Starting phenix.real_space_refine on Fri Mar 6 08:17:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oty_13069/03_2026/7oty_13069.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oty_13069/03_2026/7oty_13069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oty_13069/03_2026/7oty_13069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oty_13069/03_2026/7oty_13069.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oty_13069/03_2026/7oty_13069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oty_13069/03_2026/7oty_13069.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 191 5.16 5 Cl 1 4.86 5 C 18628 2.51 5 N 4905 2.21 5 O 5308 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29034 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 28900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3636, 28900 Classifications: {'peptide': 3636} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 158, 'TRANS': 3477} Chain breaks: 16 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 126 Chain: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 134 Unusual residues: {'1IX': 1} Classifications: {'peptide': 20, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19, None: 1} Not linked: pdbres="UNK A6020 " pdbres="1IX A6101 " Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 6.18, per 1000 atoms: 0.21 Number of scatterers: 29034 At special positions: 0 Unit cell: (125.184, 153.872, 182.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 191 16.00 F 1 9.00 O 5308 8.00 N 4905 7.00 C 18628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7012 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 4 sheets defined 71.2% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.573A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 49 through 52 Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.842A pdb=" N VAL A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.014A pdb=" N ASP A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 removed outlier: 4.226A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 97 removed outlier: 4.241A pdb=" N GLU A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 85 " --> pdb=" O CYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 3.986A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 146 removed outlier: 4.019A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N MET A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.524A pdb=" N TYR A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.489A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.811A pdb=" N GLU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.981A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.819A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.945A pdb=" N LEU A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.837A pdb=" N ASP A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 289 through 302 removed outlier: 3.966A pdb=" N LEU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 330 removed outlier: 4.093A pdb=" N ALA A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.706A pdb=" N SER A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 377 removed outlier: 3.585A pdb=" N LYS A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 396 removed outlier: 4.192A pdb=" N PHE A 383 " --> pdb=" O LYS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 409 through 424 removed outlier: 4.281A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 472 through 493 removed outlier: 4.294A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 559 through 578 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.701A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 removed outlier: 4.114A pdb=" N PHE A 642 " --> pdb=" O GLN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 660 Processing helix chain 'A' and resid 663 through 679 removed outlier: 4.380A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 724 through 734 Processing helix chain 'A' and resid 737 through 759 removed outlier: 4.376A pdb=" N LEU A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.611A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 794 through 800 removed outlier: 3.808A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY A 798 " --> pdb=" O CYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 862 Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 872 through 877 Processing helix chain 'A' and resid 910 through 921 removed outlier: 3.839A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 945 Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.607A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.757A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 997 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1007 through 1015 removed outlier: 3.896A pdb=" N LEU A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1044 Processing helix chain 'A' and resid 1045 through 1050 removed outlier: 3.668A pdb=" N GLU A1050 " --> pdb=" O PRO A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1086 removed outlier: 3.640A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 3.586A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1117 No H-bonds generated for 'chain 'A' and resid 1115 through 1117' Processing helix chain 'A' and resid 1122 through 1141 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1164 through 1175 Processing helix chain 'A' and resid 1176 through 1178 No H-bonds generated for 'chain 'A' and resid 1176 through 1178' Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1215 Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1252 through 1273 Processing helix chain 'A' and resid 1277 through 1282 Processing helix chain 'A' and resid 1289 through 1299 removed outlier: 4.041A pdb=" N GLU A1299 " --> pdb=" O ALA A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1351 removed outlier: 3.588A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1359 removed outlier: 4.313A pdb=" N LEU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1378 removed outlier: 3.576A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1383 Processing helix chain 'A' and resid 1390 through 1409 Proline residue: A1396 - end of helix removed outlier: 3.730A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1421 Processing helix chain 'A' and resid 1424 through 1433 Processing helix chain 'A' and resid 1441 through 1462 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1476 through 1481 Processing helix chain 'A' and resid 1481 through 1487 Processing helix chain 'A' and resid 1488 through 1491 removed outlier: 4.246A pdb=" N ILE A1491 " --> pdb=" O TYR A1488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1488 