" O MET A2014 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2027 removed outlier: 3.545A pdb=" N GLN A2026 " --> pdb=" O SER A2022 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2042 Processing helix chain 'A' and resid 2043 through 2048 Processing helix chain 'A' and resid 2048 through 2062 removed outlier: 4.131A pdb=" N TYR A2052 " --> pdb=" O HIS A2048 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A2062 " --> pdb=" O PHE A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2105 Processing helix chain 'A' and resid 2112 through 2121 removed outlier: 3.697A pdb=" N ARG A2121 " --> pdb=" O GLU A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2127 through 2132 Processing helix chain 'A' and resid 2137 through 2139 No H-bonds generated for 'chain 'A' and resid 2137 through 2139' Processing helix chain 'A' and resid 2140 through 2155 Processing helix chain 'A' and resid 2158 through 2178 removed outlier: 4.209A pdb=" N GLU A2162 " --> pdb=" O SER A2158 " (cutoff:3.500A) Processing helix chain 'A' and resid 2196 through 2204 removed outlier: 3.982A pdb=" N LYS A2200 " --> pdb=" O ALA A2196 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A2204 " --> pdb=" O LYS A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2207 through 2228 Proline residue: A2215 - end of helix Processing helix chain 'A' and resid 2229 through 2231 No H-bonds generated for 'chain 'A' and resid 2229 through 2231' Processing helix chain 'A' and resid 2238 through 2240 No H-bonds generated for 'chain 'A' and resid 2238 through 2240' Processing helix chain 'A' and resid 2241 through 2263 Processing helix chain 'A' and resid 2267 through 2282 Processing helix chain 'A' and resid 2284 through 2292 Processing helix chain 'A' and resid 2296 through 2313 Processing helix chain 'A' and resid 2350 through 2369 removed outlier: 3.847A pdb=" N GLU A2357 " --> pdb=" O THR A2353 " (cutoff:3.500A) Processing helix chain 'A' and resid 2375 through 2380 removed outlier: 4.305A pdb=" N GLY A2379 " --> pdb=" O ARG A2376 " (cutoff:3.500A) Processing helix chain 'A' and resid 2384 through 2397 removed outlier: 3.638A pdb=" N ARG A2397 " --> pdb=" O ILE A2393 " (cutoff:3.500A) Processing helix chain 'A' and resid 2401 through 2406 Processing helix chain 'A' and resid 2408 through 2414 removed outlier: 3.769A pdb=" N TRP A2412 " --> pdb=" O PRO A2408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2434 through 2437 removed outlier: 3.805A pdb=" N GLN A2437 " --> pdb=" O GLU A2434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2434 through 2437' Processing helix chain 'A' and resid 2438 through 2453 removed outlier: 3.722A pdb=" N PHE A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2456 through 2471 removed outlier: 4.074A pdb=" N PHE A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A2471 " --> pdb=" O LEU A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2508 Processing helix chain 'A' and resid 2539 through 2558 removed outlier: 4.164A pdb=" N LEU A2543 " --> pdb=" O PHE A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2593 Processing helix chain 'A' and resid 2614 through 2621 Processing helix chain 'A' and resid 2663 through 2680 removed outlier: 4.070A pdb=" N CYS A2667 " --> pdb=" O ASP A2663 " (cutoff:3.500A) Processing helix chain 'A' and resid 2689 through 2704 Processing helix chain 'A' and resid 2705 through 2707 No H-bonds generated for 'chain 'A' and resid 2705 through 2707' Processing helix chain 'A' and resid 2709 through 2727 removed outlier: 3.699A pdb=" N PHE A2713 " --> pdb=" O GLU A2709 " (cutoff:3.500A) Processing helix chain 'A' and resid 2731 through 2749 Proline residue: A2740 - end of helix removed outlier: 3.626A pdb=" N LEU A2749 " --> pdb=" O ALA A2745 " (cutoff:3.500A) Processing helix chain 'A' and resid 2752 through 2767 Proline residue: A2758 - end of helix Processing helix chain 'A' and resid 2771 through 2786 Processing helix chain 'A' and resid 2795 through 2799 removed outlier: 3.586A pdb=" N LEU A2798 " --> pdb=" O ALA A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2800 through 2812 removed outlier: 3.852A pdb=" N GLY A2812 " --> pdb=" O SER A2808 " (cutoff:3.500A) Processing helix chain 'A' and resid 2823 through 2839 Processing helix chain 'A' and resid 2844 through 2860 removed outlier: 3.779A pdb=" N SER A2848 " --> pdb=" O GLY A2844 " (cutoff:3.500A) Processing helix chain 'A' and resid 2867 through 2884 Processing helix chain 'A' and resid 2888 through 2903 removed outlier: 3.833A pdb=" N ALA A2892 " --> pdb=" O SER A2888 " (cutoff:3.500A) Processing helix chain 'A' and resid 2907 through 2922 removed outlier: 3.857A pdb=" N MET A2922 " --> pdb=" O MET A2918 " (cutoff:3.500A) Processing helix chain 'A' and resid 2946 through 2963 Processing helix chain 'A' and resid 2965 through 2984 Proline residue: A2977 - end of helix removed outlier: 4.223A pdb=" N PHE A2984 " --> pdb=" O LEU A2980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2985 through 2996 removed outlier: 4.391A pdb=" N ILE A2989 " --> pdb=" O PRO A2985 " (cutoff:3.500A) Processing helix chain 'A' and resid 3005 through 3018 Processing helix chain 'A' and resid 3021 through 3039 Processing helix chain 'A' and resid 3044 through 3059 removed outlier: 3.518A pdb=" N ALA A3059 " --> pdb=" O PHE A3055 " (cutoff:3.500A) Processing helix chain 'A' and resid 3065 through 3067 No H-bonds generated for 'chain 'A' and resid 3065 