Starting phenix.real_space_refine on Tue Jul 7 01:25:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9l_51156/07_2026/9g9l_51156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9l_51156/07_2026/9g9l_51156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g9l_51156/07_2026/9g9l_51156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9l_51156/07_2026/9g9l_51156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g9l_51156/07_2026/9g9l_51156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9l_51156/07_2026/9g9l_51156.map" } resolution = 4.63 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 236 5.16 5 C 25359 2.51 5 N 6723 2.21 5 O 7436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39800 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 29010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3688, 29010 Classifications: {'peptide': 3688} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 142} Link IDs: {'PTRANS': 160, 'TRANS': 3527} Chain breaks: 17 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 561 Unresolved non-hydrogen angles: 684 Unresolved non-hydrogen dihedrals: 466 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 17, 'ASN:plan1': 3, 'GLU:plan': 11, 'GLN:plan1': 9, 'PHE:plan': 7, 'TYR:plan': 5, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 295 Chain: "B" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3825 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 27, 'TRANS': 460} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 6, 'TYR:plan': 2, 'ASP:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 5093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5093 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 26, 'TRANS': 620} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'PHE:plan': 2, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "F" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 91} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 155 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 19} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Chain: "D" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 488 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "E" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 474 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Time building chain proxies: 8.79, per 1000 atoms: 0.22 Number of scatterers: 39800 At special positions: 0 Unit cell: (131.704, 165.608, 220.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 236 16.00 P 46 15.00 O 7436 8.00 N 6723 7.00 C 25359 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: 4.25 Conformation dependent library (CDL) restraints added in 1.9 seconds 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9472 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 17 sheets defined 62.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.776A pdb=" N ALA A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 45 Processing helix chain 'A' and resid 52 through 67 removed outlier: 4.467A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 Processing helix chain 'A' and resid 100 through 116 removed outlier: 3.684A pdb=" N THR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 148 through 151 Processing helix chain 'A' and resid 152 through 161 removed outlier: 3.595A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.066A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.543A pdb=" N ILE A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.566A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 4.259A pdb=" N SER A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 291 through 303 Processing helix chain 'A' and resid 305 through 330 Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.747A pdb=" N ILE A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 377 through 396 Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.150A pdb=" N TYR A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 409 through 423 Processing helix chain 'A' and resid 430 through 443 removed outlier: 4.011A pdb=" N VAL A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 469 Processing helix chain 'A' and resid 472 through 491 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.617A pdb=" N VAL A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 548 removed outlier: 3.531A pdb=" N ILE A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 579 Processing helix chain 'A' and resid 616 through 637 removed outlier: 3.640A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 633 " --> pdb=" O PHE A 629 " (cutoff:3.500A) Proline residue: A 635 - end of helix Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'A' and resid 647 through 660 removed outlier: 3.962A pdb=" N GLU A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 681 removed outlier: 4.096A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 725 through 734 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.527A pdb=" N ILE A 741 " --> pdb=" O PRO A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 760 removed outlier: 4.123A pdb=" N ALA A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 4.004A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 793 removed outlier: 4.123A pdb=" N LYS A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASP A 791 " --> pdb=" O PRO A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.095A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 861 Processing helix chain 'A' and resid 865 through 869 removed outlier: 4.214A pdb=" N ASN A 869 " --> pdb=" O ILE A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 925 through 945 Processing helix chain 'A' and resid 958 through 974 Proline residue: A 967 - end of helix removed outlier: 3.987A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 996 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 4.093A pdb=" N ALA A1008 " --> pdb=" O GLN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1037 Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1086 removed outlier: 3.725A pdb=" N ARG A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1092 Processing helix chain 'A' and resid 1099 through 1118 removed outlier: 4.095A pdb=" N ALA A1103 " --> pdb=" O PHE A1099 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A1118 " --> pdb=" O ALA A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1141 removed outlier: 4.554A pdb=" N GLN A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1147 Processing helix chain 'A' and resid 1164 through 1174 removed outlier: 3.598A pdb=" N LEU A1168 " --> pdb=" O CYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1198 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1203 through 1213 removed outlier: 3.627A pdb=" N LYS A1213 " --> pdb=" O LYS A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1223 removed outlier: 4.800A pdb=" N ILE A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1272 Processing helix chain 'A' and resid 1277 through 1283 removed outlier: 3.951A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1299 removed outlier: 4.122A pdb=" N GLU A1299 " --> pdb=" O ALA A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1352 Processing helix chain 'A' and resid 1367 through 1378 removed outlier: 4.031A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN A1374 " --> pdb=" O ARG A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1388 Processing helix chain 'A' and resid 1389 through 1409 Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1411 through 1423 Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 3.882A pdb=" N GLU A1430 " --> pdb=" O GLN A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1462 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.770A pdb=" N ILE A1467 " --> pdb=" O LEU A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1491 removed outlier: 4.643A pdb=" N GLU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS A1489 " --> pdb=" O SER A1485 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1521 Processing helix chain 'A' and resid 1524 through 1533 Processing helix chain 'A' and resid 1555 through 1574 removed outlier: 6.456A pdb=" N GLU A1565 " --> pdb=" O SER A1561 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A1566 " --> pdb=" O LEU A1562 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1585 Processing helix chain 'A' and resid 1590 through 1607 Processing helix chain 