through 1491' Processing helix chain 'A' and resid 1506 through 1520 Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.921A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1574 removed outlier: 5.877A pdb=" N GLU A1565 " --> pdb=" O SER A1561 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A1566 " --> pdb=" O LEU A1562 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1585 removed outlier: 4.620A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 Processing helix chain 'A' and resid 1611 through 1625 Processing helix chain 'A' and resid 1626 through 1630 Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.823A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 Processing helix chain 'A' and resid 1685 through 1693 Processing helix chain 'A' and resid 1695 through 1699 Processing helix chain 'A' and resid 1706 through 1722 Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1767 Processing helix chain 'A' and resid 1774 through 1786 Processing helix chain 'A' and resid 1790 through 1806 Processing helix chain 'A' and resid 1813 through 1822 removed outlier: 3.804A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1829 Processing helix chain 'A' and resid 1834 through 1853 removed outlier: 3.697A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1882 removed outlier: 4.143A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1885 through 1890 removed outlier: 4.210A pdb=" N VAL A1889 " --> pdb=" O PRO A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1925 removed outlier: 3.613A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A1925 " --> pdb=" O ASP A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1956 removed outlier: 4.112A pdb=" N ARG A1937 " --> pdb=" O LEU A1933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1974 removed outlier: 3.904A pdb=" N LYS A1973 " --> pdb=" O LYS A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2106 removed outlier: 3.796A pdb=" N ARG A2106 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2135 removed outlier: 3.678A pdb=" N LYS A2132 " --> pdb=" O PHE A2128 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 Processing helix chain 'A' and resid 2160 through 2172 removed outlier: 5.469A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2183 through 2196 Processing helix chain 'A' and resid 2205 through 2222 removed outlier: 3.853A pdb=" N ARG A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2268 through 2283 removed outlier: 4.089A pdb=" N VAL A2272 " --> pdb=" O LYS A2268 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A2273 " --> pdb=" O ASP A2269 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2306 removed outlier: 3.843A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2309 No H-bonds generated for 'chain 'A' and resid 2307 through 2309' Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.405A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A2333 " --> pdb=" O TYR A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2354 removed outlier: 3.842A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 removed outlier: 4.438A pdb=" N ILE A2361 " --> pdb=" O GLU A2357 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2377 removed outlier: 3.652A pdb=" N LEU A2374 " --> pdb=" O PHE A2371 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A2377 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.717A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2418 Processing helix chain 'A' and resid 2419 through 2425 removed outlier: 3.595A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2419 through 2425' Processing helix chain 'A' and resid 2429 through 2443 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 3.858A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2469 through 2484 removed outlier: 3.537A pdb=" N ASN A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2509 Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2526 Processing helix chain 'A' and resid 2534 through 2544 removed outlier: 3.808A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2546 No H-bonds generated for 'chain 'A' and resid 2545 through 2546' Processing helix chain 'A' and resid 2547 through 2549 No H-bonds generated for 'chain 'A' and resid 2547 through 2549' Processing helix chain 'A' and resid 2550 through 2564 removed outlier: 4.386A pdb=" N LEU A2555 " --> pdb=" O GLU A2551 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER A2556 " --> pdb=" O VAL A2552 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2799 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2824 removed outlier: 4.414A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS A2822 " --> pdb=" O LYS A2818 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A2823 " --> pdb=" O GLU A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 Processing helix chain 'A' and resid 2851 through 2865 removed outlier: 3.635A pdb=" N HIS A2865 " --> pdb=" O ILE A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 Processing helix chain 'A' and resid 2885 through 2899 removed outlier: 3.654A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2933 removed outlier: 3.598A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2947 removed outlier: 3.754A pdb=" N SER A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A2947 " --> pdb=" O PHE A2943 " (cutoff:3.500A) Processing helix chain 'A' and resid 2951 through 2962 removed outlier: 3.724A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A2956 " --> pdb=" O ILE A2952 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A2957 " --> pdb=" O THR A2953 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2977 Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 3.995A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (cutoff:3.500A) Processing helix chain 'A' and resid 3007 through 3014 Processing helix chain 'A' and resid 3040 through 3055 Processing helix chain 'A' and resid 3059 through 3070 removed outlier: 3.608A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3074 through 3080 Processing helix chain 'A' and resid 3082 through 3093 removed outlier: 3.699A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3117 Processing helix chain 'A' and resid 3121 through 3131 removed outlier: 3.681A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) Processing helix chain 'A' and resid 3132 through 3146 removed outlier: 3.513A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3167 removed outlier: 4.442A pdb=" N LEU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3194 Processing helix chain 'A' and resid 3230 through 3249 removed outlier: 3.554A pdb=" N CYS A3234 " --> pdb=" O LEU A3230 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3261 