Starting phenix.real_space_refine on Thu Sep 18 23:45:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mx1_48707/09_2025/9mx1_48707.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mx1_48707/09_2025/9mx1_48707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mx1_48707/09_2025/9mx1_48707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mx1_48707/09_2025/9mx1_48707.map" model { file = "/net/cci-nas-00/data/ceres_data/9mx1_48707/09_2025/9mx1_48707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mx1_48707/09_2025/9mx1_48707.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 13333 2.51 5 N 3379 2.21 5 O 4082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20832 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 19032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2363, 19032 Classifications: {'peptide': 2363} Link IDs: {'PTRANS': 54, 'TRANS': 2308} Chain: "B" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 960 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 840 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 4.01, per 1000 atoms: 0.19 Number of scatterers: 20832 At special positions: 0 Unit cell: (173.76, 182.448, 194.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 4082 8.00 N 3379 7.00 C 13333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 308 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 742.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4902 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 51 sheets defined 27.8% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 67 through 87 removed outlier: 4.158A pdb=" N ILE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 136 through 156 removed outlier: 3.606A pdb=" N LEU A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 removed outlier: 4.232A pdb=" N GLN A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 191 removed outlier: 4.433A pdb=" N PHE A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 216 through 234 removed outlier: 3.529A pdb=" N SER A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 263 through 279 removed outlier: 3.697A pdb=" N ILE A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 removed outlier: 3.996A pdb=" N TYR A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 392 through 419 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.651A pdb=" N ASN A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 469 through 482 Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.920A pdb=" N TRP A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 538 Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 589 through 603 Processing helix chain 'A' and resid 639 through 643 Processing helix chain 'A' and resid 669 through 685 removed outlier: 4.077A pdb=" N THR A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 728 removed outlier: 3.602A pdb=" N LYS A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 777 Processing helix chain 'A' and resid 795 through 812 Processing helix chain 'A' and resid 816 through 840 Processing helix chain 'A' and resid 848 through 878 removed outlier: 3.778A pdb=" N SER A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 936 removed outlier: 3.596A pdb=" N ILE A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 973 removed outlier: 4.164A pdb=" N ASN A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.784A pdb=" N GLN A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1037 through 1041 Processing helix chain 'A' and resid 1047 through 1055 removed outlier: 3.810A pdb=" N HIS A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1065 removed outlier: 3.692A pdb=" N LYS A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1094 Processing helix chain 'A' and resid 1118 through 1130 Processing helix chain 'A' and resid 1130 through 1135 removed outlier: 3.960A pdb=" N LYS A1134 " --> pdb=" O SER A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1162 Processing helix chain 'A' and resid 1250 through 1260 Processing helix chain 'A' and resid 1306 through 1311 Processing helix chain 'A' and resid 1433 through 1440 Processing helix chain 'A' and resid 1440 through 1452 Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1558 through 1572 Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 3.816A pdb=" N ASN A1583 " --> pdb=" O SER A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1679 Processing helix chain 'A' and resid 1771 through 1776 Processing helix chain 'A' and resid 1789 through 1797 Processing helix chain 'A' and resid 1801 through 1805 removed outlier: 4.101A pdb=" N ASN A1804 " --> pdb=" O ASN A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1828 removed outlier: 3.976A pdb=" N LYS A1828 " --> pdb=" O GLU A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 2011 through 2015 removed outlier: 3.564A pdb=" N GLY A2014 " --> pdb=" O THR A2011 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.845A pdb=" N SER A 91 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 238 removed outlier: 7.501A pdb=" N ILE A 237 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU A 128 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 97 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TRP A 129 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE A 99 " --> pdb=" O TRP A 129 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASN A 96 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 375 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLN A 384 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N LYS A 373 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 608 through 611 removed outlier: 5.985A pdb=" N VAL A 648 " --> pdb=" O GLU A 694 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN A 696 " --> pdb=" O VAL A 648 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 650 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU A 698 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE A 652 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 620 through 623 removed outlier: 3.842A pdb=" N PHE A 622 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 739 through 740 Processing sheet with id=AA6, first strand: chain 'A' and resid 746 through 748 Processing sheet with id=AA7, first strand: chain 'A' and resid 884 through 886 removed outlier: 3.528A pdb=" N VAL A 911 " --> pdb=" O PHE A 902 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 938 through 942 removed outlier: 4.083A pdb=" N THR A 940 " --> pdb=" O LEU A 947 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1069 through 1070 removed outlier: 