Starting phenix.real_space_refine on Fri Mar 6 07:43:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7otw_13068/03_2026/7otw_13068.cif Found real_map, /net/cci-nas-00/data/ceres_data/7otw_13068/03_2026/7otw_13068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7otw_13068/03_2026/7otw_13068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7otw_13068/03_2026/7otw_13068.map" model { file = "/net/cci-nas-00/data/ceres_data/7otw_13068/03_2026/7otw_13068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7otw_13068/03_2026/7otw_13068.cif" } resolution = 2.99 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= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 191 5.16 5 C 18627 2.51 5 N 4911 2.21 5 O 5309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 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: 29038 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 28910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3636, 28910 Classifications: {'peptide': 3636} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 158, 'TRANS': 3477} Chain breaks: 16 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "A" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 128 Unusual residues: {'MBW': 1} Classifications: {'peptide': 20, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19, None: 1} Not linked: pdbres="UNK A6020 " pdbres="MBW 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: 5.52, per 1000 atoms: 0.19 Number of scatterers: 29038 At special positions: 0 Unit cell: (125.184, 152.568, 183.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 191 16.00 O 5309 8.00 N 4911 7.00 C 18627 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: 2.18 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: 208 helices and 4 sheets defined 71.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 5.289A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.661A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.752A pdb=" N CYS A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 4.230A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 118 No H-bonds generated for 'chain 'A' and resid 117 through 118' Processing helix chain 'A' and resid 127 through 128 No H-bonds generated for 'chain 'A' and resid 127 through 128' Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.973A pdb=" N LYS A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.631A pdb=" N TYR A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.739A pdb=" N GLU A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.275A pdb=" N GLU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 4.178A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.833A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 241 through 255 removed outlier: 4.294A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.748A pdb=" N ASP A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 301 removed outlier: 4.662A pdb=" N VAL A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.656A pdb=" N ASN A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 removed outlier: 4.087A pdb=" N ASN A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 removed outlier: 4.050A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 377 removed outlier: 3.545A pdb=" N LYS A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 396 removed outlier: 3.732A pdb=" N MET A 384 " --> pdb=" O ASP A 380 " (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: 4.291A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 450 through 469 removed outlier: 3.781A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 4.075A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.188A 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 536 Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 559 through 579 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.635A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 660 Processing helix chain 'A' and resid 663 through 679 removed outlier: 4.373A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 removed outlier: 3.639A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) 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 723 through 736 removed outlier: 3.774A pdb=" N ALA A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 736 " --> pdb=" O PHE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 4.106A pdb=" N LEU A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 759 removed outlier: 3.556A 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: 3.719A 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: 4.312A pdb=" N GLY A 798 " --> pdb=" O CYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.823A pdb=" N ALA A 804 " --> pdb=" O LYS A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 862 Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.591A pdb=" N LEU A 871 " --> pdb=" O LYS A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 877 Processing helix chain 'A' and resid 880 through 884 removed outlier: 3.650A pdb=" N TYR A 883 " --> pdb=" O MET A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 921 removed outlier: 3.769A 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: 4.008A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.605A 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 1012 Processing helix chain 'A' and resid 1023 through 1043 Processing helix chain 'A' and resid 1045 through 1050 removed outlier: 3.919A 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: 3.707A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 5.373A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.449A 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 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 1251 through 1273 removed outlier: 3.812A pdb=" N CYS A1255 " --> pdb=" O GLN A1251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A1269 " --> pdb=" O GLU A1265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A1273 " --> pdb=" O THR A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1298 removed outlier: 4.372A pdb=" N ALA A1293 " --> pdb=" O SER A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1325 No H-bonds generated for 'chain 'A' and resid 1323 through 1325' Processing helix chain 'A' and resid 1326 through 1351 removed outlier: 3.512A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1359 removed outlier: 3.994A pdb=" N LEU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1378 removed outlier: 4.453A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1383 removed outlier: 3.625A pdb=" N GLY A1383 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1409 Proline residue: A1396 - end of helix removed outlier: 3.813A 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 removed outlier: 3.538A pdb=" N ALA A1433 " --> pdb=" O GLU A1429 " (cutoff:3.500A) 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 1486 removed outlier: 3.786A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1492 removed