Processing helix chain 'A' and resid 3271 through 3287 removed outlier: 3.736A pdb=" N ARG A3282 " --> pdb=" O GLN A3278 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3307 removed outlier: 4.115A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3344 removed outlier: 4.160A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3345 through 3352 removed outlier: 3.969A pdb=" N LEU A3348 " --> pdb=" O PRO A3345 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3364 removed outlier: 3.596A pdb=" N ARG A3357 " --> pdb=" O GLU A3353 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A3359 " --> pdb=" O LYS A3355 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A3360 " --> pdb=" O ALA A3356 " (cutoff:3.500A) Processing helix chain 'A' and resid 3369 through 3393 Processing helix chain 'A' and resid 3406 through 3429 Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.578A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 Processing helix chain 'A' and resid 3464 through 3472 removed outlier: 3.799A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A3470 " --> pdb=" O PRO A3466 " (cutoff:3.500A) Processing helix chain 'A' and resid 3475 through 3479 removed outlier: 3.793A pdb=" N GLU A3478 " --> pdb=" O TYR A3475 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3488 removed outlier: 3.642A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A3488 " --> pdb=" O THR A3484 " (cutoff:3.500A) Processing helix chain 'A' and resid 3493 through 3497 Processing helix chain 'A' and resid 3498 through 3506 removed outlier: 3.869A pdb=" N ALA A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) Processing helix chain 'A' and resid 3514 through 3525 removed outlier: 3.931A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3538 Processing helix chain 'A' and resid 3547 through 3563 removed outlier: 5.017A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A3554 " --> pdb=" O LYS A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3576 Processing helix chain 'A' and resid 3577 through 3579 No H-bonds generated for 'chain 'A' and resid 3577 through 3579' Processing helix chain 'A' and resid 3580 through 3594 Processing helix chain 'A' and resid 3608 through 3617 removed outlier: 4.279A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3636 removed outlier: 3.943A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3639 through 3644 Processing helix chain 'A' and resid 3657 through 3671 removed outlier: 3.774A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3778 Processing helix chain 'A' and resid 3778 through 3784 Processing helix chain 'A' and resid 3812 through 3818 Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3846 removed outlier: 4.303A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3862 removed outlier: 3.500A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 3.644A pdb=" N SER A3876 " --> pdb=" O ARG A3872 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3890 removed outlier: 3.657A pdb=" N ARG A3885 " --> pdb=" O ASP A3881 " (cutoff:3.500A) Processing helix chain 'A' and resid 3893 through 3919 Processing helix chain 'A' and resid 3947 through 3952 Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 4.415A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 4.349A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4008 removed outlier: 4.301A pdb=" N LEU A3998 " --> pdb=" O ASP A3994 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A4008 " --> pdb=" O VAL A4004 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4011 No H-bonds generated for 'chain 'A' and resid 4009 through 4011' Processing helix chain 'A' and resid 4012 through 4022 removed outlier: 3.799A pdb=" N LYS A4022 " --> pdb=" O GLN A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4040 through 4051 removed outlier: 3.641A pdb=" N TYR A4046 " --> pdb=" O GLN A4042 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 Processing helix chain 'A' and resid 4073 through 4083 removed outlier: 3.556A pdb=" N GLY A4083 " --> pdb=" O ALA A4079 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4113 Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 6002 through 6010 Processing helix chain 'A' and resid 6010 through 6015 Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.840A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET A3796 " --> pdb=" O LEU A3800 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3809 through 3811 1621 hydrogen bonds defined for protein. 4800 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: 7.70 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.17: 1 1.17 - 1.33: 8629 1.33 - 1.50: 10060 1.50 - 1.67: 10640 1.67 - 1.83: 299 Bond restraints: 29629 Sorted by residual: bond pdb=" C30 1IX A6101 " pdb=" O29 1IX A6101 " ideal model delta sigma weight residual 1.406 1.000 0.406 2.00e-02 2.50e+03 4.12e+02 bond pdb=" C11 1IX A6101 " pdb="CL1 1IX A6101 " ideal model delta sigma weight residual 1.728 1.825 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C LEU A1068 " pdb=" N HIS A1069 " ideal model delta sigma weight residual 1.331 1.237 0.094 2.07e-02 2.33e+03 2.05e+01 bond pdb=" C12 1IX A6101 " pdb=" C13 1IX A6101 " ideal model delta sigma weight residual 1.379 1.465 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C20 1IX A6101 " pdb=" C21 1IX A6101 " ideal model delta sigma weight residual 1.416 1.336 0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 29624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 39867 5.16 - 10.33: 198 10.33 - 15.49: 6 15.49 - 20.66: 0 20.66 - 25.82: 1 Bond angle restraints: 40072 Sorted by residual: angle pdb=" C28 1IX A6101 " pdb=" O29 1IX A6101 " pdb=" C30 1IX A6101 " ideal model delta sigma weight residual 109.87 135.69 -25.82 3.00e+00 1.11e-01 7.41e+01 angle pdb=" N GLN A3494 " pdb=" CA GLN A3494 " pdb=" C GLN A3494 " ideal model delta sigma weight residual 110.97 102.87 8.10 1.09e+00 8.42e-01 5.52e+01 angle pdb=" N CYS A3492 " pdb=" CA CYS A3492 " pdb=" C CYS A3492 " ideal model delta sigma weight residual 107.73 119.81 -12.08 1.80e+00 3.09e-01 4.51e+01 angle pdb=" N LYS A3753 " pdb=" CA LYS A3753 " pdb=" C LYS A3753 " ideal model delta sigma weight residual 109.96 100.00 9.96 1.50e+00 4.44e-01 4.41e+01 angle pdb=" C LEU A1884 " pdb=" N PRO A1885 " pdb=" CA PRO A1885 " ideal model delta sigma weight residual 120.85 113.97 6.88 1.08e+00 8.57e-01 4.06e+01 ... (remaining 40067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 16199 17.82 - 35.63: 1554 35.63 - 53.45: 269 53.45 - 71.27: 42 71.27 - 89.08: 22 Dihedral angle restraints: 18086 sinusoidal: 7329 harmonic: 10757 Sorted by residual: dihedral pdb=" C CYS A3492 " pdb=" N CYS A3492 " pdb=" CA CYS A3492 " pdb=" CB CYS A3492 " ideal model delta harmonic sigma weight residual -122.60 -137.16 14.56 0 2.50e+00 1.60e-01 3.39e+01 dihedral pdb=" CA ILE A2785 " pdb=" C ILE A2785 " pdb=" N LYS A2786 " pdb=" CA LYS A2786 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU A3714 " pdb=" C GLU A3714 " pdb=" N TYR A3715 " pdb=" CA TYR A3715 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 18083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 4426 0.131 - 0.263: 133 0.263 - 0.394: 5 0.394 - 0.525: 0 0.525 - 0.656: 1 Chirality restraints: 4565 Sorted by residual: chirality pdb=" CA CYS A3492 " pdb=" N CYS A3492 " pdb=" C CYS A3492 " pdb=" CB CYS A3492 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA GLU A3693 " pdb=" N GLU A3693 " pdb=" C GLU A3693 " pdb=" CB GLU A3693 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA GLU A 775 " pdb=" N GLU A 775 " pdb=" C GLU A 775 " pdb=" CB GLU A 775 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 4562 not shown) Planarity restraints: 5084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A3684 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO A3685 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A3685 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A3685 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A3520 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" CD GLU A3520 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU A3520 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU A3520 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A2135 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO A2136 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A2136 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A2136 " 0.044 5.00e-02 4.00e+02 ... (remaining 5081 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 2 1.92 - 2.67: 760 2.67 - 3.41: 44121 3.41 - 4.16: 69106 4.16 - 4.90: 128498 Nonbonded interactions: 242487 Sorted by model distance: nonbonded pdb=" SG CYS A1255 " pdb=" CE2 PHE A3694 " model vdw 1.177 3.700 nonbonded pdb=" SG CYS A1255 " pdb=" CD2 PHE A3694 " model vdw 1.822 3.700 nonbonded pdb=" CB CYS A1255 " pdb=" CE2 PHE A3694 " model vdw 1.948 3.740 nonbonded pdb=" O TYR A1243 " pdb=" NH1 ARG A1245 " model vdw 2.079 3.120 nonbonded pdb=" O ALA A1078 " pdb=" OH TYR A1107 " model vdw 2.083 3.040 ... (remaining 242482 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=0.00 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.160 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 28.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.013 0.406 29629 Z= 0.541 Angle : 1.081 25.820 40072 Z= 0.578 Chirality : 0.061 0.656 4565 Planarity : 0.006 0.086 5084 Dihedral : 14.426 89.081 11074 Min Nonbonded Distance : 1.177 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.13 % Favored : 89.67 % Rotamer: Outliers : 0.75 % Allowed : 0.72 % Favored : 98.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.13), residues: 3602 helix: -0.82 (0.10), residues: 2377 sheet: -1.72 (0.70), residues: 54 loop : -2.65 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A3708 TYR 0.034 0.004 TYR A 366 PHE 0.037 0.004 PHE A4011 TRP 0.037 0.004 TRP A3686 HIS 0.022 0.003 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.01273 (29629) covalent geometry : angle 1.08143 (40072) hydrogen bonds : bond 0.10815 ( 1621) hydrogen bonds : angle 5.89655 ( 4800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 321 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1004 GLN cc_start: 0.7468 (mp10) cc_final: 0.7182 (mp10) REVERT: A 1155 ARG cc_start: 0.6858 (mtp-110) cc_final: 0.6588 (ttm-80) REVERT: A 1812 LEU cc_start: 0.7089 (mt) cc_final: 0.6812 (pp) REVERT: A 2185 MET cc_start: 0.8098 (tpt) cc_final: 0.7864 (tpt) REVERT: A 2269 ASP cc_start: 0.7067 (p0) cc_final: 0.6626 (p0) REVERT: A 2307 MET cc_start: 0.7921 (mpp) cc_final: 0.7046 (mpt) REVERT: A 2328 ARG cc_start: 0.7846 (tmt-80) cc_final: 0.7491 (tpt90) REVERT: A 3695 LEU cc_start: 0.4516 (OUTLIER) cc_final: 0.4293 (tt) REVERT: A 4039 TYR cc_start: 0.5627 (t80) cc_final: 0.5285 (t80) outliers start: 24 outliers final: 4 residues processed: 335 average time/residue: 0.6852 time to fit residues: 270.9254 Evaluate side-chains 249 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 244 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1863 PHE Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3695 LEU Chi-restraints excluded: chain A residue 3803 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 442 GLN ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 HIS A2305 ASN A2365 ASN A2432 GLN A2795 GLN A3326 GLN A3390 GLN A3577 GLN ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.182731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.141215 restraints weight = 44864.497| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.49 r_work: 0.3674 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29629 Z= 0.161 Angle : 0.715 9.229 40072 Z= 0.365 Chirality : 0.043 0.164 4565 Planarity : 0.005 0.058 5084 Dihedral : 5.912 47.011 3953 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.75 % Favored : 93.11 % Rotamer: Outliers : 1.31 % Allowed : 9.61 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.14), residues: 3602 helix: -0.02 (0.11), residues: 2389 sheet: -1.55 (0.72), residues: 51 loop : -2.29 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2425 TYR 0.032 0.002 TYR A3540 PHE 0.026 0.002 PHE A2823 TRP 0.022 0.002 TRP A3686 HIS 0.011 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00358 (29629) covalent geometry : angle 0.71519 (40072) hydrogen bonds : bond 0.04399 ( 1621) hydrogen bonds : angle 4.67734 ( 4800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 302 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 775 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: A 1214 GLU cc_start: 0.7407 (pm20) cc_final: 0.7176 (pp20) REVERT: A 1369 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7512 (mmt) REVERT: A 1712 ARG cc_start: 0.7440 (ptp90) cc_final: 0.7209 (ttp-110) REVERT: A 1812 LEU cc_start: 0.6963 (mt) cc_final: 0.6583 (pp) REVERT: A 2269 ASP cc_start: 0.7565 (p0) cc_final: 0.7127 (p0) REVERT: A 2307 MET cc_start: 0.6790 (mpp) cc_final: 0.5958 (mpt) REVERT: A 2328 ARG cc_start: 0.8352 (tmt-80) cc_final: 0.7561 (tpt90) REVERT: A 2374 LEU cc_start: 0.8393 (tp) cc_final: 0.8057 (tt) REVERT: A 2396 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7193 (tm) REVERT: A 2399 GLU cc_start: 0.8496 (mp0) cc_final: 0.8278 (mp0) REVERT: A 2443 MET cc_start: 0.7690 (ttm) cc_final: 0.7389 (ttm) REVERT: A 3176 MET cc_start: 0.9054 (mmm) cc_final: 0.8747 (mmm) REVERT: A 3474 ARG cc_start: 0.7330 (ptm-80) cc_final: 0.6644 (ptm-80) REVERT: A 3483 MET cc_start: 0.5586 (tpp) cc_final: 0.5327 (tpp) REVERT: A 4005 PHE cc_start: 0.7706 (t80) cc_final: 0.7461 (t80) outliers start: 42 outliers final: 11 residues processed: 315 average time/residue: 0.6112 time to fit residues: 228.3495 Evaluate side-chains 265 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 251 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1477 HIS Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3625 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 351 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 361 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 127 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 30.