3.586A pdb=" N MET A1517 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASN A1522 " --> pdb=" O LEU A1544 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU A1544 " --> pdb=" O ASN A1522 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A1540 " --> pdb=" O GLY A1526 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N SER A1537 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU A1557 " --> pdb=" O SER A1537 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP A1539 " --> pdb=" O LEU A1555 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU A1555 " --> pdb=" O ASP A1539 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER A1541 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A1550 " --> pdb=" O ASN A1601 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1069 through 1070 removed outlier: 3.586A pdb=" N MET A1517 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASN A1522 " --> pdb=" O LEU A1544 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU A1544 " --> pdb=" O ASN A1522 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A1540 " --> pdb=" O GLY A1526 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N SER A1537 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU A1557 " --> pdb=" O SER A1537 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP A1539 " --> pdb=" O LEU A1555 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU A1555 " --> pdb=" O ASP A1539 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER A1541 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N THR A1609 " --> pdb=" O LYS A1551 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN A1553 " --> pdb=" O THR A1609 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N VAL A1611 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A1555 " --> pdb=" O VAL A1611 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE A1622 " --> pdb=" O ILE A1631 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE A1631 " --> pdb=" O ILE A1622 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1139 through 1140 Processing sheet with id=AB3, first strand: chain 'A' and resid 1169 through 1171 removed outlier: 7.530A pdb=" N ASN A1170 " --> pdb=" O PHE A1232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1173 through 1174 removed outlier: 4.160A pdb=" N ALA A1173 " --> pdb=" O SER A1196 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A1196 " --> pdb=" O ALA A1173 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1181 through 1183 removed outlier: 3.566A pdb=" N THR A1181 " --> pdb=" O HIS A1188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1221 through 1223 removed outlier: 6.590A pdb=" N MET A1222 " --> pdb=" O ILE A1300 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A1299 " --> pdb=" O LEU A1327 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR A1324 " --> pdb=" O ILE A1346 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN A1348 " --> pdb=" O TYR A1324 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A1326 " --> pdb=" O ASN A1348 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP A1345 " --> pdb=" O PHE A1404 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR A1406 " --> pdb=" O TRP A1345 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A1347 " --> pdb=" O THR A1406 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N GLU A1408 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1236 through 1237 Processing sheet with id=AB8, first strand: chain 'A' and resid 1286 through 1288 removed outlier: 3.503A pdb=" N SER A1314 " --> pdb=" O THR A1286 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A1313 " --> pdb=" O SER A1334 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN A1336 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR A1315 " --> pdb=" O ASN A1336 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASN A1338 " --> pdb=" O TYR A1315 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE A1317 " --> pdb=" O ASN A1338 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR A1335 " --> pdb=" O THR A1389 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1356 through 1357 Processing sheet with id=AC1, first strand: chain 'A' and resid 1457 through 1463 removed outlier: 5.318A pdb=" N LYS A1469 " --> pdb=" O LYS A1486 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS A1486 " --> pdb=" O LYS A1469 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1641 through 1644 removed outlier: 3.604A pdb=" N THR A1644 " --> pdb=" O VAL A1654 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL A1653 " --> pdb=" O LEU A1689 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A1688 " --> pdb=" O ILE A1715 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A1714 " --> pdb=" O ARG A1764 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A1747 " --> pdb=" O SER A1740 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A1798 " --> pdb=" O TYR A1737 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1671 through 1674 removed outlier: 6.521A pdb=" N LEU A1671 " --> pdb=" O ASN A1700 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASN A1702 " --> pdb=" O LEU A1671 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE A1673 " --> pdb=" O ASN A1702 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A1699 " --> pdb=" O ASN A1729 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A1726 " --> pdb=" O SER A1779 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASP A1781 " --> pdb=" O VAL A1726 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A1728 " --> pdb=" O ASP A1781 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1833 through 1835 Processing sheet with id=AC5, first strand: chain 'A' and resid 1853 through 1857 Processing sheet with id=AC6, first strand: chain 'A' and resid 1876 through 1878 Processing sheet with id=AC7, first strand: chain 'A' and resid 1894 through 1898 Processing sheet with id=AC8, first strand: chain 'A' and resid 1926 through 1927 Processing sheet with id=AC9, first strand: chain 'A' and resid 1945 through 1947 Processing sheet with id=AD1, first strand: chain 'A' and resid 1988 through 1991 Processing sheet with id=AD2, first strand: chain 'A' and resid 2009 through 2010 Processing sheet with id=AD3, first strand: chain 'A' and resid 2028 through 2031 removed outlier: 3.867A pdb=" N PHE A2030 " --> pdb=" O GLU A2037 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A2037 " --> pdb=" O PHE A2030 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A2052 " --> pdb=" O ALA A2040 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 2060 