through 3067' Processing helix chain 'A' and resid 3068 through 3073 Processing helix chain 'A' and resid 3080 through 3096 removed outlier: 3.598A pdb=" N ARG A3096 " --> pdb=" O THR A3092 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 64 through 80 removed outlier: 3.660A pdb=" N LEU B 80 " --> pdb=" O CYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 106 removed outlier: 3.791A pdb=" N ALA B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 136 removed outlier: 3.844A pdb=" N GLN B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 154 removed outlier: 4.010A pdb=" N ALA B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.962A pdb=" N ALA B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 194 Processing helix chain 'B' and resid 196 through 214 Processing helix chain 'B' and resid 260 through 280 removed outlier: 4.016A pdb=" N ASP B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 299 Processing helix chain 'B' and resid 315 through 332 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.513A pdb=" N ILE B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 362 1303 hydrogen bonds defined for protein. 3870 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: 7.71 Time building geometry restraints manager: 8.69 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: 6603 1.34 - 1.47: 4606 1.47 - 1.59: 9489 1.59 - 1.71: 0 1.71 - 1.84: 187 Bond restraints: 20885 Sorted by residual: bond pdb=" CG1 ILE A1002 " pdb=" CD1 ILE A1002 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.61e+00 bond pdb=" C VAL A 296 " pdb=" N PRO A 297 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.29e+00 bond pdb=" C ILE A2122 " pdb=" N PRO A2123 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.19e-02 7.06e+03 6.78e+00 bond pdb=" C VAL A 318 " pdb=" N PRO A 319 " ideal model delta sigma weight residual 1.337 1.357 -0.020 9.80e-03 1.04e+04 4.26e+00 bond pdb=" CB MET A2828 " pdb=" CG MET A2828 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.14e+00 ... (remaining 20880 not shown) Histogram of bond angle deviations from ideal: 96.63 - 104.62: 385 104.62 - 112.61: 11343 112.61 - 120.60: 10199 120.60 - 128.59: 6257 128.59 - 136.58: 190 Bond angle restraints: 28374 Sorted by residual: angle pdb=" N VAL A2514 " pdb=" CA VAL A2514 " pdb=" C VAL A2514 " ideal model delta sigma weight residual 113.10 104.81 8.29 9.70e-01 1.06e+00 7.30e+01 angle pdb=" N LEU B 63 " pdb=" CA LEU B 63 " pdb=" C LEU B 63 " ideal model delta sigma weight residual 109.81 121.05 -11.24 2.21e+00 2.05e-01 2.59e+01 angle pdb=" CA LEU A 852 " pdb=" CB LEU A 852 " pdb=" CG LEU A 852 " ideal model delta sigma weight residual 116.30 133.83 -17.53 3.50e+00 8.16e-02 2.51e+01 angle pdb=" C LEU A1130 " pdb=" N VAL A1131 " pdb=" CA VAL A1131 " ideal model delta sigma weight residual 120.43 124.97 -4.54 9.60e-01 1.09e+00 2.24e+01 angle pdb=" N VAL A2512 " pdb=" CA VAL A2512 " pdb=" C VAL A2512 " ideal model delta sigma weight residual 108.88 117.92 -9.04 2.16e+00 2.14e-01 1.75e+01 ... (remaining 28369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 11126 17.81 - 35.61: 1273 35.61 - 53.42: 225 53.42 - 71.23: 31 71.23 - 89.03: 25 Dihedral angle restraints: 12680 sinusoidal: 5006 harmonic: 7674 Sorted by residual: dihedral pdb=" CA LEU B 63 " pdb=" C LEU B 63 " pdb=" N PRO B 64 " pdb=" CA PRO B 64 " ideal model delta harmonic sigma weight residual 180.00 132.83 47.17 0 5.00e+00 4.00e-02 8.90e+01 dihedral pdb=" CA VAL A 296 " pdb=" C VAL A 296 " pdb=" N PRO A 297 " pdb=" CA PRO A 297 " ideal model delta harmonic sigma weight residual -180.00 -135.33 -44.67 0 5.00e+00 4.00e-02 7.98e+01 dihedral pdb=" CA SER A3062 " pdb=" C SER A3062 " pdb=" N PRO A3063 " pdb=" CA PRO A3063 " ideal model delta harmonic sigma weight residual -180.00 -143.40 -36.60 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2404 0.053 - 0.106: 787 0.106 - 0.158: 173 0.158 - 0.211: 23 0.211 - 0.264: 8 Chirality restraints: 3395 Sorted by residual: chirality pdb=" CB ILE A1490 " pdb=" CA ILE A1490 " pdb=" CG1 ILE A1490 " pdb=" CG2 ILE A1490 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA VAL A2512 " pdb=" N VAL A2512 " pdb=" C VAL A2512 " pdb=" CB VAL A2512 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE A2624 " pdb=" CA ILE A2624 " pdb=" CG1 ILE A2624 " pdb=" CG2 ILE A2624 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3392 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 63 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO B 64 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1138 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.19e+00 pdb=" C PHE A1138 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE A1138 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A1139 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1136 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C GLN A1136 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN A1136 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A1137 " 0.016 2.00e-02 2.50e+03 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4754 2.78 - 3.31: 19390 3.31 - 3.84: 34217 3.84 - 4.37: 38116 4.37 - 4.90: 64734 Nonbonded interactions: 161211 Sorted by model distance: nonbonded pdb=" OH TYR A 983 " pdb=" O GLN A1272 " model vdw 2.251 2.440 nonbonded pdb=" O SER A2614 " pdb=" OG SER A2617 " model vdw 2.262 2.440 nonbonded pdb=" O LEU A2400 " pdb=" OG1 THR A2426 " model vdw 2.270 2.440 nonbonded