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 250 ASN ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 HIS A2234 ASN A2348 GLN ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4000 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.183153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.142135 restraints weight = 44888.181| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.58 r_work: 0.3711 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29629 Z= 0.149 Angle : 0.658 12.675 40072 Z= 0.332 Chirality : 0.041 0.160 4565 Planarity : 0.004 0.048 5084 Dihedral : 5.351 43.454 3945 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % Rotamer: Outliers : 2.35 % Allowed : 11.77 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3602 helix: 0.30 (0.11), residues: 2405 sheet: -1.52 (0.70), residues: 51 loop : -2.16 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 746 TYR 0.028 0.002 TYR A3540 PHE 0.022 0.002 PHE A1923 TRP 0.027 0.002 TRP A3588 HIS 0.008 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00345 (29629) covalent geometry : angle 0.65775 (40072) hydrogen bonds : bond 0.04024 ( 1621) hydrogen bonds : angle 4.42887 ( 4800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 281 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1011 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 1267 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7442 (t80) REVERT: A 1408 MET cc_start: 0.8221 (tpp) cc_final: 0.7981 (mpp) REVERT: A 1812 LEU cc_start: 0.6803 (mt) cc_final: 0.6496 (pp) REVERT: A 2160 TYR cc_start: 0.6214 (m-10) cc_final: 0.5996 (m-10) REVERT: A 2185 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7968 (tpt) REVERT: A 2217 ASN cc_start: 0.7996 (m-40) cc_final: 0.7739 (m110) REVERT: A 2269 ASP cc_start: 0.7439 (p0) cc_final: 0.7043 (p0) REVERT: A 2307 MET cc_start: 0.6742 (mpp) cc_final: 0.5760 (mpt) REVERT: A 2328 ARG cc_start: 0.8321 (tmt-80) cc_final: 0.7579 (tpt90) REVERT: A 2374 LEU cc_start: 0.8447 (tp) cc_final: 0.7992 (tt) REVERT: A 2396 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7341 (tm) REVERT: A 2443 MET cc_start: 0.7733 (ttm) cc_final: 0.7207 (ttm) REVERT: A 3176 MET cc_start: 0.9041 (mmm) cc_final: 0.8779 (mmm) REVERT: A 3483 MET cc_start: 0.5493 (OUTLIER) cc_final: 0.5140 (tpp) REVERT: A 3493 TRP cc_start: 0.6643 (OUTLIER) cc_final: 0.6441 (p90) REVERT: A 3613 MET cc_start: 0.1546 (ttt) cc_final: 0.1193 (ttt) REVERT: A 4005 PHE cc_start: 0.7529 (t80) cc_final: 0.7256 (t80) REVERT: A 4017 GLU cc_start: 0.7712 (pt0) cc_final: 0.7511 (mm-30) outliers start: 75 outliers final: 18 residues processed: 313 average time/residue: 0.6107 time to fit residues: 227.4144 Evaluate side-chains 273 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1477 HIS Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2185 MET Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3493 TRP Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 294 optimal weight: 0.9990 chunk 330 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 258 optimal weight: 0.3980 chunk 338 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 322 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1435 ASN A1477 HIS A2348 GLN A3093 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.183297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.142559 restraints weight = 44766.696| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.41 r_work: 0.3710 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29629 Z= 0.156 Angle : 0.666 16.906 40072 Z= 0.331 Chirality : 0.042 0.391 4565 Planarity : 0.004 0.048 5084 Dihedral : 5.202 42.268 3945 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.89 % Favored : 93.00 % Rotamer: Outliers : 2.29 % Allowed : 13.84 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3602 helix: 0.44 (0.11), residues: 2406 sheet: -1.36 (0.69), residues: 51 loop : -2.15 (0.19), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2254 TYR 0.028 0.002 TYR A3540 PHE 0.029 0.002 PHE A1805 TRP 0.043 0.002 TRP A3588 HIS 0.006 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00367 (29629) covalent geometry : angle 0.66591 (40072) hydrogen bonds : bond 0.03932 ( 1621) hydrogen bonds : angle 4.36664 ( 4800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 269 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 PHE cc_start: 0.5531 (p90) cc_final: 0.5305 (p90) REVERT: A 1011 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 1408 MET cc_start: 0.8144 (tpp) cc_final: 0.7920 (mpp) REVERT: A 1576 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: A 1584 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8202 (mp10) REVERT: A 1794 GLN cc_start: 0.8456 (mt0) cc_final: 0.8229 (mt0) REVERT: A 2126 MET cc_start: 0.5591 (ppp) cc_final: 0.5227 (ppp) REVERT: A 2217 ASN cc_start: 0.7989 (m-40) cc_final: 0.7697 (m110) REVERT: A 2307 MET cc_start: 0.6526 (mpp) cc_final: 0.5502 (mpt) REVERT: A 2328 ARG cc_start: 0.8292 (tmt-80) cc_final: 0.7583 (tpt90) REVERT: A 2443 MET cc_start: 0.7814 (ttm) cc_final: 0.7262 (ttm) REVERT: A 2799 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8257 (tm130) REVERT: A 3176 MET cc_start: 0.9030 (mmm) cc_final: 0.8774 (mmm) REVERT: A 3483 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.5080 (tpp) REVERT: A 3493 TRP cc_start: 0.6640 (OUTLIER) cc_final: 0.6428 (p90) REVERT: A 3609 MET cc_start: 0.3628 (ptp) cc_final: 0.2491 (mmm) REVERT: A 4005 PHE cc_start: 0.7671 (t80) cc_final: 0.7442 (t80) REVERT: A 4017 GLU cc_start: 0.7755 (pt0) cc_final: 0.7478 (mm-30) outliers start: 73 outliers final: 27 residues processed: 302 average time/residue: 0.6281 time to fit residues: 223.2945 Evaluate side-chains 286 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 1477 HIS Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1584 GLN Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2189 ILE Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2274 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2501 