outlier: 3.522A pdb=" N ILE A1491 " --> pdb=" O TYR A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1520 Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.656A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1574 removed outlier: 6.342A pdb=" N GLU A1565 " --> pdb=" O SER A1561 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR A1566 " --> pdb=" O LEU A1562 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1585 removed outlier: 3.686A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 Processing helix chain 'A' and resid 1611 through 1626 Processing helix chain 'A' and resid 1627 through 1633 removed outlier: 3.685A pdb=" N ASP A1630 " --> pdb=" O LYS A1627 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER A1631 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.670A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 3.613A pdb=" N VAL A1671 " --> pdb=" O SER A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1693 Processing helix chain 'A' and resid 1695 through 1700 removed outlier: 3.655A pdb=" N PHE A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1722 removed outlier: 3.980A pdb=" N LEU A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) 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 1812 through 1823 removed outlier: 3.572A pdb=" N ARG A1816 " --> pdb=" O LEU A1812 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A1818 " --> pdb=" O PHE A1814 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A1823 " --> pdb=" O PHE A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1829 Processing helix chain 'A' and resid 1834 through 1845 removed outlier: 4.266A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1853 removed outlier: 3.633A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A1851 " --> pdb=" O ALA A1847 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1882 removed outlier: 4.063A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1924 removed outlier: 3.913A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1956 Processing helix chain 'A' and resid 1970 through 1975 removed outlier: 3.563A pdb=" N ASN A1974 " --> pdb=" O LYS A1970 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A1975 " --> pdb=" O PRO A1971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1970 through 1975' Processing helix chain 'A' and resid 2093 through 2105 Processing helix chain 'A' and resid 2123 through 2135 removed outlier: 3.826A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.707A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 3.958A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A2158 " --> pdb=" O GLU A2154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2153 through 2158' Processing helix chain 'A' and resid 2160 through 2172 removed outlier: 4.586A 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 Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2269 through 2283 removed outlier: 4.271A pdb=" N GLY A2273 " --> pdb=" O ASP A2269 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2305 Processing helix chain 'A' and resid 2306 through 2309 Processing helix chain 'A' and resid 2312 through 2331 removed outlier: 4.209A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2357 removed outlier: 4.022A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR A2355 " --> pdb=" O GLN A2351 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A2356 " --> pdb=" O HIS A2352 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2371 removed outlier: 4.214A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2374 through 2386 removed outlier: 4.227A pdb=" N PHE A2378 " --> pdb=" O LEU A2374 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN A2380 " --> pdb=" O ASP A2376 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA A2381 " --> pdb=" O ARG A2377 " (cutoff:3.500A) 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 2392 through 2404 removed outlier: 3.993A 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 2424 Processing helix chain 'A' and resid 2428 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 2456 removed outlier: 3.767A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Processing helix chain 'A' and resid 2458 through 2462 removed outlier: 3.966A pdb=" N VAL A2462 " --> pdb=" O VAL A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2469 through 2484 Processing helix chain 'A' and resid 2496 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 2543 removed outlier: 3.889A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2546 No H-bonds generated for 'chain 'A' and resid 2544 through 2546' Processing helix chain 'A' and resid 2557 through 2564 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: 4.233A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A2822 " --> pdb=" O LYS A2818 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A2823 " --> pdb=" O GLU A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2846 Processing helix chain 'A' and resid 2851 through 2865 removed outlier: 3.710A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) removed outlier: 3.749A 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 2900 removed outlier: 3.525A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2933 removed outlier: 3.631A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2946 Processing helix chain 'A' and resid 2951 through 2961 removed outlier: 3.533A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A2956 " --> pdb=" O ILE A2952 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2977 removed outlier: 3.906A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 4.049A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A3000 " --> pdb=" O LEU A2996 " (cutoff:3.500A) Processing helix chain 'A' and resid 3007 through 3013 Processing helix chain 'A' and resid 3040 through 3054 Processing helix chain 'A' and resid 3059 through 3071 removed outlier: 3.814A pdb=" N THR A3063 " --> pdb=" O GLN A3059 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A3071 " --> pdb=" O LYS A3067 " (cutoff:3.500A) Processing helix chain 'A' and resid 3074 through 3082 removed outlier: 3.779A pdb=" N LEU A3078 " --> pdb=" O GLN A3074 " (cutoff:3.500A) Processing helix chain 'A' and resid 3082 through 3094 removed outlier: 3.637A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3116 removed outlier: 3.583A pdb=" N ALA A3099 " --> pdb=" O ASP A3095 " (cutoff:3.500A) Processing helix chain 'A' and resid 3121 through 3130 removed outlier: 3.538A pdb=" N THR A3127 " --> pdb=" O GLN A3123 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A3128 " --> pdb=" O SER A3124 " (cutoff:3.500A) Processing helix chain 'A' and resid 3132 through 3146 removed outlier: 3.750A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3165 removed outlier: 4.385A pdb=" N LEU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3196 removed outlier: 3.869A pdb=" N GLU A3195 " --> pdb=" O SER A3191 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A3196 " --> pdb=" O LYS A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3231 through 3249 removed outlier: 3.858A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A3243 " --> pdb=" O LYS A3239 " (cutoff:3.500A) Processing helix chain 'A' and resid 3253 through 3262 Processing helix chain 'A' and resid 3271 through 3287 removed outlier: 4.112A pdb=" N ARG A3282 " --> pdb=" O GLN A3278 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3307 Processing helix chain 'A' and resid 3318 through 3344 removed outlier: 3.786A pdb=" N ALA A3322 " --> pdb=" O LYS A3318 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG A3324 " --> pdb=" O ILE A3320 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASP A3325 " --> pdb=" O LEU A3321 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3345 through 3352 removed outlier: 3.724A pdb=" N LEU A3348 " --> pdb=" O PRO A3345 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A3351 " --> pdb=" O LEU A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3364 removed outlier: 4.374A pdb=" N ILE A3359 " --> pdb=" O LYS A3355 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A3360 " --> pdb=" O ALA A3356 " (cutoff:3.500A) Processing helix chain 'A' and resid 3369 through 3394 removed outlier: 4.284A pdb=" N GLU A3394 " --> pdb=" O GLN A3390 " (cutoff:3.500A) Processing helix chain 'A' and resid 3406 through 3430 removed outlier: 3.666A pdb=" N ILE A3410 " --> pdb=" O ALA A3406 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.562A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3465 Processing helix chain 'A' and resid 3467 through 3472 Processing helix chain 'A' and resid 3480 through 3488 Processing helix chain 'A' and resid 3494 through 3497 removed outlier: 3.508A pdb=" N SER A3497 " --> pdb=" O GLN A3494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3494 through 3497' Processing helix chain 'A' and resid 3498 through 3506 removed outlier: 3.599A pdb=" N LEU A3505 " --> pdb=" O HIS A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3514 through 3525 removed outlier: 3.502A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3538 removed outlier: 3.669A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3547 through 3563 removed outlier: 3.824A pdb=" N PHE A3554 " --> pdb=" O LYS A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3579 removed outlier: 3.928A pdb=" N GLN A3577 " --> pdb=" O ASN A3573 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A3578 " --> pdb=" O ALA A3574 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER A3579 " --> pdb=" O LEU A3575 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3594 Processing helix chain 'A' and resid 3607 through 3615 removed outlier: 4.298A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3636 removed outlier: 3.763A 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 3649 through 3653 Processing helix chain 'A' and resid 3657 through 3673 removed outlier: 3.579A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A3673 " --> pdb=" O LYS A3669 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3684 Processing helix chain 'A' and resid 3686 through 3690 removed outlier: 3.505A pdb=" N PHE A3690 " --> pdb=" O MET A3687 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3778 Processing helix chain 'A' and resid 3779 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: 4.017A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3862 removed outlier: 3.552A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3875 Processing helix chain 'A' and resid 3881 through 3890 Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 3.744A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3952 Processing helix chain 'A' and resid 3964 through 3969 Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 4.296A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4007 removed outlier: 4.706A pdb=" N LEU A3998 " --> pdb=" O ASP A3994 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4022 removed outlier: 3.568A pdb=" N LYS A4022 " --> pdb=" O GLN A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4051 removed outlier: 3.921A pdb=" N LYS A4043 " --> pdb=" O TYR A4039 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A4044 " --> pdb=" O PRO A4040 " (cutoff:3.500A) removed outlier: 3.508A 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: 3.610A pdb=" N GLY A4083 " --> pdb=" O ALA A4079 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4113 removed outlier: 3.650A pdb=" N LEU A4107 " --> pdb=" O GLN A4103 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4121 through 4125 Processing helix chain 'A' and resid 6002 through 6010 removed outlier: 3.700A pdb=" N UNK A6008 " --> pdb=" O UNK A6004 " (cutoff:3.500A) 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 3719 through 3722 removed outlier: 5.894A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE A3722 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE A3739 " --> pdb=" O PHE A3722 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3793 through 3797 removed outlier: 3.747A pdb=" N MET A3796 " --> pdb=" O LEU A3800 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3809 through 3811 1591 hydrogen bonds defined for protein. 4707 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: 6.86 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5577 1.32 - 1.45: 6866 1.45 - 1.57: 16891 1.57 - 1.69: 1 1.69 - 1.81: 298 Bond restraints: 29633 Sorted by residual: bond pdb=" C LEU A3958 " pdb=" N MET A3959 " ideal model delta sigma weight residual 1.333 1.242 0.091 2.74e-02 1.33e+03 1.10e+01 bond pdb=" CG1 ILE A3499 " pdb=" CD1 ILE A3499 " ideal model delta sigma weight residual 1.513 1.391 0.122 3.90e-02 6.57e+02 9.77e+00 bond pdb=" CA LEU A3151 " pdb=" CB LEU A3151 " ideal model delta sigma weight residual 1.526 1.570 -0.044 1.51e-02 4.39e+03 8.40e+00 bond pdb=" N PHE A3694 " pdb=" CA PHE A3694 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.17e+00 bond pdb=" C ASP A 241 " pdb=" N PRO A 242 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.08e-02 8.57e+03 6.62e+00 ... (remaining 29628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 39049 2.59 - 5.18: 875 5.18 - 7.76: 127 7.76 - 10.35: 22 10.35 - 12.94: 4 Bond angle restraints: 40077 Sorted by residual: angle pdb=" N LYS A3455 " pdb=" CA LYS A3455 " pdb=" C LYS A3455 " ideal model delta sigma weight residual 111.36 103.46 7.90 1.09e+00 8.42e-01 5.25e+01 angle pdb=" N ILE A4028 " pdb=" CA ILE A4028 " pdb=" C ILE A4028 " ideal model delta sigma weight residual 113.71 106.90 6.81 9.50e-01 1.11e+00 5.14e+01 angle pdb=" N ILE A3231 " pdb=" CA ILE A3231 " pdb=" C ILE A3231 " ideal model delta sigma weight residual 112.96 107.14 5.82 1.00e+00 1.00e+00 3.39e+01 angle pdb=" N LYS A3753 " pdb=" CA LYS A3753 " pdb=" C LYS A3753 " ideal model delta sigma weight residual 110.10 101.66 8.44 1.49e+00 4.50e-01 3.21e+01 angle pdb=" C ILE A1085 " pdb=" N TYR A1086 " pdb=" CA TYR A1086 " ideal model delta sigma