pdb=" O SER A2378 " pdb=" OG SER A2378 " model vdw 2.306 2.440 nonbonded pdb=" O MET A1647 " pdb=" OG SER A1651 " model vdw 2.312 2.440 ... (remaining 161206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 2.150 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 57.770 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.007 0.108 20885 Z= 0.450 Angle : 1.049 17.528 28374 Z= 0.565 Chirality : 0.055 0.264 3395 Planarity : 0.008 0.081 3576 Dihedral : 15.550 89.032 7660 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.24 % Favored : 94.60 % Rotamer: Outliers : 0.48 % Allowed : 11.24 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.13), residues: 2575 helix: -2.17 (0.09), residues: 1833 sheet: None (None), residues: 0 loop : -2.84 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 184 HIS 0.010 0.002 HIS A2616 PHE 0.029 0.002 PHE B 165 TYR 0.026 0.002 TYR B 298 ARG 0.005 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 523 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9026 (mmm) cc_final: 0.8410 (mmp) REVERT: A 145 GLU cc_start: 0.8488 (pp20) cc_final: 0.7901 (pp20) REVERT: A 874 ARG cc_start: 0.8697 (ptp-110) cc_final: 0.8302 (mtt90) REVERT: A 886 LEU cc_start: 0.7822 (tp) cc_final: 0.7437 (tt) REVERT: A 1235 LEU cc_start: 0.8439 (tp) cc_final: 0.8109 (tp) REVERT: A 1284 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8683 (mptt) REVERT: A 1356 MET cc_start: 0.7288 (tpt) cc_final: 0.6721 (tpp) REVERT: A 1563 GLN cc_start: 0.8181 (mt0) cc_final: 0.7894 (mp10) REVERT: A 1652 MET cc_start: 0.8750 (tpp) cc_final: 0.8110 (tpt) REVERT: A 1988 TYR cc_start: 0.7556 (m-10) cc_final: 0.7310 (m-10) REVERT: A 1998 ARG cc_start: 0.8439 (mmp-170) cc_final: 0.8195 (tpp-160) REVERT: A 2003 MET cc_start: 0.8112 (ttp) cc_final: 0.7883 (mmt) REVERT: A 2040 GLN cc_start: 0.8303 (mm110) cc_final: 0.7856 (mm110) REVERT: A 2179 LEU cc_start: 0.8325 (mt) cc_final: 0.7980 (mt) REVERT: A 2385 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8355 (p) REVERT: A 2447 TYR cc_start: 0.8789 (t80) cc_final: 0.8588 (t80) REVERT: A 2524 GLU cc_start: 0.7497 (pp20) cc_final: 0.7238 (tm-30) REVERT: A 2593 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8170 (pp) REVERT: A 2762 LEU cc_start: 0.9053 (tt) cc_final: 0.8451 (mm) REVERT: A 2839 TYR cc_start: 0.7432 (m-80) cc_final: 0.7215 (m-10) REVERT: A 2853 GLN cc_start: 0.9075 (mt0) cc_final: 0.8769 (pt0) REVERT: A 2879 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8587 (tm-30) REVERT: A 2883 LEU cc_start: 0.9148 (mm) cc_final: 0.8421 (mm) REVERT: A 2953 ARG cc_start: 0.7809 (mpt180) cc_final: 0.7464 (mtm180) REVERT: A 2990 MET cc_start: 0.8850 (tpt) cc_final: 0.7893 (tpp) REVERT: A 3001 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8132 (tm-30) REVERT: A 3031 TRP cc_start: 0.9470 (m100) cc_final: 0.8980 (m100) REVERT: A 3047 MET cc_start: 0.8292 (mmt) cc_final: 0.7912 (mpp) REVERT: A 3055 PHE cc_start: 0.9229 (t80) cc_final: 0.8853 (t80) REVERT: B 88 LEU cc_start: 0.8485 (mm) cc_final: 0.8226 (mm) REVERT: B 99 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7055 (tpp-160) REVERT: B 116 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7304 (mm-30) REVERT: B 130 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7853 (tpm170) REVERT: B 279 LEU cc_start: 0.8945 (tp) cc_final: 0.8675 (tp) outliers start: 11 outliers final: 3 residues processed: 533 average time/residue: 0.3581 time to fit residues: 282.3035 Evaluate side-chains 355 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 350 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 148 ASN A 221 GLN A 281 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS A 399 GLN A 796 ASN A1140 HIS A1352 HIS A1708 ASN A1742 GLN A1765 HIS A1841 HIS ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1921 GLN A1959 ASN A2026 GLN A2040 GLN ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2495 ASN A2555 GLN A2568 HIS ** A2669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2838 ASN B 82 HIS B 119 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20885 Z= 0.212 Angle : 0.678 10.071 28374 Z= 0.334 Chirality : 0.041 0.172 3395 Planarity : 0.005 0.063 3576 Dihedral : 5.472 41.334 2798 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 0.13 % Allowed : 4.35 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 2575 helix: -0.28 (0.11), residues: 1853 sheet: None (None), residues: 0 loop : -2.33 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A2454 HIS 0.015 0.001 HIS A 366 PHE 0.033 0.002 PHE B 165 TYR 0.028 0.002 TYR A 857 ARG 0.008 0.001 ARG A2057 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 471 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9051 (mmm) cc_final: 0.8629 (mmm) REVERT: A 145 GLU cc_start: 0.8421 (pp20) cc_final: 0.7924 (pp20) REVERT: A 787 MET cc_start: 0.8502 (mmm) cc_final: 0.8301 (mmm) REVERT: A 813 ASP cc_start: 0.6926 (t70) cc_final: 0.6377 (t0) REVERT: A 886 LEU cc_start: 0.7970 (tp) cc_final: 0.7464 (tt) REVERT: A 1102 ARG cc_start: 0.4550 (mpt180) cc_final: 0.4169 (mmt180) REVERT: A 1235 LEU cc_start: 0.8374 (tp) cc_final: 0.8143 (tp) REVERT: A 1284 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8724 (mptt) REVERT: A 1356 MET cc_start: 0.7194 (tpt) cc_final: 0.6564 (tpp) REVERT: A 1563 GLN cc_start: 0.8229 (mt0) cc_final: 0.8013 (mp10) REVERT: A 1988 TYR cc_start: 0.7421 (m-10) cc_final: 0.7046 (m-10) REVERT: A 1998 ARG cc_start: 0.8383 (mmp-170) cc_final: 