LEU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2799 GLN Chi-restraints excluded: chain A residue 2807 GLN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3493 TRP Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 202 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 280 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.182054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.139206 restraints weight = 44842.999| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.53 r_work: 0.3693 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29629 Z= 0.173 Angle : 0.672 20.492 40072 Z= 0.334 Chirality : 0.043 0.276 4565 Planarity : 0.004 0.048 5084 Dihedral : 5.160 41.528 3945 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.30 % Favored : 92.62 % Rotamer: Outliers : 2.66 % Allowed : 14.81 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3602 helix: 0.44 (0.11), residues: 2413 sheet: -1.28 (0.70), residues: 51 loop : -2.13 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2232 TYR 0.028 0.002 TYR A3540 PHE 0.025 0.002 PHE A1219 TRP 0.039 0.002 TRP A3588 HIS 0.006 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00413 (29629) covalent geometry : angle 0.67225 (40072) hydrogen bonds : bond 0.03974 ( 1621) hydrogen bonds : angle 4.36308 ( 4800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 274 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.3629 (OUTLIER) cc_final: 0.3090 (mm) REVERT: A 1011 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7036 (mt-10) REVERT: A 1408 MET cc_start: 0.8183 (tpp) cc_final: 0.7943 (mpp) REVERT: A 1576 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7235 (m-30) REVERT: A 1584 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8255 (mp10) REVERT: A 2307 MET cc_start: 0.6544 (mpp) cc_final: 0.5481 (mpt) REVERT: A 2328 ARG cc_start: 0.8263 (tmt-80) cc_final: 0.7610 (tpt90) REVERT: A 2443 MET cc_start: 0.7859 (ttm) cc_final: 0.7259 (ttm) REVERT: A 3176 MET cc_start: 0.9009 (mmm) cc_final: 0.8782 (mmm) REVERT: A 3421 ASP cc_start: 0.7417 (t0) cc_final: 0.7048 (t0) REVERT: A 3483 MET cc_start: 0.5458 (OUTLIER) cc_final: 0.5132 (tpt) REVERT: A 3493 TRP cc_start: 0.6670 (OUTLIER) cc_final: 0.6459 (p90) REVERT: A 3609 MET cc_start: 0.3754 (ptp) cc_final: 0.2689 (mmm) REVERT: A 4005 PHE cc_start: 0.7704 (t80) cc_final: 0.7502 (t80) REVERT: A 4017 GLU cc_start: 0.7761 (pt0) cc_final: 0.7544 (pt0) outliers start: 85 outliers final: 30 residues processed: 328 average time/residue: 0.6367 time to fit residues: 247.1272 Evaluate side-chains 285 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1477 HIS Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1584 GLN Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2189 ILE Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2334 LYS Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2501 LEU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2807 GLN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3493 TRP Chi-restraints excluded: chain A residue 3890 MET Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 168 optimal weight: 6.9990 chunk 306 optimal weight: 0.7980 chunk 351 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 357 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN A1477 HIS A2348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.184548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.143696 restraints weight = 44499.513| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.45 r_work: 0.3731 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29629 Z= 0.122 Angle : 0.638 18.444 40072 Z= 0.316 Chirality : 0.041 0.239 4565 Planarity : 0.004 0.047 5084 Dihedral : 4.904 38.975 3945 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 2.04 % Allowed : 16.44 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3602 helix: 0.66 (0.11), residues: 2407 sheet: -1.24 (0.70), residues: 51 loop : -1.99 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2254 TYR 0.022 0.001 TYR A3540 PHE 0.027 0.001 PHE A1219 TRP 0.041 0.001 TRP A3588 HIS 0.004 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00274 (29629) covalent geometry : angle 0.63798 (40072) hydrogen bonds : bond 0.03507 ( 1621) hydrogen bonds : angle 4.22854 ( 4800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 287 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.3622 (OUTLIER) cc_final: 0.3100 (mm) REVERT: A 1011 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 1369 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7371 (mmt) REVERT: A 1576 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: A 1739 TYR cc_start: 0.7743 (t80) cc_final: 0.7471 (t80) REVERT: A 1812 LEU cc_start: 0.7068 (mt) cc_final: 0.6694 (mp) REVERT: A 1878 ASP cc_start: 0.8251 (t70) cc_final: 0.7954 (t0) REVERT: A 2307 MET cc_start: 0.6560 (mpp) cc_final: 0.5490 (mpt) REVERT: A 2328 ARG cc_start: 0.8204 (tmt-80) cc_final: 0.7582 (tpt90) REVERT: A 2374 LEU cc_start: 0.8514 (tp) cc_final: 0.8151 (mp) REVERT: A 2443 MET cc_start: 0.7793 (ttm) cc_final: 0.7231 (ttm) REVERT: A 3062 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8044 (pt) REVERT: A 3176 MET cc_start: 0.9055 (mmm) cc_final: 0.8822 (mmm) REVERT: A 3421 ASP cc_start: 0.7385 (t0) cc_final: 0.7009 (t0) REVERT: A 3483 MET cc_start: 0.4841 (OUTLIER) cc_final: 0.4218 (tpp) REVERT: A 3493 TRP cc_start: 0.6865 (OUTLIER) cc_final: 0.6632 (p90) REVERT: A 3609 MET cc_start: 0.3495 (ptp) cc_final: 0.2439 (mmm) REVERT: A 3796 MET cc_start: 0.8849 (mtt) cc_final: 0.7939 (mtt) REVERT: A 4017 GLU cc_start: 0.7717 (pt0) cc_final: 0.7508 (mm-30) outliers start: 65 outliers final: 27 residues processed: 326 average time/residue: 0.6411 time to fit residues: 247.2270 Evaluate side-chains 288 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2334 LYS Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2807 GLN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3493 TRP Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 182 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 350 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN A3104 GLN A3422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.184326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.143215 restraints weight = 44799.135| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.44 r_work: 0.3714 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29629 Z= 0.139 Angle : 0.656 17.771 40072 Z= 0.323 Chirality : 0.042 0.347 4565 Planarity : 0.004 0.047 5084 Dihedral : 4.880 39.632 3945 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.89 % Favored : 93.03 % Rotamer: Outliers : 2.41 % Allowed : 17.16 