'A' and resid 1608 through 1610 No H-bonds generated for 'chain 'A' and resid 1608 through 1610' Processing helix chain 'A' and resid 1612 through 1625 removed outlier: 4.031A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A1625 " --> pdb=" O THR A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1632 removed outlier: 4.101A pdb=" N SER A1631 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 Processing helix chain 'A' and resid 1657 through 1663 removed outlier: 3.573A pdb=" N PHE A1661 " --> pdb=" O SER A1657 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR A1663 " --> pdb=" O VAL A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 Processing helix chain 'A' and resid 1685 through 1693 removed outlier: 3.516A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1699 Proline residue: A1697 - end of helix No H-bonds generated for 'chain 'A' and resid 1694 through 1699' Processing helix chain 'A' and resid 1705 through 1722 removed outlier: 3.561A pdb=" N GLU A1709 " --> pdb=" O GLY A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1767 removed outlier: 3.606A pdb=" N CYS A1767 " --> pdb=" O THR A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1788 removed outlier: 3.951A pdb=" N PHE A1778 " --> pdb=" O MET A1774 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1804 removed outlier: 4.311A pdb=" N MET A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1830 removed outlier: 3.968A pdb=" N SER A1823 " --> pdb=" O PHE A1819 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N THR A1826 " --> pdb=" O ARG A1822 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS A1830 " --> pdb=" O THR A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1852 removed outlier: 3.654A pdb=" N PHE A1839 " --> pdb=" O ALA A1835 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1882 removed outlier: 3.795A pdb=" N ASP A1864 " --> pdb=" O GLU A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1924 removed outlier: 3.927A pdb=" N LYS A1917 " --> pdb=" O LYS A1913 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1955 Processing helix chain 'A' and resid 1971 through 1975 Processing helix chain 'A' and resid 2034 through 2048 Processing helix chain 'A' and resid 2093 through 2108 Processing helix chain 'A' and resid 2123 through 2132 Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.554A pdb=" N THR A2153 " --> pdb=" O LEU A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 4.190A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2160 through 2171 removed outlier: 4.508A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2185 through 2196 removed outlier: 3.865A pdb=" N ILE A2189 " --> pdb=" O MET A2185 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2221 removed outlier: 4.135A pdb=" N GLU A2209 " --> pdb=" O VAL A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2245 removed outlier: 3.922A pdb=" N TRP A2245 " --> pdb=" O LEU A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2270 through 2282 Processing helix chain 'A' and resid 2297 through 2308 Processing helix chain 'A' and resid 2313 through 2327 removed outlier: 5.173A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) Processing helix chain 'A' and resid 2339 through 2351 removed outlier: 3.604A pdb=" N GLU A2343 " --> pdb=" O GLU A2339 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 removed outlier: 3.934A pdb=" N LYS A2369 " --> pdb=" O ASN A2365 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2377 removed outlier: 4.033A pdb=" N ARG A2377 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.990A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 removed outlier: 3.888A pdb=" N LEU A2415 " --> pdb=" O LEU A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2419 through 2424 removed outlier: 3.837A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) 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 2459 removed outlier: 4.131A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2462 No H-bonds generated for 'chain 'A' and resid 2460 through 2462' Processing helix chain 'A' and resid 2468 through 2485 removed outlier: 3.772A pdb=" N GLN A2472 " --> pdb=" O THR A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 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 2527 Processing helix chain 'A' and resid 2534 through 2540 Processing helix chain 'A' and resid 2541 through 2546 removed outlier: 3.882A pdb=" N TYR A2546 " --> pdb=" O ASN A2543 " (cutoff:3.500A) Processing helix chain 'A' and resid 2553 through 2566 removed outlier: 3.788A pdb=" N LEU A2557 " --> pdb=" O HIS A2553 " (cutoff:3.500A) Processing helix chain 'A' and resid 2567 through 2569 No H-bonds generated for 'chain 'A' and resid 2567 through 2569' Processing helix chain 'A' and resid 2786 through 2799 removed outlier: 4.100A pdb=" N LEU A2790 " --> pdb=" O LYS A2786 " (cutoff:3.500A) Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2821 Processing helix chain 'A' and resid 2825 through 2847 Processing helix chain 'A' and resid 2851 through 2865 removed outlier: 4.156A pdb=" N HIS A2865 " --> pdb=" O ILE A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2883 removed outlier: 3.616A pdb=" N VAL A2876 " --> pdb=" O ASP A2872 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2901 Processing helix chain 'A' and resid 2919 through 2934 Processing helix chain 'A' and resid 2936 through 2947 Processing helix chain 'A' and resid 2950 through 2962 Processing helix chain 'A' and resid 2964 through 2978 Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3008 through 3017 Processing helix chain 'A' and resid 3034 through 3054 Proline residue: A3042 - end of helix Processing helix chain 'A' and resid 3059 through 3068 Processing helix chain 'A' and resid 3070 through 3093 removed outlier: 4.110A pdb=" N GLN A3074 " --> pdb=" O HIS A3070 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A3078 " --> pdb=" O GLN A3074 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU A3079 " --> pdb=" O LYS A3075 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLN A3084 " --> pdb=" O LEU A3080 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU A3085 " --> pdb=" O HIS A3081 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3117 Processing helix chain 'A' and resid 3121 through 3130 Processing helix chain 'A' and resid 3131 through 3146 Processing helix chain 'A' and resid 3147 through 3153 Processing helix chain 'A' and resid 3153 through 3167 removed outlier: 3.950A pdb=" N LEU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3194 removed outlier: 3.668A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3249 Processing helix chain 'A' and resid 3251 through 3269 removed outlier: 3.790A pdb=" N ALA A3255 " --> pdb=" O ASN A3251 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A3260 " --> pdb=" O MET A3256 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU A3261 " --> pdb=" O LYS A3257 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A3262 " --> pdb=" O LEU A3258 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS A3264 " --> pdb=" O LYS A3260 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU A3265 " --> pdb=" O GLU A3261 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3287 Processing helix chain 'A' and resid 3290 through 3306 removed outlier: 3.970A pdb=" N GLN A3296 " --> pdb=" O GLY A3292 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A3306 " --> pdb=" O LYS A3302 " (cutoff:3.500A) Processing helix chain 'A' and resid 3313 through 3319 Processing helix chain 'A' and resid 3319 through 3344 removed outlier: 3.721A pdb=" N PHE A3323 " --> pdb=" O ASN A3319 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3359 through 3364 Processing helix chain 'A' and resid 3370 through 3394 removed outlier: 3.849A pdb=" N GLU A3394 " --> pdb=" O GLN A3390 " (cutoff:3.500A) Processing helix chain 'A' and resid 3407 through 3428 Processing helix chain 'A' and resid 3441 through 3455 removed outlier: 3.996A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3475 Proline residue: A3466 - end of helix Processing helix chain 'A' and resid 3480 through 3489 removed outlier: 3.521A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3505 Processing helix chain 'A' and resid 3506 through 3508 No H-bonds generated for 'chain 'A' and resid 3506 through 3508' Processing helix chain 'A' and resid 3511 through 3522 Processing