0.8150 (tpp-160) REVERT: A 2040 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7909 (mm-40) REVERT: A 2176 VAL cc_start: 0.9262 (t) cc_final: 0.9061 (m) REVERT: A 2179 LEU cc_start: 0.8378 (mt) cc_final: 0.8071 (mt) REVERT: A 2201 LEU cc_start: 0.8875 (tp) cc_final: 0.8495 (tp) REVERT: A 2459 GLN cc_start: 0.7604 (mp10) cc_final: 0.7244 (mp10) REVERT: A 2524 GLU cc_start: 0.7799 (pp20) cc_final: 0.7296 (tm-30) REVERT: A 2762 LEU cc_start: 0.8879 (tt) cc_final: 0.8335 (mm) REVERT: A 2875 LEU cc_start: 0.9242 (tp) cc_final: 0.9025 (tp) REVERT: A 2922 MET cc_start: 0.7843 (ptp) cc_final: 0.7458 (ppp) REVERT: A 2990 MET cc_start: 0.8923 (tpt) cc_final: 0.7963 (tpp) REVERT: A 3001 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8132 (tm-30) REVERT: A 3031 TRP cc_start: 0.9454 (m100) cc_final: 0.8992 (m100) REVERT: A 3047 MET cc_start: 0.8340 (mmt) cc_final: 0.7877 (mpp) REVERT: A 3052 LEU cc_start: 0.9567 (tp) cc_final: 0.9069 (mt) REVERT: B 68 TRP cc_start: 0.7176 (t-100) cc_final: 0.6915 (t60) REVERT: B 88 LEU cc_start: 0.8659 (mm) cc_final: 0.8373 (mm) REVERT: B 99 ARG cc_start: 0.7658 (ttm170) cc_final: 0.6837 (tpp-160) REVERT: B 279 LEU cc_start: 0.8646 (tp) cc_final: 0.8440 (tp) outliers start: 3 outliers final: 0 residues processed: 474 average time/residue: 0.2683 time to fit residues: 199.7237 Evaluate side-chains 318 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 0.0000 chunk 73 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 256 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 322 GLN A 755 HIS A1150 HIS A1272 GLN ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 HIS A1834 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2367 GLN ** A2377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2820 HIS ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20885 Z= 0.281 Angle : 0.691 9.843 28374 Z= 0.342 Chirality : 0.042 0.154 3395 Planarity : 0.005 0.065 3576 Dihedral : 5.241 39.422 2798 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Rotamer: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2575 helix: 0.43 (0.12), residues: 1857 sheet: None (None), residues: 0 loop : -2.07 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 786 HIS 0.010 0.001 HIS A2771 PHE 0.031 0.002 PHE A2833 TYR 0.023 0.002 TYR A2737 ARG 0.014 0.001 ARG A2698 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9068 (mmm) cc_final: 0.8643 (mmm) REVERT: A 145 GLU cc_start: 0.8340 (pp20) cc_final: 0.7884 (pp20) REVERT: A 831 MET cc_start: 0.8293 (tpp) cc_final: 0.8020 (mmm) REVERT: A 868 LEU cc_start: 0.8864 (mt) cc_final: 0.8498 (mt) REVERT: A 886 LEU cc_start: 0.7929 (tp) cc_final: 0.7474 (tt) REVERT: A 1065 MET cc_start: 0.6091 (tpt) cc_final: 0.5886 (tpt) REVERT: A 1102 ARG cc_start: 0.4719 (mpt180) cc_final: 0.4167 (mmt180) REVERT: A 1235 LEU cc_start: 0.8364 (tp) cc_final: 0.8131 (tp) REVERT: A 1284 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8763 (mptt) REVERT: A 1356 MET cc_start: 0.7199 (tpt) cc_final: 0.6610 (tpp) REVERT: A 1570 MET cc_start: 0.8525 (mtm) cc_final: 0.8210 (mtt) REVERT: A 1988 TYR cc_start: 0.7301 (m-10) cc_final: 0.6964 (m-10) REVERT: A 2040 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7852 (mm110) REVERT: A 2176 VAL cc_start: 0.9269 (t) cc_final: 0.8995 (m) REVERT: A 2201 LEU cc_start: 0.8809 (tp) cc_final: 0.8540 (tp) REVERT: A 2524 GLU cc_start: 0.7868 (pp20) cc_final: 0.7367 (tm-30) REVERT: A 2696 VAL cc_start: 0.9341 (p) cc_final: 0.8524 (p) REVERT: A 2699 SER cc_start: 0.8168 (t) cc_final: 0.7832 (p) REVERT: A 2716 MET cc_start: 0.9309 (tpt) cc_final: 0.9100 (tpt) REVERT: A 2753 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8038 (tptp) REVERT: A 2762 LEU cc_start: 0.8906 (tt) cc_final: 0.8242 (mm) REVERT: A 2833 PHE cc_start: 0.8508 (m-80) cc_final: 0.8288 (m-80) REVERT: A 2854 MET cc_start: 0.7744 (mtt) cc_final: 0.7442 (mtp) REVERT: A 2875 LEU cc_start: 0.9164 (tp) cc_final: 0.8912 (tp) REVERT: A 2879 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8716 (tm-30) REVERT: A 2883 LEU cc_start: 0.9019 (mm) cc_final: 0.8688 (mm) REVERT: A 2992 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8704 (mmtm) REVERT: A 3001 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 3031 TRP cc_start: 0.9452 (m100) cc_final: 0.8780 (m100) REVERT: A 3047 MET cc_start: 0.8422 (mmt) cc_final: 0.7879 (mpp) REVERT: B 88 LEU cc_start: 0.8685 (mm) cc_final: 0.8373 (mm) REVERT: B 99 ARG cc_start: 0.7743 (ttm170) cc_final: 0.6947 (tpp-160) REVERT: B 279 LEU cc_start: 0.8809 (tp) cc_final: 0.8424 (tp) outliers start: 1 outliers final: 0 residues processed: 439 average time/residue: 0.3081 time to fit residues: 213.6291 Evaluate side-chains 322 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 159 optimal weight: 0.0770 chunk 238 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 ASN A1834 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2048 HIS ** A2259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2824 HIS B 77 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20885 Z= 0.230 Angle : 0.669 12.619 28374 Z= 0.328 Chirality : 0.042 0.174 3395 Planarity : 0.005 0.108 3576 Dihedral : 5.078 39.559 2798 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2575 helix: 0.81 (0.12), residues: 1855 sheet: None (None), residues: 0 loop : -1.94 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 184 HIS 0.008 0.001 HIS A2616 PHE 0.049 0.002 PHE A 128 TYR 0.017 0.001 TYR A 857 