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3602 helix: 0.67 (0.11), residues: 2407 sheet: -1.25 (0.70), residues: 51 loop : -1.99 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2522 TYR 0.024 0.001 TYR A3540 PHE 0.026 0.001 PHE A1219 TRP 0.043 0.001 TRP A3588 HIS 0.004 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00326 (29629) covalent geometry : angle 0.65594 (40072) hydrogen bonds : bond 0.03627 ( 1621) hydrogen bonds : angle 4.24775 ( 4800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 265 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.3613 (OUTLIER) cc_final: 0.3096 (mm) REVERT: A 171 LEU cc_start: 0.3457 (OUTLIER) cc_final: 0.3189 (mm) REVERT: A 672 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7793 (pt) REVERT: A 1011 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7019 (mt-10) REVERT: A 1576 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: A 1878 ASP cc_start: 0.8192 (t70) cc_final: 0.7885 (t0) REVERT: A 2307 MET cc_start: 0.6589 (mpp) cc_final: 0.5506 (mpt) REVERT: A 2328 ARG cc_start: 0.8197 (tmt-80) cc_final: 0.7586 (tpt90) REVERT: A 2443 MET cc_start: 0.7847 (ttm) cc_final: 0.7263 (ttm) REVERT: A 3062 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8080 (pt) REVERT: A 3159 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7573 (ptp90) REVERT: A 3421 ASP cc_start: 0.7397 (t0) cc_final: 0.7006 (t0) REVERT: A 3483 MET cc_start: 0.4630 (OUTLIER) cc_final: 0.4032 (tpp) REVERT: A 3493 TRP cc_start: 0.6914 (OUTLIER) cc_final: 0.6699 (p90) REVERT: A 3609 MET cc_start: 0.3420 (ptp) cc_final: 0.2334 (mmm) REVERT: A 4017 GLU cc_start: 0.7728 (pt0) cc_final: 0.7520 (mm-30) REVERT: A 4039 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6663 (t80) outliers start: 77 outliers final: 31 residues processed: 314 average time/residue: 0.6089 time to fit residues: 229.6161 Evaluate side-chains 287 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1477 HIS Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2334 LYS Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2501 LEU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2807 GLN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3471 ILE Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3493 TRP Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 134 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 312 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 113 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN A 982 GLN ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN A2348 GLN A3104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.185194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.144490 restraints weight = 44820.391| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.56 r_work: 0.3732 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29629 Z= 0.123 Angle : 0.658 17.035 40072 Z= 0.322 Chirality : 0.041 0.319 4565 Planarity : 0.004 0.046 5084 Dihedral : 4.775 38.945 3945 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 2.16 % Allowed : 17.94 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3602 helix: 0.77 (0.11), residues: 2401 sheet: -1.05 (0.68), residues: 60 loop : -1.98 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2522 TYR 0.024 0.001 TYR A1873 PHE 0.025 0.001 PHE A1814 TRP 0.047 0.001 TRP A3588 HIS 0.005 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00279 (29629) covalent geometry : angle 0.65802 (40072) hydrogen bonds : bond 0.03486 ( 1621) hydrogen bonds : angle 4.18382 ( 4800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 268 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.3581 (OUTLIER) cc_final: 0.3079 (mm) REVERT: A 171 LEU cc_start: 0.3648 (OUTLIER) cc_final: 0.3352 (mm) REVERT: A 775 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: A 1011 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7091 (mt-10) REVERT: A 1576 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7253 (m-30) REVERT: A 1812 LEU cc_start: 0.7079 (mt) cc_final: 0.6657 (mp) REVERT: A 1878 ASP cc_start: 0.8199 (t70) cc_final: 0.7905 (t0) REVERT: A 2307 MET cc_start: 0.6472 (mpp) cc_final: 0.5518 (mpt) REVERT: A 2328 ARG cc_start: 0.8176 (tmt-80) cc_final: 0.7585 (tpt90) REVERT: A 2443 MET cc_start: 0.7797 (ttm) cc_final: 0.7255 (ttm) REVERT: A 3062 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8167 (pt) REVERT: A 3159 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7595 (ptp90) REVERT: A 3319 ASN cc_start: 0.7327 (p0) cc_final: 0.6814 (t0) REVERT: A 3421 ASP cc_start: 0.7390 (t0) cc_final: 0.7008 (t0) REVERT: A 3483 MET cc_start: 0.4440 (OUTLIER) cc_final: 0.3931 (tpp) REVERT: A 3493 TRP cc_start: 0.6863 (OUTLIER) cc_final: 0.6662 (p90) REVERT: A 3609 MET cc_start: 0.3273 (ptp) cc_final: 0.2447 (mmm) REVERT: A 3796 MET cc_start: 0.8846 (mtt) cc_final: 0.8003 (mtt) REVERT: A 4039 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.6612 (t80) outliers start: 69 outliers final: 36 residues processed: 310 average time/residue: 0.6536 time to fit residues: 240.3126 Evaluate side-chains 296 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1477 HIS Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2160 TYR Chi-restraints excluded: chain A residue 2241 LEU Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2274 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2334 LYS Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2501 LEU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2807 GLN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3459 ASN Chi-restraints excluded: chain A residue 3471 ILE Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3493 TRP Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 7 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 347 optimal weight: 0.3980 chunk 288 optimal weight: 0.7980 chunk 240 optimal weight: 0.7980 chunk 225 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 338 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN A2217 ASN A2348 GLN A3104 GLN A3422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.185753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.146288 restraints weight = 44688.629| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.89 r_work: 0.3774 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29629 Z= 0.125 Angle : 0.656 16.790 40072 Z= 0.322 Chirality : 0.041 0.301 4565 Planarity : 0.004 0.046 5084 Dihedral : 4.715 38.823 3945 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 1.85 % Allowed : 18.44 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3602 helix: 0.79 (0.11), residues: 2402 sheet: -1.05 (0.67), residues: 60 loop : -1.97 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2522 TYR 0.024 0.001 