helix chain 'A' and resid 3529 through 3538 Processing helix chain 'A' and resid 3548 through 3562 Processing helix chain 'A' and resid 3567 through 3579 Processing helix chain 'A' and resid 3580 through 3599 removed outlier: 3.988A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR A3599 " --> pdb=" O GLU A3595 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3618 removed outlier: 4.190A pdb=" N MET A3609 " --> pdb=" O ASN A3605 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3637 Processing helix chain 'A' and resid 3638 through 3643 removed outlier: 3.737A pdb=" N HIS A3643 " --> pdb=" O GLU A3639 " (cutoff:3.500A) Processing helix chain 'A' and resid 3658 through 3672 removed outlier: 3.567A pdb=" N ILE A3662 " --> pdb=" O ASP A3658 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3683 Processing helix chain 'A' and resid 3684 through 3690 Processing helix chain 'A' and resid 3758 through 3778 removed outlier: 3.528A pdb=" N GLN A3762 " --> pdb=" O LEU A3758 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3784 Processing helix chain 'A' and resid 3812 through 3820 Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3847 removed outlier: 4.212A pdb=" N MET A3846 " --> pdb=" O TRP A3842 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3858 Processing helix chain 'A' and resid 3863 through 3878 Processing helix chain 'A' and resid 3881 through 3891 Processing helix chain 'A' and resid 3893 through 3918 Processing helix chain 'A' and resid 3947 through 3953 removed outlier: 3.795A pdb=" N GLN A3951 " --> pdb=" O GLY A3947 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 3.732A pdb=" N ILE A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 3.580A pdb=" N SER A3982 " --> pdb=" O GLY A3978 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4007 removed outlier: 3.737A pdb=" N LYS A4007 " --> pdb=" O ASP A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4023 Processing helix chain 'A' and resid 4039 through 4052 removed outlier: 3.730A pdb=" N LYS A4043 " --> pdb=" O TYR A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4069 removed outlier: 3.663A pdb=" N GLU A4069 " --> pdb=" O LEU A4065 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4088 through 4093 Processing helix chain 'A' and resid 4099 through 4113 Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4119 through 4120 No H-bonds generated for 'chain 'A' and resid 4119 through 4120' Processing helix chain 'A' and resid 4121 through 4125 Processing helix chain 'B' and resid 58 through 77 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 136 Processing helix chain 'B' and resid 142 through 155 Processing helix chain 'B' and resid 179 through 197 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.651A pdb=" N LYS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 455 through 468 removed outlier: 3.733A pdb=" N LYS B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 4.394A pdb=" N PHE B 478 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 removed outlier: 3.522A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 519 removed outlier: 4.940A pdb=" N LYS B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.852A pdb=" N GLU B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 49 Processing helix chain 'C' and resid 87 through 98 Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 198 through 216 Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 324 through 332 removed outlier: 3.622A pdb=" N GLU C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 330 " --> pdb=" O VAL C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 370 through 388 removed outlier: 3.649A pdb=" N ALA C 374 " --> pdb=" O ASP C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 484 through 500 removed outlier: 3.934A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS C 496 " --> pdb=" O GLN C 492 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG C 497 " --> pdb=" O CYS C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.617A pdb=" N TRP C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 537 removed outlier: 3.809A pdb=" N THR C 523 " --> pdb=" O PRO C 519 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing helix chain 'C' and resid 594 through 606 removed outlier: 3.685A pdb=" N LYS C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 622 removed outlier: 4.243A pdb=" N GLN C 622 " --> pdb=" O ASN C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 649 Processing helix chain 'C' and resid 651 through 668 Processing helix chain 'C' and resid 675 through 682 Processing helix chain 'C' and resid 693 through 703 Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'F' and resid 40 through 44 removed outlier: 3.649A pdb=" N SER F 43 " --> pdb=" O TRP F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 68 Processing helix chain 'F' and resid 90 through 98 Processing helix chain 'F' and resid 111 through 122 removed outlier: 3.829A pdb=" N LEU F 115 " --> pdb=" O LYS F 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AA2, first strand: chain 'A' and resid 894 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 1538 through 1539 Processing sheet with id=AA4, first strand: chain 'A' and resid 2587 through 2588 Processing sheet with id=AA5, first strand: chain 'A' and resid 3719 through 3721 removed outlier: 6.250A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3719 through 3721 removed outlier: 6.250A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET A3796 " --> pdb=" O LEU A3800 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A3802 " --> pdb=" O VAL A3794 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3810 through 3811 Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 109 removed outlier: 6.067A pdb=" N VAL B 85 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLU B 107 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU B 83 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N ALA B 84 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 38 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TYR B 88 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 201 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 258 through 262 removed outlier: 3.721A pdb=" N LEU B 413 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA B 396 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG B 399 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 347 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 401 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU B 345 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU B 345 " --> pdb=" O LYS B 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 287 through 289 Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 329 Processing sheet with id=AB3, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 15 removed outlier: 7.434A pdb=" N VAL C 10 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N VAL C 57 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU C 12 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE C 59 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET C 14 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE C 54 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N HIS C 82 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU C 56 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AB6, first strand: chain 'C' and resid 362 through 366 removed outlier: 9.350A pdb=" N PHE C 340 " --> pdb=" O PRO C 248 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ARG C 250 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL C 342 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR C 252 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N GLY C 344 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N PHE C 340 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ALA C 396 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL C 342 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG C 394 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N MET C 389 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA C 391 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA C 408 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 393 " --> pdb=" O GLY C 406 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 406 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 314 through 316 Processing sheet with id=AB8, first strand: chain 'C' and resid 464 through 468 removed outlier: 4.649A pdb=" N ASP C 467 " --> pdb=" O THR C 472 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR C 472 " --> pdb=" O ASP C 467 " (cutoff:3.500A) 2087 hydrogen bonds defined for protein. 