ARG 0.008 0.000 ARG A2057 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 435 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9072 (mmm) cc_final: 0.8506 (mmp) REVERT: A 145 GLU cc_start: 0.8392 (pp20) cc_final: 0.7902 (pp20) REVERT: A 210 THR cc_start: 0.9221 (p) cc_final: 0.8578 (p) REVERT: A 787 MET cc_start: 0.8370 (mmm) cc_final: 0.7726 (mmm) REVERT: A 831 MET cc_start: 0.8160 (tpp) cc_final: 0.7668 (tmm) REVERT: A 886 LEU cc_start: 0.7919 (tp) cc_final: 0.7492 (tt) REVERT: A 1065 MET cc_start: 0.6084 (tpt) cc_final: 0.5878 (tpt) REVERT: A 1102 ARG cc_start: 0.5189 (mpt180) cc_final: 0.4699 (mmt180) REVERT: A 1235 LEU cc_start: 0.8356 (tp) cc_final: 0.8055 (tp) REVERT: A 1284 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8750 (mptt) REVERT: A 1356 MET cc_start: 0.7200 (tpt) cc_final: 0.6570 (tpp) REVERT: A 1570 MET cc_start: 0.8472 (mtm) cc_final: 0.8174 (mtt) REVERT: A 1926 LEU cc_start: 0.8866 (mt) cc_final: 0.8479 (pp) REVERT: A 1932 VAL cc_start: 0.8045 (p) cc_final: 0.7773 (p) REVERT: A 1988 TYR cc_start: 0.7348 (m-10) cc_final: 0.6921 (m-10) REVERT: A 2003 MET cc_start: 0.6682 (mmt) cc_final: 0.5831 (mmt) REVERT: A 2040 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7823 (mm110) REVERT: A 2524 GLU cc_start: 0.7794 (pp20) cc_final: 0.7356 (tm-30) REVERT: A 2620 LEU cc_start: 0.9043 (pp) cc_final: 0.8830 (tt) REVERT: A 2696 VAL cc_start: 0.9392 (p) cc_final: 0.9144 (p) REVERT: A 2716 MET cc_start: 0.9303 (tpt) cc_final: 0.9050 (tpt) REVERT: A 2753 LYS cc_start: 0.8322 (mmtm) cc_final: 0.7948 (tptp) REVERT: A 2833 PHE cc_start: 0.8521 (m-80) cc_final: 0.8206 (m-80) REVERT: A 2854 MET cc_start: 0.7894 (mtt) cc_final: 0.7469 (mtp) REVERT: A 2875 LEU cc_start: 0.9175 (tp) cc_final: 0.8939 (tp) REVERT: A 2878 LEU cc_start: 0.9230 (mp) cc_final: 0.8801 (tp) REVERT: A 2879 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8731 (tm-30) REVERT: A 2990 MET cc_start: 0.8793 (tpt) cc_final: 0.8520 (mmm) REVERT: A 2992 LYS cc_start: 0.8993 (mmtm) cc_final: 0.8745 (mmtm) REVERT: A 3001 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8118 (tm-30) REVERT: A 3031 TRP cc_start: 0.9415 (m100) cc_final: 0.9069 (m100) REVERT: A 3032 VAL cc_start: 0.9582 (t) cc_final: 0.9344 (t) REVERT: A 3047 MET cc_start: 0.8517 (mmt) cc_final: 0.7996 (mpp) REVERT: B 88 LEU cc_start: 0.8602 (mm) cc_final: 0.8300 (mm) REVERT: B 99 ARG cc_start: 0.7721 (ttm170) cc_final: 0.6947 (tpp-160) REVERT: B 114 TYR cc_start: 0.7323 (p90) cc_final: 0.7013 (p90) REVERT: B 279 LEU cc_start: 0.8876 (tp) cc_final: 0.8506 (tp) outliers start: 1 outliers final: 0 residues processed: 436 average time/residue: 0.2948 time to fit residues: 205.6136 Evaluate side-chains 320 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1236 HIS ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2212 GLN ** A2259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2283 GLN A2348 ASN ** A2377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20885 Z= 0.192 Angle : 0.645 11.385 28374 Z= 0.312 Chirality : 0.040 0.162 3395 Planarity : 0.005 0.066 3576 Dihedral : 4.876 39.305 2798 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2575 helix: 1.05 (0.12), residues: 1855 sheet: None (None), residues: 0 loop : -1.88 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 184 HIS 0.008 0.001 HIS A2616 PHE 0.032 0.002 PHE A1475 TYR 0.042 0.002 TYR B 298 ARG 0.010 0.000 ARG A2057 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 448 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9061 (mmm) cc_final: 0.8495 (mmp) REVERT: A 145 GLU cc_start: 0.8314 (pp20) cc_final: 0.7871 (pp20) REVERT: A 210 THR cc_start: 0.9176 (p) cc_final: 0.8533 (p) REVERT: A 224 LEU cc_start: 0.8977 (tp) cc_final: 0.8759 (tp) REVERT: A 232 MET cc_start: 0.8659 (mmm) cc_final: 0.8183 (tpt) REVERT: A 269 SER cc_start: 0.8886 (m) cc_final: 0.8335 (p) REVERT: A 787 MET cc_start: 0.7995 (mmm) cc_final: 0.7475 (mmm) REVERT: A 886 LEU cc_start: 0.8128 (tp) cc_final: 0.7484 (tt) REVERT: A 1065 MET cc_start: 0.6053 (tpt) cc_final: 0.5845 (tpt) REVERT: A 1102 ARG cc_start: 0.5264 (mpt180) cc_final: 0.4843 (mmt180) REVERT: A 1284 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8709 (mptt) REVERT: A 1356 MET cc_start: 0.7100 (tpt) cc_final: 0.6567 (tpp) REVERT: A 1528 ARG cc_start: 0.6852 (mmm-85) cc_final: 0.6085 (mmp80) REVERT: A 1929 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7191 (mt-10) REVERT: A 1988 TYR cc_start: 0.7372 (m-10) cc_final: 0.6948 (m-10) REVERT: A 2040 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8044 (mm110) REVERT: A 2356 CYS cc_start: 0.8393 (p) cc_final: 0.8188 (p) REVERT: A 2358 MET cc_start: 0.9103 (mmm) cc_final: 0.8811 (mmm) REVERT: A 2447 TYR cc_start: 0.8481 (t80) cc_final: 0.8151 (t80) REVERT: A 2524 GLU cc_start: 0.7828 (pp20) cc_final: 0.7474 (tm-30) REVERT: A 2696 VAL cc_start: 0.9377 (p) cc_final: 0.9131 (p) REVERT: A 2753 LYS cc_start: 0.8313 (mmtm) cc_final: 0.7943 (tptp) REVERT: A 2833 PHE cc_start: 0.8566 (m-80) cc_final: 0.8345 (m-80) REVERT: A 2854 MET cc_start: 0.8066 (mtt) cc_final: 0.7520 (mtp) REVERT: A 2875 LEU cc_start: 0.9297 (tp) cc_final: 0.9088 (tp) REVERT: A 2878 LEU cc_start: 0.9263 (mp) cc_final: 0.8823 (tp) REVERT: A 2990 MET cc_start: 0.8799 (tpt) cc_final: 0.8459 (mmm) REVERT: A 2992 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8645 (mmtm) REVERT: A 3001 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8231 (tm-30) REVERT: A 3031 TRP cc_start: 0.9378 (m100) cc_final: 0.9052 (m100) REVERT: A 3032 VAL cc_start: 0.9586 (t) cc_final: 0.9340 (t) REVERT: A 3047 MET cc_start: 0.8475 (mmt) cc_final: 0.7801 (mmt) REVERT: B 68 TRP cc_start: 0.7450 (t-100) cc_final: 0.7225 (t-100) REVERT: B 99 ARG cc_start: 0.7708 (ttm170) cc_final: 0.6937 (tpp-160) REVERT: B 114 TYR cc_start: 0.7315 (p90) cc_final: 0.7020 (p90) REVERT: B 279 LEU cc_start: 0.8690 (tp) cc_final: 0.8377 (tp) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.3022 time to fit residues: 214.3957 Evaluate side-chains 331 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 GLN ** A2259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2283 GLN ** A2377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20885 Z= 0.249 Angle : 0.680 10.333 28374 Z= 0.330 Chirality : 0.042 0.371 3395 Planarity : 0.005 0.070 3576 Dihedral : 4.848 38.595 2798 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2575 helix: 1.14 (0.12), residues: 1857 sheet: None (None), residues: 0 loop : -1.82 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A2454 HIS 0.009 0.001 HIS A1236 PHE 0.038 0.002 PHE B 165 TYR 0.032 0.002 TYR A2737 ARG 0.005 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9060 (mmm) cc_final: 0.8487 (mmp) REVERT: A 145 GLU cc_start: 0.8383 (pp20) cc_final: 0.7921 (pp20) REVERT: A 210 THR cc_start: 0.9220 (p) cc_final: 0.8675 (p) REVERT: A 232 MET cc_start: 0.8725 (mmm) cc_final: 0.8204 (tpt) REVERT: A 269 SER cc_start: 0.8906 (m) cc_final: 0.8425 (p) REVERT: A 787 MET cc_start: 0.8124 (mmm) cc_final: 0.7704 (mmm) REVERT: A 886 LEU cc_start: 0.8091 (tp) cc_final: 0.7485 (tt) REVERT: A 1065 MET cc_start: 0.6141 (tpt) cc_final: 0.5915 (tpt) REVERT: A 1102 ARG cc_start: 0.5171 (mpt180) cc_final: 0.4713 (mmt180) REVERT: A 1284 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8681 (mptt) REVERT: A 1356 MET cc_start: 0.7194 (tpt) cc_final: 0.6646 (tpp) REVERT: A 1988 TYR cc_start: 0.7366 (m-10) cc_final: 0.6957 (m-10) REVERT: A 2014 MET cc_start: 0.8329 (ptm) cc_final: 0.7873 (ppp) REVERT: A 2040 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8066 (mm110) REVERT: A 2358 MET cc_start: 0.9120 (mmm) cc_final: 0.8786 (mmm) REVERT: A 2459 GLN cc_start: 0.7584 (mp10) cc_final: 0.7347 (mp10) REVERT: A 2524 GLU cc_start: 0.7883 (pp20) cc_final: 0.7513 (tm-30) REVERT: A 2677 ARG cc_start: 0.8467 (tmt170) cc_final: 0.8163 (tmt-80) REVERT: A 2696 VAL cc_start: 0.9363 (p) cc_final: 0.8988 (p) REVERT: A 2753 LYS cc_start: 0.8387 (mmtm) cc_final: 0.7996 (tptp) REVERT: A 2854 MET cc_start: 0.8193 (mtt) cc_final: 0.7715 (mtp) REVERT: A 2875 LEU cc_start: 0.9312 (tp) cc_final: 0.9090 (tp) REVERT: A 2883 LEU cc_start: 0.9137 (mm) cc_final: 0.8860 (mm) REVERT: A 2990 MET cc_start: 0.8805 (tpt) cc_final: 0.8493 (mmm) REVERT: A 2992 LYS cc_start: 0.9010 (mmtm) cc_final: 0.8665 (mmtm) REVERT: A 3001 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 3031 TRP cc_start: 0.9386 (m100) cc_final: 0.9066 (m100) REVERT: A 3032 VAL cc_start: 0.9583 (t) cc_final: 0.9325 (t) REVERT: A 3047 MET cc_start: 0.8481 (mmt) cc_final: 0.7775 (mmt) REVERT: B 88 LEU cc_start: 0.8537 (mm) cc_final: 0.8269 (mm) REVERT: B 99 ARG cc_start: 0.7728 (ttm170) cc_final: 0.6958 (tpp-160) REVERT: B 279 LEU cc_start: 0.8762 (tp) cc_final: 0.8433 (tp) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.3090 time to fit residues: 214.3189 Evaluate side-chains 308 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 143 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 251 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2872 HIS ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 20885 Z= 0.315 Angle : 0.713 10.740 28374 Z= 0.350 Chirality : 0.044 0.267 3395 Planarity : 0.005 0.072 3576 Dihedral : 4.913 38.371 2798 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 0.04 % Allowed : 1.89 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2575 helix: 1.12 (0.12), residues: 1855 sheet: None (None), residues: 0 loop : -1.75 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A2454 HIS 0.009 0.001 HIS A2616 PHE 0.031 0.002 PHE A 238 TYR 0.030 0.002 TYR A 354 ARG 0.010 0.001 ARG A2057 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 408 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9057 (mmm) cc_final: 0.8488 (mmp) REVERT: A 145 GLU cc_start: 0.8430 (pp20) cc_final: 0.7964 (pp20) REVERT: A 232 MET cc_start: 0.8769 (mmm) cc_final: 0.8256 (tpt) REVERT: A 269 SER cc_start: 0.8999 (m) cc_final: 0.8487 (p) REVERT: A 787 MET cc_start: 0.8313 (mmm) cc_final: 0.7767 (mmm) REVERT: A 886 LEU cc_start: 0.8147 (tp) cc_final: 0.7565 (tt) REVERT: A 1065 MET cc_start: 0.6178 (tpt) cc_final: 0.5928 (tpt) REVERT: A 1284 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8694 (mptt) REVERT: A 1356 MET cc_start: 0.7186 (tpt) cc_final: 0.6621 (tpp) REVERT: A 1613 MET cc_start: 0.8834 (tpp) cc_final: 0.8600 (tpp) REVERT: A 1619 MET cc_start: 0.8318 (mtp) cc_final: 0.8013 (mtp) REVERT: A 1988 TYR cc_start: 0.7322 (m-10) cc_final: 0.7052 (m-10) REVERT: A 2014 MET cc_start: 0.8078 (ptm) cc_final: 0.7664 (ppp) REVERT: A 2040 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8083 (mm110) REVERT: A 2358 MET cc_start: 0.9052 (mmm) cc_final: 0.8809 (mmm) REVERT: A 2459 GLN cc_start: 0.7693 (mp10) cc_final: 0.7351 (mp10) REVERT: A 2524 GLU cc_start: 0.8014 (pp20) cc_final: 0.7603 (tm-30) REVERT: A 2675 TYR cc_start: 0.8812 (m-10) cc_final: 0.8603 (m-80) REVERT: A 2696 VAL cc_start: 0.9207 (p) cc_final: 0.8836 (p) REVERT: A 2872 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.8421 (m90) REVERT: A 2875 LEU cc_start: 0.9279 (tp) cc_final: 0.9052 (tp) REVERT: A 2990 MET cc_start: 0.8753 (tpt) cc_final: 0.8016 (mmm) REVERT: A 2992 LYS cc_start: 0.9037 (mmtm) cc_final: 0.8699 (mmtm) REVERT: A 3001 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 3031 TRP cc_start: 0.9416 (m100) cc_final: 0.9053 (m100) REVERT: A 3032 VAL cc_start: 0.9580 (t) cc_final: 0.9331 (t) REVERT: A 3047 MET cc_start: 0.8682 (mmt) cc_final: 0.8188 (mmt) REVERT: B 88 LEU cc_start: 0.8481 (mm) cc_final: 0.8245 (mm) REVERT: B 99 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7004 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 409 average time/residue: 0.2949 time to fit residues: 192.4138 Evaluate side-chains 296 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 295 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 159 optimal weight: 0.0170 chunk 171 optimal weight: 0.2980 chunk 124 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 197 optimal weight: 0.3980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1533 HIS ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 GLN ** A2259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2283 GLN A2555 GLN ** A2669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20885 Z= 0.180 Angle : 0.673 13.245 28374 Z= 0.318 Chirality : 0.041 0.247 3395 Planarity : 0.004 0.063 3576 Dihedral : 4.753 39.059 2798 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2575 helix: 1.32 (0.12), residues: 1856 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 786 HIS 0.009 0.001 HIS A2824 PHE 0.026 0.001 PHE A 238 TYR 0.023 0.001 TYR A1768 ARG 0.007 0.000 ARG A2057 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9033 (mmm) cc_final: 0.8462 (mmp) REVERT: A 145 GLU cc_start: 0.8342 (pp20) cc_final: 0.7843 (pp20) REVERT: A 210 THR cc_start: 0.9181 (p) cc_final: 0.8576 (p) REVERT: A 224 LEU cc_start: 0.8971 (tp) cc_final: 0.8736 (tp) REVERT: A 232 MET cc_start: 0.8729 (mmm) cc_final: 0.8205 (tpt) REVERT: A 269 SER cc_start: 0.8884 (m) cc_final: 0.8326 (p) REVERT: A 886 LEU cc_start: 0.8053 (tp) cc_final: 0.7454 (tt) REVERT: A 1065 MET cc_start: 0.6192 (tpt) cc_final: 0.5975 (tpt) REVERT: A 1102 ARG cc_start: 0.5657 (mmt180) cc_final: 0.5422 (mmt180) REVERT: A 1235 LEU cc_start: 0.8319 (tp) cc_final: 0.7919 (tp) REVERT: A 1263 LEU cc_start: 0.8670 (tp) cc_final: 0.8391 (tp) REVERT: A 1284 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8664 (mptt) REVERT: A 1356 MET cc_start: 0.6964 (tpt) cc_final: 0.6415 (tpp) REVERT: A 1528 ARG cc_start: 0.6656 (mmm-85) cc_final: 0.5998 (mmp80) REVERT: A 1988 TYR cc_start: 0.7289 (m-10) cc_final: 0.6887 (m-10) REVERT: A 2014 MET cc_start: 0.8073 (ptm) cc_final: 0.7626 (ppp) REVERT: A 2040 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8080 (mm110) REVERT: A 2356 CYS cc_start: 0.8234 (p) cc_final: 0.7804 (p) REVERT: A 2357 GLU cc_start: 0.8232 (pm20) cc_final: 0.7894 (pm20) REVERT: A 2524 GLU cc_start: 0.7880 (pp20) cc_final: 0.7470 (tm-30) REVERT: A 2675 TYR cc_start: 0.8760 (m-10) cc_final: 0.8546 (m-10) REVERT: A 2696 VAL cc_start: 0.9123 (p) cc_final: 0.8790 (p) REVERT: A 2753 LYS cc_start: 0.8407 (mmtm) cc_final: 0.7993 (tptp) REVERT: A 2810 LEU cc_start: 0.8208 (mm) cc_final: 0.7954 (mm) REVERT: A 2854 MET cc_start: 0.6983 (mtp) cc_final: 0.6161 (mtp) REVERT: A 2864 GLU cc_start: 0.7318 (pt0) cc_final: 0.6624 (tm-30) REVERT: A 2879 GLU cc_start: 0.8471 (pp20) cc_final: 0.8003 (pp20) REVERT: A 2881 LEU cc_start: 0.9429 (mt) cc_final: 0.9228 (mt) REVERT: A 2990 MET cc_start: 0.8729 (tpt) cc_final: 0.7948 (mmm) REVERT: A 2992 LYS cc_start: 0.9000 (mmtm) cc_final: 0.8670 (mmtm) REVERT: A 3001 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 3031 TRP cc_start: 0.9367 (m100) cc_final: 0.8959 (m100) REVERT: A 3032 VAL cc_start: 0.9550 (t) cc_final: 0.9256 (t) REVERT: A 3047 MET cc_start: 0.8617 (mmt) cc_final: 0.8140 (mmt) REVERT: B 97 PHE cc_start: 0.8360 (m-80) cc_final: 0.8082 (m-80) REVERT: B 99 ARG cc_start: 0.7734 (ttm170) cc_final: 0.6944 (tpp-160) REVERT: B 147 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7545 (tm-30) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.3056 time to fit residues: 212.1947 Evaluate side-chains 318 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 234 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 71 optimal weight: 0.0470 chunk 211 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 overall best weight: 1.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1309 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2283 GLN ** A2377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20885 Z= 0.227 Angle : 0.684 13.012 28374 Z= 0.329 Chirality : 0.042 0.176 3395 Planarity : 0.005 0.115 3576 Dihedral : 4.741 37.585 2798 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.32 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2575 helix: 1.30 (0.12), residues: 1863 sheet: None (None), residues: 0 loop : -1.68 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 786 HIS 0.017 0.001 HIS A2771 PHE 0.051 0.002 PHE A 128 TYR 0.028 0.001 TYR A1768 ARG 0.010 0.000 ARG A2698 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9025 (mmm) cc_final: 0.8455 (mmp) REVERT: A 145 GLU cc_start: 0.8506 (pp20) cc_final: 0.7981 (pp20) REVERT: A 232 MET cc_start: 