TYR A3013 PHE 0.021 0.001 PHE A2260 TRP 0.051 0.002 TRP A3588 HIS 0.004 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00285 (29629) covalent geometry : angle 0.65647 (40072) hydrogen bonds : bond 0.03475 ( 1621) hydrogen bonds : angle 4.17098 ( 4800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 262 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.3374 (OUTLIER) cc_final: 0.2737 (mm) REVERT: A 171 LEU cc_start: 0.3445 (OUTLIER) cc_final: 0.3176 (mm) REVERT: A 775 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: A 1011 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7133 (mt-10) REVERT: A 1576 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: A 1712 ARG cc_start: 0.7118 (ttp-110) cc_final: 0.6853 (ptm-80) REVERT: A 1812 LEU cc_start: 0.7121 (mt) cc_final: 0.6682 (mp) REVERT: A 1878 ASP cc_start: 0.8164 (t70) cc_final: 0.7896 (t0) REVERT: A 2225 HIS cc_start: 0.7936 (t-90) cc_final: 0.7530 (t-90) REVERT: A 2307 MET cc_start: 0.6623 (mpp) cc_final: 0.5666 (mpt) REVERT: A 2328 ARG cc_start: 0.8289 (tmt-80) cc_final: 0.7605 (tpt90) REVERT: A 2443 MET cc_start: 0.7772 (ttm) cc_final: 0.7272 (ttm) REVERT: A 3062 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8159 (pt) REVERT: A 3159 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7497 (ptp90) REVERT: A 3319 ASN cc_start: 0.7056 (p0) cc_final: 0.6646 (t0) REVERT: A 3421 ASP cc_start: 0.7330 (t0) cc_final: 0.6895 (t0) REVERT: A 3483 MET cc_start: 0.4295 (OUTLIER) cc_final: 0.4051 (tpt) REVERT: A 3609 MET cc_start: 0.3362 (ptp) cc_final: 0.2407 (mmm) REVERT: A 3796 MET cc_start: 0.8797 (mtt) cc_final: 0.7961 (mtt) REVERT: A 4039 TYR cc_start: 0.6694 (OUTLIER) cc_final: 0.6429 (t80) outliers start: 59 outliers final: 38 residues processed: 301 average time/residue: 0.5978 time to fit residues: 214.0596 Evaluate side-chains 297 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1477 HIS Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2160 TYR Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2274 ILE Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2334 LYS Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2501 LEU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3459 ASN Chi-restraints excluded: chain A residue 3471 ILE Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 169 optimal weight: 8.9990 chunk 248 optimal weight: 0.7980 chunk 347 optimal weight: 0.9980 chunk 342 optimal weight: 0.9980 chunk 340 optimal weight: 0.3980 chunk 199 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 255 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 327 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN A1048 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 ASN A4018 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.185641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.146039 restraints weight = 44591.019| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.94 r_work: 0.3777 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29629 Z= 0.125 Angle : 0.670 16.571 40072 Z= 0.328 Chirality : 0.041 0.337 4565 Planarity : 0.004 0.046 5084 Dihedral : 4.670 38.567 3945 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.34 % Rotamer: Outliers : 1.41 % Allowed : 19.04 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3602 helix: 0.82 (0.11), residues: 2401 sheet: -1.09 (0.67), residues: 60 loop : -1.96 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2522 TYR 0.021 0.001 TYR A3540 PHE 0.022 0.001 PHE A2260 TRP 0.072 0.002 TRP A3588 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00286 (29629) covalent geometry : angle 0.67003 (40072) hydrogen bonds : bond 0.03467 ( 1621) hydrogen bonds : angle 4.17283 ( 4800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 775 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: A 1011 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7096 (mt-10) REVERT: A 1369 MET cc_start: 0.7803 (mpt) cc_final: 0.7485 (mmt) REVERT: A 1576 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: A 1812 LEU cc_start: 0.7083 (mt) cc_final: 0.6666 (mp) REVERT: A 1878 ASP cc_start: 0.8190 (t70) cc_final: 0.7922 (t0) REVERT: A 2307 MET cc_start: 0.6573 (mpp) cc_final: 0.5615 (mpt) REVERT: A 2328 ARG cc_start: 0.8311 (tmt-80) cc_final: 0.7642 (tpt90) REVERT: A 2443 MET cc_start: 0.7751 (ttm) cc_final: 0.7271 (ttm) REVERT: A 3062 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8150 (pt) REVERT: A 3159 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7633 (ppt-90) REVERT: A 3319 ASN cc_start: 0.7150 (p0) cc_final: 0.6737 (t0) REVERT: A 3421 ASP cc_start: 0.7392 (t0) cc_final: 0.6984 (t0) REVERT: A 3609 MET cc_start: 0.3085 (ptp) cc_final: 0.2280 (mmm) REVERT: A 3796 MET cc_start: 0.8792 (mtt) cc_final: 0.7977 (mtt) REVERT: A 4039 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.6385 (t80) outliers start: 45 outliers final: 31 residues processed: 291 average time/residue: 0.6137 time to fit residues: 212.8345 Evaluate side-chains 283 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2160 TYR Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2334 LYS Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3459 ASN Chi-restraints excluded: chain A residue 3471 ILE Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 6 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 354 optimal weight: 0.7980 chunk 150 optimal weight: 0.0980 chunk 214 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 301 optimal weight: 0.1980 chunk 230 optimal weight: 0.0270 chunk 145 optimal weight: 0.9980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 GLN A2787 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.186886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.146494 restraints weight = 44774.705| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.38 r_work: 0.3784 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29629 Z= 0.119 Angle : 0.668 16.402 40072 Z= 0.325 Chirality : 0.041 0.341 4565 Planarity : 0.004 0.046 5084 Dihedral : 4.585 37.957 3945 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 1.22 % Allowed : 19.19 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3602 helix: 0.86 (0.11), residues: 2404 sheet: -0.89 (0.71), residues: 54 loop : -1.94 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1712 TYR 0.025 0.001 TYR A3013 PHE 0.031 0.001 PHE A1805 TRP 0.076 0.002 TRP A3588 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00264 (29629) covalent geometry : angle 0.66775 (40072) hydrogen bonds : bond 0.03368 ( 1621) hydrogen bonds : angle 4.14014 ( 4800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11275.58 seconds wall clock time: 192 minutes 24.65 seconds (11544.65 seconds total)