weight residual 121.66 111.84 9.82 1.92e+00 2.71e-01 2.61e+01 ... (remaining 40072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.34: 17064 24.34 - 48.68: 927 48.68 - 73.03: 76 73.03 - 97.37: 17 97.37 - 121.71: 1 Dihedral angle restraints: 18085 sinusoidal: 7328 harmonic: 10757 Sorted by residual: dihedral pdb=" CA GLN A3037 " pdb=" C GLN A3037 " pdb=" N GLU A3038 " pdb=" CA GLU A3038 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+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 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLY A1016 " pdb=" C GLY A1016 " pdb=" N ILE A1017 " pdb=" CA ILE A1017 " ideal model delta harmonic sigma weight residual -180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 18082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3876 0.072 - 0.144: 638 0.144 - 0.216: 43 0.216 - 0.287: 6 0.287 - 0.359: 2 Chirality restraints: 4565 Sorted by residual: chirality pdb=" CA PHE A3694 " pdb=" N PHE A3694 " pdb=" C PHE A3694 " pdb=" CB PHE A3694 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 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 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CG LEU A1010 " pdb=" CB LEU A1010 " pdb=" CD1 LEU A1010 " pdb=" CD2 LEU A1010 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4562 not shown) Planarity restraints: 5085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A4008 " -0.059 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO A4009 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A4009 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A4009 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 697 " 0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 698 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 698 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 698 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A3710 " -0.053 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO A3711 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A3711 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A3711 " -0.045 5.00e-02 4.00e+02 ... (remaining 5082 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 59 2.32 - 2.96: 14677 2.96 - 3.61: 45295 3.61 - 4.25: 67880 4.25 - 4.90: 113132 Nonbonded interactions: 241043 Sorted by model distance: nonbonded pdb=" CE2 TYR A 721 " pdb=" SG CYS A 729 " model vdw 1.672 3.700 nonbonded pdb=" O SER A3288 " pdb=" NH1 ARG A3289 " model vdw 2.061 3.120 nonbonded pdb=" O ALA A1078 " pdb=" OH TYR A1107 " model vdw 2.160 3.040 nonbonded pdb=" OE2 GLU A3137 " pdb=" NH2 ARG A3186 " model vdw 2.176 3.120 nonbonded pdb=" OH TYR A 423 " pdb=" O ALA A 549 " model vdw 2.178 3.040 ... (remaining 241038 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: 1.020 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.510 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.009 0.122 29633 Z= 0.382 Angle : 0.944 12.941 40077 Z= 0.507 Chirality : 0.053 0.359 4565 Planarity : 0.006 0.087 5085 Dihedral : 14.286 121.712 11073 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.97 % Favored : 89.87 % Rotamer: Outliers : 0.28 % Allowed : 0.72 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.13), residues: 3602 helix: -0.75 (0.10), residues: 2384 sheet: -2.69 (0.84), residues: 37 loop : -2.98 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A3741 TYR 0.032 0.003 TYR A3540 PHE 0.052 0.003 PHE A3571 TRP 0.023 0.003 TRP A4127 HIS 0.011 0.002 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00899 (29633) covalent geometry : angle 0.94372 (40077) hydrogen bonds : bond 0.09375 ( 1591) hydrogen bonds : angle 5.53614 ( 4707) *********************** 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 234 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3044 MET cc_start: 0.6667 (tmm) cc_final: 0.6285 (ttp) outliers start: 9 outliers final: 3 residues processed: 232 average time/residue: 0.7261 time to fit residues: 194.9151 Evaluate side-chains 165 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1751 GLU Chi-restraints excluded: chain A residue 1757 MET Chi-restraints excluded: chain A residue 3693 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A1115 HIS ** A1568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1574 ASN A2217 ASN A2301 GLN ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3004 HIS ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS A4110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.095257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.062645 restraints weight = 112199.431| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.42 r_work: 0.3096 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29633 Z= 0.162 Angle : 0.733 12.292 40077 Z= 0.369 Chirality : 0.043 0.195 4565 Planarity : 0.005 0.065 5085 Dihedral : 6.140 122.536 3944 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.58 % Favored : 92.37 % Rotamer: Outliers : 0.97 % Allowed : 8.35 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3602 helix: -0.04 (0.11), residues: 2381 sheet: -2.12 (0.88), residues: 38 loop : -2.48 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1938 TYR 0.045 0.002 TYR A2572 PHE 0.026 0.002 PHE A3542 TRP 0.025 0.002 TRP A3031 HIS 0.010 0.001 HIS A2105 Details of bonding type rmsd covalent geometry : bond 0.00359 (29633) covalent geometry : angle 0.73344 (40077) hydrogen bonds : bond 0.04212 ( 1591) hydrogen bonds : angle 4.69610 ( 4707) *********************** 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 206 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 TRP cc_start: 0.8785 (m100) cc_final: 0.8017 (m100) REVERT: A 939 MET cc_start: 0.9293 (mmm) cc_final: 0.9090 (mmm) REVERT: A 1583 MET cc_start: 0.7752 (ptm) cc_final: 0.7048 (tmt) REVERT: A 1829 TRP cc_start: 0.9352 (m100) cc_final: 0.8658 (m100) REVERT: A 1881 TYR cc_start: 0.9281 (m-80) cc_final: 0.9022 (m-80) REVERT: A 1945 TYR cc_start: 0.8852 (t80) cc_final: 0.8526 (t80) REVERT: A 2126 MET cc_start: 0.8759 (tmm) cc_final: 0.8448 (ppp) REVERT: A 2341 LEU cc_start: 0.9613 (mt) cc_final: 0.9272 (pp) REVERT: A 2408 MET cc_start: 0.6867 (tmt) cc_final: 0.6627 (tmt) REVERT: A 2443 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8542 (tmm) REVERT: A 2565 MET cc_start: 0.8656 (tpp) cc_final: 0.8271 (tpp) REVERT: A 2572 TYR cc_start: 0.7486 (t80) cc_final: 0.7255 (t80) REVERT: A 2576 MET cc_start: 0.7462 (pmt) cc_final: 0.7227 (pmt) outliers start: 31 outliers final: 5 residues processed: 187 average time/residue: 0.6721 time to fit residues: 146.9684 Evaluate side-chains 158 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1219 PHE Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3712 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 142 optimal weight: 0.7980 chunk 259 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 361 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 307 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1568 ASN ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 ASN ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3564 GLN A3643 HIS A4042 GLN A4110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.093347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.061426 restraints weight = 113393.592| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.76 r_work: 0.3025 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 29633 Z= 0.245 Angle : 0.733 13.137 40077 Z= 0.368 Chirality : 0.044 0.194 4565 Planarity : 0.005 0.060 5085 Dihedral : 5.427 52.347 3935 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.05 % Favored : 91.89 % Rotamer: Outliers : 1.22 % Allowed : 11.48 % Favored : 87.30 % 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: -0.95 (0.14), residues: 3602 helix: 0.25 (0.11), residues: 2389 sheet: -2.08 (0.89), residues: 38 loop : -2.37 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1783 TYR 0.027 0.002 TYR A2572 PHE 0.024 0.002 PHE A1219 TRP 0.014 0.002 TRP A3276 HIS 0.011 0.001 HIS A2105 Details of bonding type rmsd covalent geometry : bond 0.00552 (29633) covalent geometry : angle 0.73305 (40077) hydrogen bonds : bond 0.04148 ( 1591) hydrogen bonds : angle 4.57947 ( 4707) *********************** 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 203 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.5359 (mmp) cc_final: 0.4070 (ppp) REVERT: A 300 TRP cc_start: 0.8776 (m100) cc_final: 0.7970 (m100) REVERT: A 1829 TRP cc_start: 0.9335 (m100) cc_final: 0.8667 (m100) REVERT: A 1945 TYR cc_start: 0.8764 (t80) cc_final: 0.8486 (t80) REVERT: A 2408 MET cc_start: 0.7133 (tmt) cc_final: 0.6761 (tmt) REVERT: A 2565 MET cc_start: 0.8767 (tpp) cc_final: 0.7766 (tmm) REVERT: A 3538 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8479 (pm20) outliers start: 39 outliers final: 13 residues processed: 184 average time/residue: 0.6442 time to fit residues: 139.0922 Evaluate side-chains 162 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3538 GLU Chi-restraints excluded: chain A residue 3638 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 241 optimal weight: 0.6980 chunk 214 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 310 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 272 optimal weight: 0.4980 chunk 240 optimal weight: 0.5980 chunk 273 optimal weight: 0.5980 chunk 334 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1568 ASN ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2787 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.094996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.063157 restraints weight = 112428.248| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.92 r_work: 0.3072 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29633 Z= 0.125 Angle : 0.666 13.531 40077 Z= 0.330 Chirality : 0.041 0.180 4565 Planarity : 0.004 0.060 5085 Dihedral : 5.138 53.833 3935 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 1.41 % Allowed : 13.49 % Favored : 85.11 % 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: -0.57 (0.15), residues: 3602 helix: 0.55 (0.11), residues: 2381 sheet: -2.27 (0.86), residues: 40 loop : -2.21 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1783 TYR 0.024 0.001 TYR A2572 PHE 0.043 0.001 PHE A2231 TRP 0.016 0.001 TRP A3031 HIS 0.009 0.001 HIS A2105 Details of bonding type rmsd covalent geometry : bond 0.00273 (29633) covalent geometry : angle 0.66635 (40077) hydrogen bonds : bond 0.03645 ( 1591) hydrogen bonds : angle 4.36809 ( 4707) *********************** 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 213 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.5148 (tpt) cc_final: 0.4919 (tpt) REVERT: A 300 TRP cc_start: 0.8920 (m100) cc_final: 0.8282 (m100) REVERT: A 1743 MET cc_start: 0.6859 (mmt) cc_final: 0.6464 (mmt) REVERT: A 1829 TRP cc_start: 0.9336 (m100) cc_final: 0.8661 (m100) REVERT: A 1945 TYR cc_start: 0.8714 (t80) cc_final: 0.8436 (t80) REVERT: A 2092 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: A 2126 MET cc_start: 0.8830 (tmm) cc_final: 0.8466 (ppp) REVERT: A 2408 MET cc_start: 0.7189 (tmt) cc_final: 0.6886 (tmt) REVERT: A 2443 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8715 (tmm) REVERT: A 2565 MET cc_start: 0.8516 (tpp) cc_final: 0.7603 (tmm) REVERT: A 3031 TRP cc_start: 0.7660 (t-100) cc_final: 0.7340 (t-100) REVERT: A 3538 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: A 3694 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6711 (t80) outliers start: 45 outliers final: 8 residues processed: 200 average time/residue: 0.6287 time to fit residues: 148.6868 Evaluate side-chains 160 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2209 GLU Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3538 GLU Chi-restraints excluded: chain A residue 3694 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 301 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 312 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 298 optimal weight: 0.3980 chunk 183 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 166 optimal weight: 30.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1568 ASN ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.093606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.061168 restraints weight = 112691.958| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.39 r_work: 0.3071 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29633 Z= 0.191 Angle : 0.692 15.106 40077 Z= 0.341 Chirality : 0.042 0.208 4565 Planarity : 0.004 0.059 5085 Dihedral : 5.041 50.595 3935 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.19 % Favored : 92.75 % Rotamer: Outliers : 1.78 % Allowed : 14.52 % Favored : 83.70 % 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: -0.41 (0.15), residues: 3602 helix: 0.67 (0.11), residues: 2394 sheet: -2.18 (0.89), residues: 40 loop : -2.20 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.020 0.001 TYR A2572 PHE 0.029 0.001 PHE A2231 TRP 0.011 0.001 TRP A3276 HIS 0.009 0.001 HIS A2105 Details of bonding type rmsd covalent geometry : bond 0.00435 (29633) covalent geometry : angle 0.69222 (40077) hydrogen bonds : bond 0.03703 ( 1591) hydrogen bonds : angle 4.36698 ( 4707) *********************** 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 211 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 154 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.4558 (tpt) cc_final: 0.4226 (tpt) REVERT: A 300 TRP cc_start: 0.8892 (m100) cc_final: 0.8210 (m100) REVERT: A 384 MET cc_start: 0.9516 (ptp) cc_final: 0.9148 (ppp) REVERT: A 1013 ILE cc_start: 0.9022 (pp) cc_final: 0.8806 (mt) REVERT: A 1774 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8823 (pmm) REVERT: A 1829 TRP cc_start: 0.9338 (m100) cc_final: 0.8654 (m100) REVERT: A 1945 TYR cc_start: 0.8700 (t80) cc_final: 0.8412 (t80) REVERT: A 1975 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6298 (pt) REVERT: A 2092 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.6929 (pm20) REVERT: A 2285 LEU cc_start: 0.9252 (mm) cc_final: 0.8868 (pp) REVERT: A 2408 MET cc_start: 0.7066 (tmt) cc_final: 0.6766 (ppp) REVERT: A 2565 MET cc_start: 0.8449 (tpp) cc_final: 0.7606 (tmm) REVERT: A 2576 MET cc_start: 0.7098 (pmt) cc_final: 0.6879 (pmt) REVERT: A 3031 TRP cc_start: 0.7746 (t-100) cc_final: 0.7446 (t-100) REVERT: A 3694 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6855 (t80) REVERT: A 3974 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8810 (mpp) REVERT: A 4008 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: A 4028 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8198 (mm) outliers start: 57 outliers final: 20 residues processed: 196 average time/residue: 0.6006 time to fit residues: 140.2004 Evaluate side-chains 175 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 MET Chi-restraints excluded: chain A residue 1774 MET Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2209 GLU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3333 THR Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3445 LEU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3811 THR Chi-restraints excluded: chain A residue 3974 MET Chi-restraints excluded: chain A residue 4008 GLU Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 10.0000 chunk 340 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 19 optimal weight: 30.0000 chunk 294 optimal weight: 8.9990 chunk 318 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 354 optimal weight: 0.6980 chunk 253 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1568 ASN ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.094164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.061850 restraints weight = 112337.698| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.38 r_work: 0.3093 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29633 Z= 0.143 Angle : 0.677 14.341 40077 Z= 0.330 Chirality : 0.041 0.195 4565 Planarity : 0.004 0.057 5085 Dihedral : 4.930 51.737 3935 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.16 % Favored : 92.78 % Rotamer: Outliers : 1.63 % Allowed : 15.49 % Favored : 82.88 % 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: -0.24 (0.15), residues: 3602 helix: 0.82 (0.11), residues: 2375 sheet: -2.20 (0.88), residues: 40 loop : -2.12 (0.19), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.019 0.001 TYR A2572 PHE 0.025 0.001 PHE A2231 TRP 0.012 0.001 TRP A3276 HIS 0.009 0.001 HIS A2105 Details of bonding type rmsd covalent geometry : bond 0.00325 (29633) covalent geometry : angle 0.67677 (40077) hydrogen bonds : bond 0.03520 ( 1591) hydrogen bonds : angle 4.28583 ( 4707) *********************** 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 202 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.4953 (mmp) cc_final: 0.4163 (pp-130) REVERT: A 189 MET cc_start: 0.4404 (tpt) cc_final: 0.4014 (tpt) REVERT: A 238 MET cc_start: 0.4376 (mtm) cc_final: 0.4035 (mtp) REVERT: A 300 TRP cc_start: 0.8859 (m100) cc_final: 0.8186 (m100) REVERT: A 384 MET cc_start: 0.9504 (ptp) cc_final: 0.9159 (ppp) REVERT: A 438 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9381 (mm) REVERT: A 1013 ILE cc_start: 0.8952 (pp) cc_final: 0.8735 (mt) REVERT: A 1392 MET cc_start: 0.7543 (mmm) cc_final: 0.7100 (mmp) REVERT: A 1774 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8898 (pmm) REVERT: A 1975 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6647 (pt) REVERT: A 2092 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: A 2104 MET cc_start: 0.3892 (tmm) cc_final: 0.3667 (ppp) REVERT: A 2126 MET cc_start: 0.8907 (tmm) cc_final: 0.8547 (ppp) REVERT: A 2285 LEU cc_start: 0.9316 (mm) cc_final: 0.8936 (pp) REVERT: A 2408 MET cc_start: 0.7252 (tmt) cc_final: 0.6995 (ppp) REVERT: A 2565 MET cc_start: 0.8354 (tpp) cc_final: 0.7771 (tmm) REVERT: A 2576 MET cc_start: 0.7145 (pmt) cc_final: 0.6876 (pmt) REVERT: A 3031 TRP cc_start: 0.7596 (t-100) cc_final: 0.7245 (t-100) REVERT: A 3538 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: A 3694 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6834 (t80) REVERT: A 4028 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8286 (mm) outliers start: 52 outliers final: 22 residues processed: 187 average time/residue: 0.6500 time to fit residues: 144.2505 Evaluate side-chains 172 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 MET Chi-restraints excluded: chain A residue 1774 MET Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2209 GLU Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3333 THR Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3538 GLU Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3811 THR Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 229 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 231 optimal weight: 0.0670 chunk 24 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1568 ASN ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.094126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.061764 restraints weight = 112646.922| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.38 r_work: 0.3091 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29633 Z= 0.148 Angle : 0.684 14.426 40077 Z= 0.332 Chirality : 0.041 0.195 4565 Planarity : 0.004 0.056 5085 Dihedral : 4.845 50.772 3935 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.08 % Favored : 92.87 % Rotamer: Outliers : 1.69 % Allowed : 15.89 % Favored : 82.42 % 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: 0.86 (0.11), residues: 2381 sheet: -2.21 (0.86), residues: 40 loop : -2.11 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3696 TYR 0.018 0.001 TYR A2572 PHE 0.028 0.001 PHE A1219 TRP 0.012 0.001 TRP A3276 HIS 0.009 0.001 HIS A2105 Details of bonding type rmsd covalent geometry : bond 0.00338 (29633) covalent geometry : angle 0.68363 (40077) hydrogen bonds : bond 0.03484 ( 1591) hydrogen bonds : angle 4.25966 ( 4707) *********************** 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 200 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.4682 (tpt) cc_final: 0.4169 (tpt) REVERT: A 238 MET cc_start: 0.4339 (mtm) cc_final: 0.4095 (mtp) REVERT: A 300 TRP cc_start: 0.8830 (m100) cc_final: 0.8140 (m100) REVERT: A 438 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9374 (mm) REVERT: A 1013 ILE cc_start: 0.8959 (pp) cc_final: 0.8748 (mt) REVERT: A 1583 MET cc_start: 0.7915 (ttt) cc_final: 0.7484 (tmt) REVERT: A 1774 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8954 (pmm) REVERT: A 1829 TRP cc_start: 0.9358 (m100) cc_final: 0.8628 (m100) REVERT: A 1975 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6787 (pt) REVERT: A 2092 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: A 2094 MET cc_start: 0.9319 (ppp) cc_final: 0.9106 (ppp) REVERT: A 2126 MET cc_start: 0.8896 (tmm) cc_final: 0.8625 (ppp) REVERT: A 2285 LEU cc_start: 0.9245 (mm) cc_final: 0.8871 (pp) REVERT: A 2341 LEU cc_start: 0.9743 (mm) cc_final: 0.9421 (pp) REVERT: A 2408 MET cc_start: 0.6896 (tmt) cc_final: 0.6524 (tmt) REVERT: A 2443 MET cc_start: 0.8738 (tmm) cc_final: 0.8505 (tmm) REVERT: A 2565 MET cc_start: 0.8678 (tpp) cc_final: 0.7318 (tmm) REVERT: A 2576 MET cc_start: 0.7184 (pmt) cc_final: 0.6859 (pmt) REVERT: A 3031 TRP cc_start: 0.7497 (t-100) cc_final: 0.7213 (t-100) REVERT: A 3538 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: A 3694 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6843 (t80) REVERT: A 3858 MET cc_start: 0.9170 (ttp) cc_final: 0.8687 (tmm) REVERT: A 3932 MET cc_start: 0.9002 (mmm) cc_final: 0.8465 (mmm) REVERT: A 4008 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: A 4028 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8285 (mm) outliers start: 54 outliers final: 21 residues processed: 187 average time/residue: 0.6628 time to fit residues: 146.4668 Evaluate side-chains 174 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1437 TYR Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1757 MET Chi-restraints excluded: chain A residue 1774 MET Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3333 THR Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3445 LEU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3538 GLU Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3811 THR Chi-restraints excluded: chain A residue 4008 GLU Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 42 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 23 optimal weight: 30.0000 chunk 119 optimal weight: 0.9980 chunk 126 optimal weight: 0.2980 chunk 20 optimal weight: 50.0000 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 326 optimal weight: 0.0670 chunk 203 optimal weight: 20.0000 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1568 ASN ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.094888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.062413 restraints weight = 113442.121| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.43 r_work: 0.3113 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 29633 Z= 0.120 Angle : 0.685 14.375 40077 Z= 0.330 Chirality : 0.041 0.189 4565 Planarity : 0.004 0.057 5085 Dihedral : 4.740 50.715 3935 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 1.22 % Allowed : 16.74 % Favored : 82.04 % 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: -0.08 (0.15), residues: 3602 helix: 0.95 (0.11), residues: 2390 sheet: -2.23 (0.82), residues: 40 loop : -2.09 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1606 TYR 0.020 0.001 TYR A2184 PHE 0.021 0.001 PHE A2231 TRP 0.014 0.001 TRP A3276 HIS 0.008 0.001 HIS A2105 Details of bonding type rmsd covalent geometry : bond 0.00268 (29633) covalent geometry : angle 0.68536 (40077) hydrogen bonds : bond 0.03299 ( 1591) hydrogen bonds : angle 4.20210 ( 4707) *********************** 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 194 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.5406 (mmp) cc_final: 0.4401 (pp-130) REVERT: A 189 MET cc_start: 0.4611 (tpt) cc_final: 0.4036 (tpt) REVERT: A 300 TRP cc_start: 0.8839 (m100) cc_final: 0.8222 (m100) REVERT: A 326 MET cc_start: 0.7850 (mpm) cc_final: 0.7432 (pp-130) REVERT: A 384 MET cc_start: 0.9431 (ptp) cc_final: 0.9035 (ppp) REVERT: A 438 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9373 (mm) REVERT: A 1392 MET cc_start: 0.7394 (mmm) cc_final: 0.6869 (mmp) REVERT: A 1431 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9232 (pp) REVERT: A 1583 MET cc_start: 0.7913 (ttt) cc_final: 0.7422 (tmt) REVERT: A 1774 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8990 (pmm) REVERT: A 1829 TRP cc_start: 0.9359 (m100) cc_final: 0.8692 (m100) REVERT: A 1975 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6548 (pt) REVERT: A 2092 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.6744 (pm20) REVERT: A 2094 MET cc_start: 0.9344 (ppp) cc_final: 0.9143 (ptm) REVERT: A 2126 MET cc_start: 0.8894 (tmm) cc_final: 0.8447 (ppp) REVERT: A 2285 LEU cc_start: 0.9213 (mm) cc_final: 0.8822 (pp) REVERT: A 2341 LEU cc_start: 0.9654 (mm) cc_final: 0.9313 (pp) REVERT: A 2408 MET cc_start: 0.6903 (tmt) cc_final: 0.6088 (tmt) REVERT: A 2565 MET cc_start: 0.8373 (tpp) cc_final: 0.7328 (tmm) REVERT: A 2576 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6844 (pmt) REVERT: A 3031 TRP cc_start: 0.7369 (t-100) cc_final: 0.7018 (t-100) REVERT: A 3104 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8593 (mp10) REVERT: A 3483 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8242 (tpt) REVERT: A 3538 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: A 3613 MET cc_start: 0.9457 (tmm) cc_final: 0.9033 (pp-130) REVERT: A 3694 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6751 (t80) REVERT: A 3932 MET cc_start: 0.8992 (mmm) cc_final: 0.8476 (mmm) REVERT: A 4008 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: A 4028 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8242 (mm) outliers start: 39 outliers final: 13 residues processed: 186 average time/residue: 0.7000 time to fit residues: 152.2884 Evaluate side-chains 173 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1437 TYR Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1751 GLU Chi-restraints excluded: chain A residue 1757 MET Chi-restraints excluded: chain A residue 1774 MET Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2576 MET Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3538 GLU Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 4008 GLU Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 82 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 135 optimal weight: 0.0470 chunk 53 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.093986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.061609 restraints weight = 112761.409| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.41 r_work: 0.3088 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29633 Z= 0.167 Angle : 0.721 18.023 40077 Z= 0.346 Chirality : 0.042 0.195 4565 Planarity : 0.004 0.056 5085 Dihedral : 4.721 49.100 3935 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.83 % Favored : 93.11 % Rotamer: Outliers : 1.22 % Allowed : 16.99 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3602 helix: 0.91 (0.11), residues: 2407 sheet: -1.94 (0.86), residues: 38 loop : -2.11 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1606 TYR 0.020 0.001 TYR A2184 PHE 0.021 0.001 PHE A2231 TRP 0.010 0.001 TRP A3031 HIS 0.011 0.001 HIS A2183 Details of bonding type rmsd covalent geometry : bond 0.00383 (29633) covalent geometry : angle 0.72140 (40077) hydrogen bonds : bond 0.03413 ( 1591) hydrogen bonds : angle 4.26848 ( 4707) *********************** 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 188 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.4617 (mmp) cc_final: 0.4036 (pp-130) REVERT: A 189 MET cc_start: 0.4495 (tpt) cc_final: 0.3906 (tpt) REVERT: A 300 TRP cc_start: 0.8828 (m100) cc_final: 0.8203 (m100) REVERT: A 326 MET