6102 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: 12.27 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8854 1.33 - 1.45: 8391 1.45 - 1.57: 22987 1.57 - 1.69: 91 1.69 - 1.81: 372 Bond restraints: 40695 Sorted by residual: bond pdb=" C LEU B 311 " pdb=" N LEU B 312 " ideal model delta sigma weight residual 1.331 1.272 0.058 1.48e-02 4.57e+03 1.55e+01 bond pdb=" C3' DA D 25 " pdb=" C2' DA D 25 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.16e+00 bond pdb=" C5' DA E 33 " pdb=" C4' DA E 33 " ideal model delta sigma weight residual 1.512 1.532 -0.020 7.00e-03 2.04e+04 8.51e+00 bond pdb=" N ILE B 425 " pdb=" CA ILE B 425 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.30e+00 bond pdb=" N LEU A2446 " pdb=" CA LEU A2446 " ideal model delta sigma weight residual 1.453 1.490 -0.036 1.27e-02 6.20e+03 8.22e+00 ... (remaining 40690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 54408 2.71 - 5.41: 732 5.41 - 8.12: 109 8.12 - 10.83: 11 10.83 - 13.53: 2 Bond angle restraints: 55262 Sorted by residual: angle pdb=" N PRO A 126 " pdb=" CA PRO A 126 " pdb=" CB PRO A 126 " ideal model delta sigma weight residual 103.33 110.57 -7.24 1.10e+00 8.26e-01 4.33e+01 angle pdb=" N SER A2297 " pdb=" CA SER A2297 " pdb=" C SER A2297 " ideal model delta sigma weight residual 114.56 107.77 6.79 1.27e+00 6.20e-01 2.86e+01 angle pdb=" C LEU B 281 " pdb=" N LYS B 282 " pdb=" CA LYS B 282 " ideal model delta sigma weight residual 120.94 130.90 -9.96 1.90e+00 2.77e-01 2.75e+01 angle pdb=" O4' DA D 22 " pdb=" C4' DA D 22 " pdb=" C3' DA D 22 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.38e+01 angle pdb=" N GLN A 857 " pdb=" CA GLN A 857 " pdb=" CB GLN A 857 " ideal model delta sigma weight residual 110.22 117.67 -7.45 1.54e+00 4.22e-01 2.34e+01 ... (remaining 55257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.09: 23719 29.09 - 58.18: 900 58.18 - 87.26: 130 87.26 - 116.35: 9 116.35 - 145.44: 2 Dihedral angle restraints: 24760 sinusoidal: 10237 harmonic: 14523 Sorted by residual: dihedral pdb=" CA MET A3858 " pdb=" C MET A3858 " pdb=" N TYR A3859 " pdb=" CA TYR A3859 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA GLU A1354 " pdb=" C GLU A1354 " pdb=" N GLY A1355 " pdb=" CA GLY A1355 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA LEU A3027 " pdb=" C LEU A3027 " pdb=" N ASN A3028 " pdb=" CA ASN A3028 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 24757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4696 0.050 - 0.100: 1350 0.100 - 0.150: 219 0.150 - 0.200: 32 0.200 - 0.250: 3 Chirality restraints: 6300 Sorted by residual: chirality pdb=" CB ILE B 321 " pdb=" CA ILE B 321 " pdb=" CG1 ILE B 321 " pdb=" CG2 ILE B 321 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL B 459 " pdb=" CA VAL B 459 " pdb=" CG1 VAL B 459 " pdb=" CG2 VAL B 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 126 " pdb=" N PRO A 126 " pdb=" C PRO A 126 " pdb=" CB PRO A 126 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 6297 not shown) Planarity restraints: 6909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A4125 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" CD GLU A4125 " 0.050 2.00e-02 2.50e+03 pdb=" OE1 GLU A4125 " -0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU A4125 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 39 " -0.035 2.00e-02 2.50e+03 1.73e-02 8.24e+00 pdb=" N9 DA D 39 " 0.035 2.00e-02 2.50e+03 pdb=" C8 DA D 39 " 0.009 2.00e-02 2.50e+03 pdb=" N7 DA D 39 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA D 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA D 39 " -0.008 2.00e-02 2.50e+03 pdb=" N6 DA D 39 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA D 39 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DA D 39 " 0.022 2.00e-02 2.50e+03 pdb=" N3 DA D 39 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA D 39 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 165 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO C 166 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 166 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 166 " 0.037 5.00e-02 4.00e+02 ... (remaining 6906 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3643 2.74 - 3.28: 47438 3.28 - 3.82: 73396 3.82 - 4.36: 88955 4.36 - 4.90: 135188 Nonbonded interactions: 348620 Sorted by model distance: nonbonded pdb=" O ILE A 443 " pdb=" OH TYR A 527 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR B 369 " pdb=" O SER C 436 " model vdw 2.199 3.040 nonbonded pdb=" O LYS A3485 " pdb=" OG SER A3488 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR B 298 " pdb=" OG1 THR B 300 " model vdw 2.202 3.040 nonbonded pdb=" O MET C 20 " pdb=" OG SER C 29 " model vdw 2.203 3.040 ... (remaining 348615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 43.170 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.004 0.073 40695 Z= 0.217 Angle : 0.813 13.532 55262 Z= 0.464 Chirality : 0.046 0.250 6300 Planarity : 0.005 0.066 6909 Dihedral : 15.530 145.438 15288 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.34 % Favored : 92.42 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.12), residues: 4892 helix: -0.47 (0.10), residues: 2757 sheet: -1.84 (0.38), residues: 158 loop : -2.24 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A4082 TYR 0.020 0.002 TYR A1873 PHE 0.031 0.002 PHE A 249 TRP 0.044 0.002 TRP B 148 HIS 0.018 0.001 HIS A2553 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.22 (40695) covalent geometry : angle 0.81321 / 0.46 (55262) hydrogen bonds : bond 0.14884 / 10.10 ( 2086) hydrogen bonds : angle 6.75424 / 4.76 ( 6102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 226 time to evaluate : 1.555 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: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A4128 " (corrupted residue). Skipping it. 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 410 MET cc_start: 0.8872 (mmp) cc_final: 0.8657 (mmm) REVERT: A 933 LEU cc_start: 0.8761 (pp) cc_final: 0.8426 (mt) REVERT: A 1880 MET cc_start: 0.7877 (pmm) cc_final: 0.7463 (pmm) REVERT: A 3670 MET cc_start: 0.8593 (ppp) cc_final: 0.8295 (ppp) REVERT: A 3687 MET cc_start: 0.8486 (mmp) cc_final: 0.8252 (mmm) REVERT: A 3846 MET cc_start: 0.8994 (pmm) cc_final: 0.8731 (pmm) REVERT: B 48 MET cc_start: 0.8310 (pmm) cc_final: 0.7912 (pmm) REVERT: B 520 SER cc_start: 0.9499 (m) cc_final: 0.9228 (p) REVERT: C 115 MET cc_start: 0.6979 (mpp) cc_final: 0.6678 (mpp) REVERT: C 212 MET cc_start: 0.7020 (ptt) cc_final: 0.6696 (tpp) REVERT: C 434 MET cc_start: 0.9181 (tmm) cc_final: 0.8630 (mmp) outliers start: 3 outliers final: 2 residues processed: 228 average time/residue: 0.2371 time to fit residues: 91.7530 Evaluate side-chains 182 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 432 optimal weight: 0.0770 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 30.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0000 chunk 207 optimal weight: 0.0070 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1457 GLN ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2414 GLN ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3150 ASN A3249 GLN ** A3524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN C 146 GLN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.038870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.029479 restraints weight = 562654.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.030331 restraints weight = 399308.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.030959 restraints weight = 303454.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.031438 restraints weight = 243088.