0.8788 (mmm) cc_final: 0.8241 (tpt) REVERT: A 269 SER cc_start: 0.8921 (m) cc_final: 0.8433 (p) REVERT: A 886 LEU cc_start: 0.8056 (tp) cc_final: 0.7487 (tt) REVERT: A 1102 ARG cc_start: 0.5712 (mmt180) cc_final: 0.5482 (mmt180) REVERT: A 1235 LEU cc_start: 0.8346 (tp) cc_final: 0.7944 (tp) REVERT: A 1356 MET cc_start: 0.7143 (tpt) cc_final: 0.6616 (tpp) REVERT: A 2024 MET cc_start: 0.8892 (ptp) cc_final: 0.8446 (ppp) REVERT: A 2137 ASN cc_start: 0.8187 (t0) cc_final: 0.7768 (t0) REVERT: A 2357 GLU cc_start: 0.8233 (pm20) cc_final: 0.7799 (pm20) REVERT: A 2447 TYR cc_start: 0.8589 (t80) cc_final: 0.8192 (t80) REVERT: A 2524 GLU cc_start: 0.7912 (pp20) cc_final: 0.7498 (tm-30) REVERT: A 2696 VAL cc_start: 0.9049 (p) cc_final: 0.8813 (p) REVERT: A 2699 SER cc_start: 0.7306 (p) cc_final: 0.5969 (p) REVERT: A 2732 GLU cc_start: 0.7567 (mp0) cc_final: 0.7319 (pm20) REVERT: A 2753 LYS cc_start: 0.8418 (mmtm) cc_final: 0.7995 (tptp) REVERT: A 2786 LEU cc_start: 0.9125 (mt) cc_final: 0.8909 (mt) REVERT: A 2834 TYR cc_start: 0.8110 (t80) cc_final: 0.7710 (t80) REVERT: A 2854 MET cc_start: 0.7421 (mtp) cc_final: 0.6403 (mtp) REVERT: A 2864 GLU cc_start: 0.7365 (pt0) cc_final: 0.6667 (tm-30) REVERT: A 2879 GLU cc_start: 0.8502 (pp20) cc_final: 0.8128 (pp20) REVERT: A 2990 MET cc_start: 0.8722 (tpt) cc_final: 0.7985 (mmm) REVERT: A 2992 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8696 (mmtm) REVERT: A 3001 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8132 (tm-30) REVERT: A 3031 TRP cc_start: 0.9427 (m100) cc_final: 0.9099 (m100) REVERT: A 3032 VAL cc_start: 0.9544 (t) cc_final: 0.9267 (t) REVERT: A 3047 MET cc_start: 0.8599 (mmt) cc_final: 0.8130 (mmt) REVERT: B 97 PHE cc_start: 0.8351 (m-80) cc_final: 0.8121 (m-80) REVERT: B 99 ARG cc_start: 0.7744 (ttm170) cc_final: 0.6973 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.3230 time to fit residues: 221.4015 Evaluate side-chains 302 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 GLN A2128 ASN ** A2259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20885 Z= 0.303 Angle : 0.727 12.976 28374 Z= 0.354 Chirality : 0.044 0.175 3395 Planarity : 0.005 0.114 3576 Dihedral : 4.868 38.597 2798 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2575 helix: 1.20 (0.12), residues: 1867 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 68 HIS 0.008 0.001 HIS A2616 PHE 0.040 0.002 PHE A 128 TYR 0.030 0.002 TYR B 298 ARG 0.006 0.000 ARG A2698 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9037 (mmm) cc_final: 0.8549 (mmp) REVERT: A 269 SER cc_start: 0.8940 (m) cc_final: 0.8495 (p) REVERT: A 886 LEU cc_start: 0.8137 (tp) cc_final: 0.7592 (tt) REVERT: A 1235 LEU cc_start: 0.8279 (tp) cc_final: 0.7894 (tp) REVERT: A 1356 MET cc_start: 0.7216 (tpt) cc_final: 0.6673 (tpp) REVERT: A 1746 ILE cc_start: 0.9319 (mt) cc_final: 0.9072 (tp) REVERT: A 2456 SER cc_start: 0.8314 (p) cc_final: 0.7837 (p) REVERT: A 2459 GLN cc_start: 0.7655 (mp10) cc_final: 0.7286 (mp10) REVERT: A 2696 VAL cc_start: 0.9153 (p) cc_final: 0.8715 (p) REVERT: A 2699 SER cc_start: 0.7653 (p) cc_final: 0.6081 (p) REVERT: A 2753 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8051 (tptp) REVERT: A 2834 TYR cc_start: 0.8032 (t80) cc_final: 0.7623 (t80) REVERT: A 2879 GLU cc_start: 0.8566 (pp20) cc_final: 0.8194 (pp20) REVERT: A 2906 HIS cc_start: 0.7300 (p-80) cc_final: 0.7032 (p-80) REVERT: A 2953 ARG cc_start: 0.8995 (mtm180) cc_final: 0.8565 (mtm-85) REVERT: A 2990 MET cc_start: 0.8715 (tpt) cc_final: 0.7980 (mmm) REVERT: A 2992 LYS cc_start: 0.9039 (mmtm) cc_final: 0.8654 (mmtm) REVERT: A 3001 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 3031 TRP cc_start: 0.9418 (m100) cc_final: 0.9057 (m100) REVERT: A 3032 VAL cc_start: 0.9547 (t) cc_final: 0.9284 (t) REVERT: A 3047 MET cc_start: 0.8669 (mmt) cc_final: 0.8353 (mmt) REVERT: B 88 LEU cc_start: 0.8542 (mm) cc_final: 0.8276 (mm) REVERT: B 99 ARG cc_start: 0.7829 (ttm170) cc_final: 0.7042 (tpp-160) REVERT: B 114 TYR cc_start: 0.7300 (p90) cc_final: 0.7063 (p90) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.2928 time to fit residues: 189.0488 Evaluate side-chains 295 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 57 optimal weight: 0.0060 chunk 207 optimal weight: 0.9990 chunk 86 optimal weight: 0.0870 chunk 212 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1453 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2283 GLN ** A2568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2872 HIS A2886 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.124670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100803 restraints weight = 43138.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.101341 restraints weight = 35768.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.101456 restraints weight = 27459.914| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20885 Z= 0.182 Angle : 0.679 12.443 28374 Z= 0.322 Chirality : 0.041 0.159 3395 Planarity : 0.005 0.109 3576 Dihedral : 4.721 38.789 2798 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2575 helix: 1.36 (0.12), residues: 1863 sheet: None (None), residues: 0 loop : -1.62 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2454 HIS 0.010 0.001 HIS A2824 PHE 0.045 0.002 PHE A 128 TYR 0.021 0.001 TYR A1768 ARG 0.007 0.000 ARG A2698 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4421.00 seconds wall clock time: 80 minutes 48.64 seconds (4848.64 seconds total)