cc_start: 0.8021 (mpm) cc_final: 0.7472 (pp-130) REVERT: A 384 MET cc_start: 0.9443 (ptp) cc_final: 0.9044 (ppp) REVERT: A 438 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9382 (mm) REVERT: A 1392 MET cc_start: 0.7668 (mmm) cc_final: 0.7187 (mmp) REVERT: A 1431 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9245 (pp) REVERT: A 1583 MET cc_start: 0.8013 (ttt) cc_final: 0.7629 (ptm) REVERT: A 1774 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8974 (pmm) REVERT: A 1829 TRP cc_start: 0.9358 (m100) cc_final: 0.8679 (m100) REVERT: A 1871 MET cc_start: 0.8853 (pp-130) cc_final: 0.8389 (pmt) REVERT: A 1881 TYR cc_start: 0.9442 (m-10) cc_final: 0.9208 (m-10) REVERT: A 2126 MET cc_start: 0.8904 (tmm) cc_final: 0.8694 (ppp) REVERT: A 2341 LEU cc_start: 0.9640 (mm) cc_final: 0.9301 (pp) REVERT: A 2408 MET cc_start: 0.6597 (tmt) cc_final: 0.6235 (tmt) REVERT: A 2565 MET cc_start: 0.8374 (tpp) cc_final: 0.7392 (tmm) REVERT: A 2576 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6990 (pmt) REVERT: A 3031 TRP cc_start: 0.7570 (t-100) cc_final: 0.7280 (t-100) REVERT: A 3483 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8212 (tpt) REVERT: A 3538 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8360 (pm20) REVERT: A 3694 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6845 (t80) REVERT: A 4008 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8253 (mt-10) REVERT: A 4028 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8267 (mm) outliers start: 39 outliers final: 18 residues processed: 179 average time/residue: 0.6753 time to fit residues: 141.8093 Evaluate side-chains 173 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1437 TYR Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1757 MET Chi-restraints excluded: chain A residue 1774 MET Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 2576 MET Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3333 THR Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3445 LEU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3538 GLU Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 4008 GLU Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 213 optimal weight: 6.9990 chunk 293 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 345 optimal weight: 7.9990 chunk 348 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 276 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.093563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.060808 restraints weight = 113536.148| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.39 r_work: 0.3072 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29633 Z= 0.191 Angle : 0.741 17.507 40077 Z= 0.354 Chirality : 0.042 0.217 4565 Planarity : 0.004 0.055 5085 Dihedral : 4.768 50.796 3935 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.08 % Favored : 92.87 % Rotamer: Outliers : 1.00 % Allowed : 17.30 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3602 helix: 0.91 (0.11), residues: 2398 sheet: -1.84 (0.86), residues: 38 loop : -2.10 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1606 TYR 0.019 0.001 TYR A2184 PHE 0.035 0.001 PHE A1219 TRP 0.013 0.001 TRP A3031 HIS 0.010 0.001 HIS A2105 Details of bonding type rmsd covalent geometry : bond 0.00436 (29633) covalent geometry : angle 0.74069 (40077) hydrogen bonds : bond 0.03503 ( 1591) hydrogen bonds : angle 4.31008 ( 4707) ********************** 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 180 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.4549 (mmp) cc_final: 0.4046 (pp-130) REVERT: A 189 MET cc_start: 0.4566 (tpt) cc_final: 0.4007 (tpt) REVERT: A 238 MET cc_start: 0.3885 (mtm) cc_final: 0.3607 (mtp) REVERT: A 300 TRP cc_start: 0.8869 (m100) cc_final: 0.8230 (m100) REVERT: A 326 MET cc_start: 0.8033 (mpm) cc_final: 0.7478 (pp-130) REVERT: A 438 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9294 (mm) REVERT: A 1392 MET cc_start: 0.7720 (mmm) cc_final: 0.7223 (mmp) REVERT: A 1431 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9253 (pp) REVERT: A 1583 MET cc_start: 0.8052 (ttt) cc_final: 0.7620 (ptm) REVERT: A 1608 ARG cc_start: 0.8667 (mtm180) cc_final: 0.8393 (mmp-170) REVERT: A 1774 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8939 (pmm) REVERT: A 1829 TRP cc_start: 0.9336 (m100) cc_final: 0.8682 (m100) REVERT: A 1871 MET cc_start: 0.8874 (pp-130) cc_final: 0.8611 (pmt) REVERT: A 1881 TYR cc_start: 0.9422 (m-10) cc_final: 0.9181 (m-10) REVERT: A 2094 MET cc_start: 0.9343 (ptm) cc_final: 0.9107 (ptt) REVERT: A 2285 LEU cc_start: 0.9132 (mm) cc_final: 0.8693 (pp) REVERT: A 2341 LEU cc_start: 0.9643 (mm) cc_final: 0.9305 (pp) REVERT: A 2565 MET cc_start: 0.8294 (tpp) cc_final: 0.7378 (tmm) REVERT: A 3031 TRP cc_start: 0.7689 (t-100) cc_final: 0.7476 (t-100) REVERT: A 3483 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8206 (tpt) REVERT: A 3538 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8337 (pm20) REVERT: A 4008 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: A 4028 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8287 (mm) outliers start: 32 outliers final: 18 residues processed: 174 average time/residue: 0.7013 time to fit residues: 142.9694 Evaluate side-chains 172 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1437 TYR Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1757 MET Chi-restraints excluded: chain A residue 1774 MET Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3155 VAL Chi-restraints excluded: chain A residue 3333 THR Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3445 LEU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3538 GLU Chi-restraints excluded: chain A residue 4008 GLU Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 248 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 232 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 170 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.094263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.061671 restraints weight = 113877.434| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.42 r_work: 0.3102 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29633 Z= 0.133 Angle : 0.737 17.277 40077 Z= 0.349 Chirality : 0.041 0.190 4565 Planarity : 0.004 0.054 5085 Dihedral : 4.711 51.111 3935 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 0.94 % Allowed : 17.65 % Favored : 81.41 % 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: 0.94 (0.11), residues: 2395 sheet: -2.07 (0.82), residues: 40 loop : -2.05 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1606 TYR 0.019 0.001 TYR A2184 PHE 0.021 0.001 PHE A2231 TRP 0.012 0.001 TRP A3276 HIS 0.009 0.001 HIS A2183 Details of bonding type rmsd covalent geometry : bond 0.00304 (29633) covalent geometry : angle 0.73681 (40077) hydrogen bonds : bond 0.03360 ( 1591) hydrogen bonds : angle 4.25249 ( 4707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11443.49 seconds wall clock time: 194 minutes 46.34 seconds (11686.34 seconds total)