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.031794 restraints weight = 202394.009| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40695 Z= 0.147 Angle : 0.712 10.537 55262 Z= 0.368 Chirality : 0.044 0.196 6300 Planarity : 0.005 0.055 6909 Dihedral : 12.582 143.031 5812 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.81 % Favored : 93.17 % Rotamer: Outliers : 0.17 % Allowed : 5.14 % Favored : 94.70 % 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: -1.68 (0.12), residues: 4892 helix: -0.34 (0.09), residues: 2829 sheet: -1.38 (0.39), residues: 156 loop : -2.23 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1768 TYR 0.022 0.001 TYR A3610 PHE 0.031 0.002 PHE C 598 TRP 0.024 0.002 TRP B 148 HIS 0.010 0.001 HIS A2553 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (40695) covalent geometry : angle 0.71228 / 0.37 (55262) hydrogen bonds : bond 0.04813 / 3.23 ( 2086) hydrogen bonds : angle 5.69794 / 4.03 ( 6102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 211 time to evaluate : 1.682 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: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A4128 " (corrupted residue). Skipping it. 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 156 PHE cc_start: 0.9666 (m-80) cc_final: 0.9445 (m-80) REVERT: A 238 MET cc_start: 0.9139 (pmm) cc_final: 0.8910 (pmm) REVERT: A 326 MET cc_start: 0.9667 (mpp) cc_final: 0.9455 (ptp) REVERT: A 410 MET cc_start: 0.9021 (mmp) cc_final: 0.8735 (mmm) REVERT: A 933 LEU cc_start: 0.8834 (pp) cc_final: 0.8522 (mt) REVERT: A 1342 MET cc_start: 0.9733 (mmp) cc_final: 0.9137 (tmm) REVERT: A 1880 MET cc_start: 0.8106 (pmm) cc_final: 0.7836 (pmm) REVERT: A 3670 MET cc_start: 0.8576 (ppp) cc_final: 0.8211 (ppp) REVERT: A 3687 MET cc_start: 0.8427 (mmp) cc_final: 0.8096 (mmm) REVERT: A 3971 MET cc_start: 0.9222 (tpt) cc_final: 0.9017 (tpp) REVERT: B 48 MET cc_start: 0.8095 (pmm) cc_final: 0.7652 (pmm) REVERT: B 346 MET cc_start: 0.7913 (mpp) cc_final: 0.7647 (mpp) REVERT: C 434 MET cc_start: 0.9052 (tmm) cc_final: 0.8438 (mmp) REVERT: F 84 VAL cc_start: 0.7199 (p) cc_final: 0.6949 (m) outliers start: 7 outliers final: 4 residues processed: 218 average time/residue: 0.2386 time to fit residues: 88.9326 Evaluate side-chains 183 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 74 optimal weight: 20.0000 chunk 419 optimal weight: 6.9990 chunk 314 optimal weight: 8.9990 chunk 371 optimal weight: 10.0000 chunk 183 optimal weight: 0.3980 chunk 143 optimal weight: 20.0000 chunk 472 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 327 optimal weight: 2.9990 chunk 414 optimal weight: 40.0000 chunk 51 optimal weight: 7.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1738 ASN ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2834 GLN A2845 ASN ** A3524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN C 146 GLN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.036688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.027480 restraints weight = 585901.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.028282 restraints weight = 414157.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.028865 restraints weight = 315493.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.029307 restraints weight = 253838.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.029652 restraints weight = 212379.777| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40695 Z= 0.174 Angle : 0.681 9.108 55262 Z= 0.359 Chirality : 0.043 0.218 6300 Planarity : 0.005 0.050 6909 Dihedral : 12.528 142.124 5812 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.77 % Favored : 93.21 % Rotamer: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.93 % 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: -1.44 (0.12), residues: 4892 helix: -0.14 (0.10), residues: 2839 sheet: -1.40 (0.40), residues: 152 loop : -2.13 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2530 TYR 0.027 0.001 TYR A1739 PHE 0.023 0.002 PHE A2561 TRP 0.021 0.002 TRP B 148 HIS 0.010 0.001 HIS A2553 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (40695) covalent geometry : angle 0.68112 / 0.36 (55262) hydrogen bonds : bond 0.04506 / 3.03 ( 2086) hydrogen bonds : angle 5.49420 / 3.89 ( 6102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 202 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.9266 (pmm) cc_final: 0.8973 (pmm) REVERT: A 933 LEU cc_start: 0.9233 (pp) cc_final: 0.8963 (mt) REVERT: A 989 MET cc_start: 0.9132 (tpt) cc_final: 0.8681 (tpt) REVERT: A 1342 MET cc_start: 0.9648 (mmp) cc_final: 0.9074 (tmm) REVERT: A 1757 MET cc_start: 0.9150 (ppp) cc_final: 0.8917 (ppp) REVERT: A 1880 MET cc_start: 0.8166 (pmm) cc_final: 0.7869 (pmm) REVERT: A 2220 MET cc_start: 0.8700 (mtm) cc_final: 0.8463 (mtp) REVERT: A 2424 MET cc_start: 0.9240 (mmp) cc_final: 0.8844 (mmm) REVERT: A 2473 MET cc_start: 0.8643 (ptm) cc_final: 0.8290 (ptm) REVERT: A 2813 PHE cc_start: 0.8666 (t80) cc_final: 0.8143 (t80) REVERT: A 3670 MET cc_start: 0.8367 (ppp) cc_final: 0.8084 (ppp) REVERT: A 3687 MET cc_start: 0.8708 (mmp) cc_final: 0.8386 (mmm) REVERT: A 3771 MET cc_start: 0.9825 (mmp) cc_final: 0.9487 (mmm) REVERT: A 3788 LEU cc_start: 0.9033 (mm) cc_final: 0.8824 (mm) REVERT: A 3846 MET cc_start: 0.8242 (pmm) cc_final: 0.8028 (pmm) REVERT: A 3890 MET cc_start: 0.9535 (pmm) cc_final: 0.9260 (pmm) REVERT: B 48 MET cc_start: 0.8240 (pmm) cc_final: 0.7714 (pmm) REVERT: B 346 MET cc_start: 0.8796 (mpp) cc_final: 0.8591 (mpp) REVERT: C 434 MET cc_start: 0.9069 (tmm) cc_final: 0.8479 (mmp) outliers start: 4 outliers final: 2 residues processed: 206 average time/residue: 0.2311 time to fit residues: 82.0575 Evaluate side-chains 171 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 95 optimal weight: 0.0870 chunk 90 optimal weight: 20.0000 chunk 392 optimal weight: 30.0000 chunk 149 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 427 optimal weight: 20.0000 chunk 383 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS A 739 ASN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1534 ASN A1687 HIS A2270 ASN ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3108 GLN A3150 ASN A3524 ASN ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.037659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.028374 restraints weight = 571410.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.029215 restraints weight = 397133.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.029839 restraints weight = 298844.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.030296 restraints weight = 237353.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.030642 restraints weight = 197143.341| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 40695 Z= 0.133 Angle : 0.671 9.079 55262 Z= 0.343 Chirality : 0.043 0.248 6300 Planarity : 0.004 0.061 6909 Dihedral : 12.443 140.680 5812 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.38 % Favored : 93.60 % Rotamer: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % 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: -1.33 (0.12), residues: 4892 helix: -0.08 (0.10), residues: 2844 sheet: -1.21 (0.39), residues: 162 loop : -2.06 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 659 TYR 0.023 0.001 TYR A4077 PHE 0.021 0.001 PHE A2554 TRP 0.018 0.001 TRP B 148 HIS 0.010 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (40695) covalent geometry : angle 0.67137 / 0.34 (55262) hydrogen bonds : bond 0.04032 / 2.72 ( 2086) hydrogen bonds : angle 5.31618 / 3.77 ( 6102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 198 time to evaluate : 1.476 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 TARDY: cannot create tardy model for: "MET A4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.9168 (pmm) cc_final: 0.8923 (pmm) REVERT: A 410 MET cc_start: 0.8942 (mmp) cc_final: 0.8690 (mmm) REVERT: A 933 LEU cc_start: 0.9180 (pp) cc_final: 0.8906 (mt) REVERT: A 989 MET cc_start: 0.9107 (tpt) cc_final: 0.8717 (tpt) REVERT: A 1342 MET cc_start: 0.9666 (mmp) cc_final: 0.9148 (tmm) REVERT: A 1390 GLN cc_start: 0.9713 (pm20) cc_final: 0.9234 (tm-30) REVERT: A 1757 MET cc_start: 0.9225 (ppp) cc_final: 0.8818 (ppp) REVERT: A 1880 MET cc_start: 0.7950 (pmm) cc_final: 0.7575 (pmm) REVERT: A 2220 MET cc_start: 0.8710 (mtm) cc_final: 0.8458 (mtp) REVERT: A 2424 MET cc_start: 0.9220 (mmp) cc_final: 0.8782 (mmm) REVERT: A 2473 MET cc_start: 0.8594 (ptm) cc_final: 0.8158 (ptm) REVERT: A 2813 PHE cc_start: 0.8631 (t80) cc_final: 0.8088 (t80) REVERT: A 3176 MET cc_start: 0.9506 (pmm) cc_final: 0.9170 (pmm) REVERT: A 3670 MET cc_start: 0.8377 (ppp) cc_final: 0.8140 (ppp) REVERT: A 3687 MET cc_start: 0.8725 (mmp) cc_final: 0.8415 (mmm) REVERT: A 3771 MET cc_start: 0.9815 (mmp) cc_final: 0.9490 (mmm) REVERT: A 3788 LEU cc_start: 0.9027 (mm) cc_final: 0.8817 (mm) REVERT: A 3890 MET cc_start: 0.9580 (pmm) cc_final: 0.9215 (pmm) REVERT: B 48 MET cc_start: 0.8135 (pmm) cc_final: 0.7647 (pmm) REVERT: B 346 MET cc_start: 0.8848 (mpp) cc_final: 0.8601 (mpp) REVERT: C 434 MET cc_start: 0.9002 (tmm) cc_final: 0.8387 (mmp) REVERT: F 89 MET cc_start: 0.3142 (ppp) cc_final: 0.2905 (ppp) outliers start: 2 outliers final: 2 residues processed: 200 average time/residue: 0.2336 time to fit residues: 80.3126 Evaluate side-chains 175 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 336 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 351 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 367 optimal weight: 5.9990 chunk 392 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 352 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS ** A1457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2834 GLN A3148 GLN A3150 ASN ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 330 GLN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.034585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.025625 restraints weight = 603037.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.026405 restraints weight = 423834.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.026944 restraints weight = 320578.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.027357 restraints weight = 257551.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.027666 restraints weight = 215938.109| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 40695 Z= 0.230 Angle : 0.711 8.550 55262 Z= 0.375 Chirality : 0.044 0.223 6300 Planarity : 0.005 0.051 6909 Dihedral : 12.447 140.732 5812 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.13 % Favored : 92.85 % Rotamer: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.12), residues: 4892 helix: -0.01 (0.10), residues: 2828 sheet: -1.42 (0.41), residues: 150 loop : -2.02 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 290 TYR 0.047 0.002 TYR C 395 PHE 0.021 0.002 PHE A 465 TRP 0.057 0.003 TRP A2479 HIS 0.009 0.001 HIS A2553 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.23 (40695) covalent geometry : angle 0.71130 / 0.38 (55262) hydrogen bonds : bond 0.04223 / 2.83 ( 2086) hydrogen bonds : angle 5.40577 / 3.83 ( 6102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.9224 (pmm) cc_final: 0.8937 (pmm) REVERT: A 410 MET cc_start: 0.9154 (mmp) cc_final: 0.8950 (mmm) REVERT: A 901 MET cc_start: 0.7724 (pmm) cc_final: 0.7439 (pmm) REVERT: A 989 MET cc_start: 0.9170 (tpt) cc_final: 0.8733 (tpt) REVERT: A 1342 MET cc_start: 0.9706 (mmp) cc_final: 0.9170 (tmm) REVERT: A 1390 GLN cc_start: 0.9708 (pm20) cc_final: 0.9217 (tm-30) REVERT: A 1757 MET cc_start: 0.9312 (ppp) cc_final: 0.8895 (ppp) REVERT: A 1799 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9029 (mp0) REVERT: A 2220 MET cc_start: 0.8672 (mtm) cc_final: 0.8432 (mtp) REVERT: A 2424 MET cc_start: 0.9229 (mmp) cc_final: 0.8788 (mmm) REVERT: A 2473 MET cc_start: 0.9016 (ptm) cc_final: 0.8735 (ptm) REVERT: A 2813 PHE cc_start: 0.8829 (t80) cc_final: 0.8271 (t80) REVERT: A 3111 MET cc_start: 0.9514 (ptp) cc_final: 0.9238 (ptp) REVERT: A 3670 MET cc_start: 0.8396 (ppp) cc_final: 0.8155 (ppp) REVERT: A 3687 MET cc_start: 0.8917 (mmp) cc_final: 0.8483 (mmm) REVERT: A 3771 MET cc_start: 0.9811 (mmp) cc_final: 0.9491 (mmm) REVERT: A 3788 LEU cc_start: 0.9295 (mm) cc_final: 0.9081 (mm) REVERT: A 3846 MET cc_start: 0.8566 (pmm) cc_final: 0.8010 (pmm) REVERT: A 3890 MET cc_start: 0.9536 (pmm) cc_final: 0.9276 (pmm) REVERT: B 48 MET cc_start: 0.8411 (pmm) cc_final: 0.7883 (pmm) REVERT: B 346 MET cc_start: 0.8927 (mpp) cc_final: 0.8680 (mpp) REVERT: C 434 MET cc_start: 0.9134 (tmm) cc_final: 0.8510 (mmp) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.2336 time to fit residues: 77.4243 Evaluate side-chains 165 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 467 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 423 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 109 optimal weight: 0.0000 chunk 445 optimal weight: 0.9990 chunk 56 optimal weight: 40.0000 chunk 388 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1738 ASN ** A2163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2834 GLN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN A3766 GLN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.035348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.026323 restraints weight = 590489.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.027138 restraints weight = 404109.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.027725 restraints weight = 301712.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.028155 restraints weight = 239016.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.028474 restraints weight = 198672.615| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40695 Z= 0.141 Angle : 0.660 8.639 55262 Z= 0.342 Chirality : 0.043 0.226 6300 Planarity : 0.004 0.050 6909 Dihedral : 12.378 139.272 5812 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.62 % Favored : 93.36 % Rotamer: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.51 % 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: -1.13 (0.12), residues: 4892 helix: 0.08 (0.10), residues: 2838 sheet: -1.38 (0.41), residues: 149 loop : -1.94 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 517 TYR 0.018 0.001 TYR A3610 PHE 0.023 0.001 PHE C 340 TRP 0.029 0.002 TRP A2479 HIS 0.007 0.001 HIS A2553 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (40695) covalent geometry : angle 0.65989 / 0.34 (55262) hydrogen bonds : bond 0.03825 / 2.57 ( 2086) hydrogen bonds : angle 5.26886 / 3.75 ( 6102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.9649 (mpp) cc_final: 0.9385 (ptp) REVERT: A 410 MET cc_start: 0.9120 (mmp) cc_final: 0.8912 (mmm) REVERT: A 441 MET cc_start: 0.7202 (mmt) cc_final: 0.6961 (mmt) REVERT: A 901 MET cc_start: 0.7711 (pmm) cc_final: 0.7424 (pmm) REVERT: A 933 LEU cc_start: 0.9447 (pp) cc_final: 0.9232 (mt) REVERT: A 989 MET cc_start: 0.9250 (tpt) cc_final: 0.8858 (tpt) REVERT: A 1390 GLN cc_start: 0.9709 (pm20) cc_final: 0.9237 (tm-30) REVERT: A 1757 MET cc_start: 0.9275 (ppp) cc_final: 0.8827 (ppp) REVERT: A 1880 MET cc_start: 0.8417 (pmm) cc_final: 0.8180 (pmm) REVERT: A 2220 MET cc_start: 0.8797 (mtm) cc_final: 0.8567 (mtp) REVERT: A 2424 MET cc_start: 0.9276 (mmp) cc_final: 0.8908 (mmm) REVERT: A 2473 MET cc_start: 0.9016 (ptm) cc_final: 0.8691 (ptm) REVERT: A 2813 PHE cc_start: 0.8827 (t80) cc_final: 0.8266 (t80) REVERT: A 3111 MET cc_start: 0.9492 (ptp) cc_final: 0.9203 (ptp) REVERT: A 3176 MET cc_start: 0.9523 (pmm) cc_final: 0.9225 (pmm) REVERT: A 3670 MET cc_start: 0.8427 (ppp) cc_final: 0.8175 (ppp) REVERT: A 3687 MET cc_start: 0.8924 (mmp) cc_final: 0.8545 (mmm) REVERT: A 3771 MET cc_start: 0.9805 (mmp) cc_final: 0.9488 (mmm) REVERT: A 3846 MET cc_start: 0.8423 (pmm) cc_final: 0.7953 (pmm) REVERT: B 48 MET cc_start: 0.8339 (pmm) cc_final: 0.7831 (pmm) REVERT: B 135 MET cc_start: 0.9082 (ppp) cc_final: 0.8676 (ppp) REVERT: B 346 MET cc_start: 0.8925 (mpp) cc_final: 0.8688 (mpp) REVERT: C 115 MET cc_start: 0.6568 (mpp) cc_final: 0.6231 (mpp) REVERT: C 434 MET cc_start: 0.9130 (tmm) cc_final: 0.8504 (mmp) REVERT: F 89 MET cc_start: 0.3620 (ppp) cc_final: 0.3117 (ppp) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.2308 time to fit residues: 77.4134 Evaluate side-chains 167 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 421 optimal weight: 20.0000 chunk 391 optimal weight: 6.9990 chunk 433 optimal weight: 30.0000 chunk 296 optimal weight: 6.9990 chunk 411 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 476 optimal weight: 5.9990 chunk 375 optimal weight: 0.9980 chunk 461 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 GLN ** A1457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1738 ASN ** A2163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2834 GLN A3150 ASN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN A3766 GLN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.035216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.026216 restraints weight = 590839.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.027011 restraints weight = 399591.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.027600 restraints weight = 296947.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.028028 restraints weight = 234378.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.028350 restraints weight = 194444.809| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40695 Z= 0.134 Angle : 0.657 10.565 55262 Z= 0.338 Chirality : 0.043 0.220 6300 Planarity : 0.004 0.051 6909 Dihedral : 12.275 138.579 5812 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.66 % Favored : 93.32 % Rotamer: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % 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: -1.05 (0.12), residues: 4892 helix: 0.16 (0.10), residues: 2843 sheet: -1.50 (0.41), residues: 159 loop : -1.91 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 782 TYR 0.022 0.001 TYR A3315 PHE 0.017 0.001 PHE C 340 TRP 0.025 0.002 TRP A2479 HIS 0.015 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (40695) covalent geometry : angle 0.65738 / 0.34 (55262) hydrogen bonds : bond 0.03692 / 2.48 ( 2086) hydrogen bonds : angle 5.15432 / 3.67 ( 6102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.9580 (mpp) cc_final: 0.9348 (ptp) REVERT: A 333 MET cc_start: 0.9437 (ttp) cc_final: 0.9079 (ttm) REVERT: A 441 MET cc_start: 0.7406 (mmt) cc_final: 0.7158 (mmt) REVERT: A 629 PHE cc_start: 0.8878 (t80) cc_final: 0.8579 (t80) REVERT: A 901 MET cc_start: 0.7678 (pmm) cc_final: 0.7398 (pmm) REVERT: A 933 LEU cc_start: 0.9439 (pp) cc_final: 0.9229 (mt) REVERT: A 989 MET cc_start: 0.9230 (tpt) cc_final: 0.8839 (tpt) REVERT: A 1390 GLN cc_start: 0.9705 (pm20) cc_final: 0.9233 (tm-30) REVERT: A 1724 MET cc_start: 0.9115 (tpt) cc_final: 0.8368 (tpt) REVERT: A 1757 MET cc_start: 0.9283 (ppp) cc_final: 0.8805 (ppp) REVERT: A 1871 MET cc_start: 0.9448 (mtm) cc_final: 0.9136 (mtp) REVERT: A 1880 MET cc_start: 0.8392 (pmm) cc_final: 0.8028 (pmm) REVERT: A 2220 MET cc_start: 0.8888 (mtm) cc_final: 0.8655 (mtp) REVERT: A 2281 MET cc_start: 0.9094 (tpt) cc_final: 0.8790 (tpt) REVERT: A 2424 MET cc_start: 0.9253 (mmp) cc_final: 0.8855 (mmm) REVERT: A 2473 MET cc_start: 0.9035 (ptm) cc_final: 0.8641 (ptm) REVERT: A 2813 PHE cc_start: 0.8839 (t80) cc_final: 0.8263 (t80) REVERT: A 3111 MET cc_start: 0.9489 (ptp) cc_final: 0.9185 (ptp) REVERT: A 3176 MET cc_start: 0.9522 (pmm) cc_final: 0.9199 (pmm) REVERT: A 3670 MET cc_start: 0.8487 (ppp) cc_final: 0.8187 (ppp) REVERT: A 3687 MET cc_start: 0.8972 (mmp) cc_final: 0.8619 (mmm) REVERT: A 3771 MET cc_start: 0.9789 (mmp) cc_final: 0.9476 (mmm) REVERT: A 3846 MET cc_start: 0.8082 (pmm) cc_final: 0.7460 (pmm) REVERT: A 3971 MET cc_start: 0.9082 (tpt) cc_final: 0.8658 (tpp) REVERT: A 3974 MET cc_start: 0.8164 (tmm) cc_final: 0.7926 (tmm) REVERT: B 48 MET cc_start: 0.8316 (pmm) cc_final: 0.7821 (pmm) REVERT: B 135 MET cc_start: 0.9057 (ppp) cc_final: 0.8627 (ppp) REVERT: B 161 MET cc_start: 0.9024 (tmm) cc_final: 0.8590 (tmm) REVERT: B 346 MET cc_start: 0.8854 (mpp) cc_final: 0.8587 (mpp) REVERT: B 520 SER cc_start: 0.9400 (p) cc_final: 0.9178 (p) REVERT: C 389 MET cc_start: 0.8680 (tpp) cc_final: 0.8377 (tpp) REVERT: C 434 MET cc_start: 0.9082 (tmm) cc_final: 0.8524 (mmp) REVERT: F 89 MET cc_start: 0.3617 (ppp) cc_final: 0.3073 (ppp) outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.2340 time to fit residues: 77.6636 Evaluate side-chains 166 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 341 optimal weight: 5.9990 chunk 336 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 79 optimal weight: 0.0040 chunk 43 optimal weight: 0.9980 chunk 465 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN ** A1457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2834 GLN A3150 ASN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.034608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.025723 restraints weight = 596107.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.026510 restraints weight = 401841.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.027084 restraints weight = 297448.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.027499 restraints weight = 235213.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.027821 restraints weight = 195159.864| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40695 Z= 0.145 Angle : 0.673 11.765 55262 Z= 0.346 Chirality : 0.043 0.215 6300 Planarity : 0.004 0.054 6909 Dihedral : 12.225 137.812 5812 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.56 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 4892 helix: 0.19 (0.10), residues: 2841 sheet: -1.53 (0.40), residues: 158 loop : -1.88 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 123 TYR 0.021 0.001 TYR A3315 PHE 0.019 0.001 PHE A4074 TRP 0.024 0.002 TRP B 148 HIS 0.016 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (40695) covalent geometry : angle 0.67260 / 0.35 (55262) hydrogen bonds : bond 0.03649 / 2.45 ( 2086) hydrogen bonds : angle 5.17026 / 3.69 ( 6102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.9442 (ttp) cc_final: 0.9120 (ttm) REVERT: A 410 MET cc_start: 0.9051 (mmp) cc_final: 0.8745 (mmm) REVERT: A 441 MET cc_start: 0.7411 (mmt) cc_final: 0.7161 (mmt) REVERT: A 718 MET cc_start: 0.9372 (ppp) cc_final: 0.9105 (ppp) REVERT: A 901 MET cc_start: 0.7727 (pmm) cc_final: 0.7435 (pmm) REVERT: A 933 LEU cc_start: 0.9467 (pp) cc_final: 0.9258 (mt) REVERT: A 989 MET cc_start: 0.9264 (tpt) cc_final: 0.8880 (tpt) REVERT: A 1342 MET cc_start: 0.9726 (mmp) cc_final: 0.9234 (tmm) REVERT: A 1390 GLN cc_start: 0.9718 (pm20) cc_final: 0.9259 (tm-30) REVERT: A 1757 MET cc_start: 0.9290 (ppp) cc_final: 0.8802 (ppp) REVERT: A 1880 MET cc_start: 0.8532 (pmm) cc_final: 0.8034 (pmm) REVERT: A 2220 MET cc_start: 0.8953 (mtm) cc_final: 0.8726 (mtp) REVERT: A 2281 MET cc_start: 0.9189 (tpt) cc_final: 0.8949 (tpt) REVERT: A 2424 MET cc_start: 0.9235 (mmp) cc_final: 0.8865 (mmm) REVERT: A 2473 MET cc_start: 0.9112 (ptm) cc_final: 0.8698 (ptm) REVERT: A 2813 PHE cc_start: 0.8856 (t80) cc_final: 0.8284 (t80) REVERT: A 3111 MET cc_start: 0.9484 (ptp) cc_final: 0.9244 (ptp) REVERT: A 3176 MET cc_start: 0.9532 (pmm) cc_final: 0.9205 (pmm) REVERT: A 3670 MET cc_start: 0.8463 (ppp) cc_final: 0.8164 (ppp) REVERT: A 3687 MET cc_start: 0.9021 (mmp) cc_final: 0.8687 (mmp) REVERT: A 3771 MET cc_start: 0.9782 (mmp) cc_final: 0.9526 (mmm) REVERT: A 3788 LEU cc_start: 0.9448 (mm) cc_final: 0.9129 (tp) REVERT: A 3846 MET cc_start: 0.8255 (pmm) cc_final: 0.7623 (pmm) REVERT: A 3890 MET cc_start: 0.9454 (pmm) cc_final: 0.9230 (pmm) REVERT: A 3929 MET cc_start: 0.8486 (ptt) cc_final: 0.8086 (ptt) REVERT: A 4002 MET cc_start: 0.8740 (ptm) cc_final: 0.8535 (ppp) REVERT: B 48 MET cc_start: 0.8329 (pmm) cc_final: 0.7845 (pmm) REVERT: B 135 MET cc_start: 0.9093 (ppp) cc_final: 0.8649 (ppp) REVERT: B 161 MET cc_start: 0.9011 (tmm) cc_final: 0.8705 (tmm) REVERT: B 346 MET cc_start: 0.8826 (mpp) cc_final: 0.8498 (mpp) REVERT: F 89 MET cc_start: 0.3570 (ppp) cc_final: 0.3238 (ppp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2281 time to fit residues: 74.8512 Evaluate side-chains 165 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 123 optimal weight: 5.9990 chunk 334 optimal weight: 10.0000 chunk 486 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 279 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 ASN ** A1457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2834 GLN A3054 GLN A3150 ASN A3249 GLN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3501 HIS ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.034709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.025759 restraints weight = 595741.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.026563 restraints weight = 399615.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.027147 restraints weight = 293828.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.027576 restraints weight = 230933.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.027892 restraints weight = 190793.186| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40695 Z= 0.135 Angle : 0.672 12.337 55262 Z= 0.345 Chirality : 0.043 0.215 6300 Planarity : 0.004 0.057 6909 Dihedral : 12.179 137.066 5812 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.52 % Favored : 93.46 % Rotamer: Outliers : 0.05 % Allowed : 0.80 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4892 helix: 0.21 (0.10), residues: 2840 sheet: -1.52 (0.40), residues: 156 loop : -1.84 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A2530 TYR 0.018 0.001 TYR A3610 PHE 0.017 0.001 PHE B 436 TRP 0.018 0.002 TRP B 148 HIS 0.014 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (40695) covalent geometry : angle 0.67221 / 0.34 (55262) hydrogen bonds : bond 0.03617 / 2.43 ( 2086) hydrogen bonds : angle 5.18716 / 3.71 ( 6102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.9411 (ttp) cc_final: 0.9075 (ttm) REVERT: A 410 MET cc_start: 0.9086 (mmp) cc_final: 0.8799 (mmm) REVERT: A 441 MET cc_start: 0.7519 (mmt) cc_final: 0.7281 (mmt) REVERT: A 901 MET cc_start: 0.7612 (pmm) cc_final: 0.7318 (pmm) REVERT: A 989 MET cc_start: 0.9275 (tpt) cc_final: 0.8898 (tpt) REVERT: A 1342 MET cc_start: 0.9707 (mmp) cc_final: 0.9225 (tmm) REVERT: A 1390 GLN cc_start: 0.9717 (pm20) cc_final: 0.9282 (tm-30) REVERT: A 1757 MET cc_start: 0.9286 (ppp) cc_final: 0.8792 (ppp) REVERT: A 1871 MET cc_start: 0.9453 (mtm) cc_final: 0.9149 (mtp) REVERT: A 1880 MET cc_start: 0.8436 (pmm) cc_final: 0.8009 (pmm) REVERT: A 2281 MET cc_start: 0.9156 (tpt) cc_final: 0.8920 (tpt) REVERT: A 2424 MET cc_start: 0.9267 (mmp) cc_final: 0.8848 (mmm) REVERT: A 2473 MET cc_start: 0.9123 (ptm) cc_final: 0.8682 (ptm) REVERT: A 2813 PHE cc_start: 0.8868 (t80) cc_final: 0.8372 (t80) REVERT: A 3176 MET cc_start: 0.9505 (pmm) cc_final: 0.9181 (pmm) REVERT: A 3240 MET cc_start: 0.9488 (tpt) cc_final: 0.9277 (tpp) REVERT: A 3670 MET cc_start: 0.8457 (ppp) cc_final: 0.8148 (ppp) REVERT: A 3687 MET cc_start: 0.9012 (mmp) cc_final: 0.8675 (mmp) REVERT: A 3771 MET cc_start: 0.9780 (mmp) cc_final: 0.9468 (mmm) REVERT: A 3846 MET cc_start: 0.8172 (pmm) cc_final: 0.7587 (pmm) REVERT: A 3890 MET cc_start: 0.9441 (pmm) cc_final: 0.9209 (pmm) REVERT: A 3971 MET cc_start: 0.8895 (tpt) cc_final: 0.8619 (tpp) REVERT: B 48 MET cc_start: 0.8328 (pmm) cc_final: 0.7816 (pmm) REVERT: B 135 MET cc_start: 0.9004 (ppp) cc_final: 0.8541 (ppp) REVERT: B 161 MET cc_start: 0.8952 (tmm) cc_final: 0.8643 (tmm) REVERT: B 346 MET cc_start: 0.8865 (mpp) cc_final: 0.8544 (mpp) REVERT: C 434 MET cc_start: 0.9292 (tpt) cc_final: 0.8711 (mmp) REVERT: F 89 MET cc_start: 0.3469 (ppp) cc_final: 0.3115 (ppp) outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 0.2334 time to fit residues: 77.3560 Evaluate side-chains 165 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 114 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 449 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 394 optimal weight: 5.9990 chunk 341 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 409 optimal weight: 5.9990 chunk 304 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2834 GLN A3150 ASN ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS C 146 GLN C 330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.033919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.025077 restraints weight = 601130.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.025826 restraints weight = 405448.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.026391 restraints weight = 298088.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.026815 restraints weight = 234385.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.027125 restraints weight = 193818.138| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40695 Z= 0.150 Angle : 0.681 18.726 55262 Z= 0.349 Chirality : 0.043 0.219 6300 Planarity : 0.004 0.056 6909 Dihedral : 12.127 136.432 5812 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.66 % Favored : 93.32 % Rotamer: Outliers : 0.02 % Allowed : 0.45 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4892 helix: 0.22 (0.10), residues: 2844 sheet: -1.44 (0.40), residues: 155 loop : -1.80 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 971 TYR 0.020 0.001 TYR A3610 PHE 0.017 0.002 PHE A 465 TRP 0.021 0.002 TRP F 114 HIS 0.013 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (40695) covalent geometry : angle 0.68082 / 0.35 (55262) hydrogen bonds : bond 0.03593 / 2.42 ( 2086) hydrogen bonds : angle 5.16986 / 3.70 ( 6102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9784 Ramachandran restraints generated. 4892 Oldfield, 0 Emsley, 4892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 1.601 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 TARDY: cannot create tardy model for: "MET A4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.9455 (ttp) cc_final: 0.9119 (ttm) REVERT: A 410 MET cc_start: 0.9165 (mmp) cc_final: 0.8848 (mmm) REVERT: A 441 MET cc_start: 0.7449 (mmt) cc_final: 0.7235 (mmt) REVERT: A 718 MET cc_start: 0.9344 (ppp) cc_final: 0.9086 (ppp) REVERT: A 901 MET cc_start: 0.7851 (pmm) cc_final: 0.7563 (pmm) REVERT: A 989 MET cc_start: 0.9316 (tpt) cc_final: 0.8959 (tpt) REVERT: A 1342 MET cc_start: 0.9733 (mmp) cc_final: 0.9273 (tmm) REVERT: A 1390 GLN cc_start: 0.9714 (pm20) cc_final: 0.9276 (tm-30) REVERT: A 1757 MET cc_start: 0.9351 (ppp) cc_final: 0.8870 (pmm) REVERT: A 1871 MET cc_start: 0.9460 (mtm) cc_final: 0.9165 (mtp) REVERT: A 1880 MET cc_start: 0.8631 (pmm) cc_final: 0.8302 (pmm) REVERT: A 2281 MET cc_start: 0.9289 (tpt) cc_final: 0.9080 (tpt) REVERT: A 2424 MET cc_start: 0.9289 (mmp) cc_final: 0.8883 (mmm) REVERT: A 2473 MET cc_start: 0.9220 (ptm) cc_final: 0.8680 (ptm) REVERT: A 2813 PHE cc_start: 0.8930 (t80) cc_final: 0.8358 (t80) REVERT: A 3176 MET cc_start: 0.9524 (pmm) cc_final: 0.9203 (pmm) REVERT: A 3240 MET cc_start: 0.9498 (tpt) cc_final: 0.9283 (tpp) REVERT: A 3670 MET cc_start: 0.8199 (ppp) cc_final: 0.7852 (ppp) REVERT: A 3687 MET cc_start: 0.9035 (mmp) cc_final: 0.8641 (mmp) REVERT: A 3771 MET cc_start: 0.9778 (mmp) cc_final: 0.9485 (mmm) REVERT: A 3846 MET cc_start: 0.8167 (pmm) cc_final: 0.7520 (pmm) REVERT: A 3929 MET cc_start: 0.8552 (ptt) cc_final: 0.8167 (ptt) REVERT: A 3971 MET cc_start: 0.8907 (tpt) cc_final: 0.8660 (tpp) REVERT: B 48 MET cc_start: 0.8262 (pmm) cc_final: 0.7703 (pmm) REVERT: B 135 MET cc_start: 0.9051 (ppp) cc_final: 0.8576 (ppp) REVERT: B 161 MET cc_start: 0.8960 (tmm) cc_final: 0.8686 (tmm) REVERT: B 346 MET cc_start: 0.8814 (mpp) cc_final: 0.8498 (mpp) REVERT: C 115 MET cc_start: 0.6830 (mpp) cc_final: 0.6559 (mpp) REVERT: C 389 MET cc_start: 0.8682 (tpp) cc_final: 0.8372 (tpp) REVERT: C 434 MET cc_start: 0.9313 (tpt) cc_final: 0.8723 (mmp) REVERT: F 89 MET cc_start: 0.3606 (ppp) cc_final: 0.3166 (ppp) outliers start: 1 outliers final: 1 residues processed: 187 average time/residue: 0.2451 time to fit residues: 79.2186 Evaluate side-chains 167 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 213 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 240 optimal weight: 0.1980 chunk 344 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 486 optimal weight: 0.2980 chunk 291 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 HIS ** A1457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A2163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2834 GLN A3150 ASN ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN A3766 GLN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.034751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.025870 restraints weight = 593099.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.026682 restraints weight = 389142.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.027276 restraints weight = 283225.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.027705 restraints weight = 220915.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.028017 restraints weight = 181655.516| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 40695 Z= 0.123 Angle : 0.682 14.008 55262 Z= 0.342 Chirality : 0.043 0.226 6300 Planarity : 0.004 0.057 6909 Dihedral : 12.030 135.274 5812 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.11 % Favored : 93.87 % Rotamer: Outliers : 0.05 % Allowed : 0.36 % Favored : 99.60 % 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: -0.84 (0.12), residues: 4892 helix: 0.27 (0.10), residues: 2842 sheet: -1.34 (0.41), residues: 155 loop : -1.72 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2530 TYR 0.018 0.001 TYR A3610 PHE 0.028 0.001 PHE A 138 TRP 0.025 0.001 TRP F 114 HIS 0.012 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (40695) covalent geometry : angle 0.68208 / 0.34 (55262) hydrogen bonds : bond 0.03470 / 2.33 ( 2086) hydrogen bonds : angle 5.06148 / 3.62 ( 6102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7305.65 seconds wall clock time: 128 minutes 17.48 seconds (7697.48 seconds total)