through 2063 removed outlier: 3.839A pdb=" N LYS A2066 " --> pdb=" O LEU A2063 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2100 through 2104 Processing sheet with id=AD6, first strand: chain 'A' and resid 2124 through 2125 Processing sheet with id=AD7, first strand: chain 'A' and resid 2143 through 2146 Processing sheet with id=AD8, first strand: chain 'A' and resid 2162 through 2165 removed outlier: 3.690A pdb=" N GLY A2162 " --> pdb=" O PHE A2173 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A2186 " --> pdb=" O ALA A2174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 2194 through 2195 Processing sheet with id=AE1, first strand: chain 'A' and resid 2213 through 2216 Processing sheet with id=AE2, first strand: chain 'A' and resid 2235 through 2237 Processing sheet with id=AE3, first strand: chain 'A' and resid 2254 through 2258 removed outlier: 3.594A pdb=" N ILE A2256 " --> pdb=" O PHE A2263 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A2272 " --> pdb=" O ASP A2266 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 2276 through 2279 Processing sheet with id=AE5, first strand: chain 'A' and resid 2308 through 2310 Processing sheet with id=AE6, first strand: chain 'A' and resid 2328 through 2331 Processing sheet with id=AE7, first strand: chain 'A' and resid 2348 through 2352 removed outlier: 4.021A pdb=" N GLN A2350 " --> pdb=" O TYR A2357 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A2357 " --> pdb=" O GLN A2350 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.590A pdb=" N SER B 25 " --> pdb=" O LYS B 3 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.496A pdb=" N GLY B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.496A pdb=" N GLY B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS B 96 " --> pdb=" O TRP B 113 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TRP B 113 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG B 98 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.541A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 81 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AF4, first strand: chain 'C' and resid 224 through 226 removed outlier: 3.595A pdb=" N VAL C 239 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 230 through 233 Processing sheet with id=AF6, first strand: chain 'C' and resid 273 through 274 removed outlier: 6.445A pdb=" N TRP C 255 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR C 269 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 253 " --> pdb=" O TYR C 269 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2037 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.62 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6605 1.34 - 1.46: 4978 1.46 - 1.58: 9619 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 21268 Sorted by residual: bond pdb=" CA ILE A1509 " pdb=" CB ILE A1509 " ideal model delta sigma weight residual 1.530 1.550 -0.019 1.05e-02 9.07e+03 3.44e+00 bond pdb=" C ALA A 450 " pdb=" N PRO A 451 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.96e+00 bond pdb=" N ASP A2126 " pdb=" CA ASP A2126 " ideal model delta sigma weight residual 1.460 1.484 -0.024 1.54e-02 4.22e+03 2.48e+00 bond pdb=" N GLU A1736 " pdb=" CA GLU A1736 " ideal model delta sigma weight residual 1.462 1.484 -0.022 1.54e-02 4.22e+03 2.05e+00 bond pdb=" CB ASP A1498 " pdb=" CG ASP A1498 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.04e+00 ... (remaining 21263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 28503 3.02 - 6.04: 232 6.04 - 9.06: 52 9.06 - 12.08: 7 12.08 - 15.11: 1 Bond angle restraints: 28795 Sorted by residual: angle pdb=" N ILE A1047 " pdb=" CA ILE A1047 " pdb=" C ILE A1047 " ideal model delta sigma weight residual 112.96 105.61 7.35 1.00e+00 1.00e+00 5.41e+01 angle pdb=" C ASN A1497 " pdb=" N ASP A1498 " pdb=" CA ASP A1498 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" C ILE A2125 " pdb=" N ASP A2126 " pdb=" CA ASP A2126 " ideal model delta sigma weight residual 122.46 129.13 -6.67 1.41e+00 5.03e-01 2.24e+01 angle pdb=" N ASN B 31 " pdb=" CA ASN B 31 " pdb=" C ASN B 31 " ideal model delta sigma weight residual 114.56 108.84 5.72 1.27e+00 6.20e-01 2.03e+01 angle pdb=" C GLY A1030 " pdb=" N ILE A1031 " pdb=" CA ILE A1031 " ideal model delta sigma weight residual 122.13 130.13 -8.00 1.85e+00 2.92e-01 1.87e+01 ... (remaining 28790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11322 17.98 - 35.95: 1170 35.95 - 53.93: 163 53.93 - 71.90: 17 71.90 - 89.88: 14 Dihedral angle restraints: 12686 sinusoidal: 5037 harmonic: 7649 Sorted by residual: dihedral pdb=" CA ILE A1199 " pdb=" C ILE A1199 " pdb=" N PRO A1200 " pdb=" CA PRO A1200 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LYS A 323 " pdb=" C LYS A 323 " pdb=" N LYS A 324 " pdb=" CA LYS A 324 " ideal model delta harmonic sigma weight residual 180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PRO A1200 " pdb=" C PRO A1200 " pdb=" N SER A1201 " pdb=" CA SER A1201 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 12683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2909 0.094 - 0.188: 266 0.188 - 0.283: 13 0.283 - 0.377: 2 0.377 - 0.471: 1 Chirality restraints: 3191 Sorted by residual: chirality pdb=" CB ILE A1033 " pdb=" CA ILE A1033 " pdb=" CG1 ILE A1033 " pdb=" CG2 ILE A1033 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CG LEU A 394 " pdb=" CB LEU A 394 " pdb=" CD1 LEU A 394 " pdb=" CD2 LEU A 394 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE A1815 " pdb=" CA ILE A1815 " pdb=" CG1 ILE A1815 " pdb=" CG2 ILE A1815 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 3188 not shown) Planarity restraints: 3692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1045 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C ALA A1045 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA A1045 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A1046 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 414 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO A 415 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1217 " -0.014 2.00e-02 2.50e+03 1.51e-02 4.01e+00 pdb=" CG PHE A1217 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A1217 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A1217 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A1217 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A1217 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A1217 " 0.004 2.00e-02 2.50e+03 ... (remaining 3689 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6157 2.82 - 3.34: 17756 3.34 - 3.86: 34356 3.86 - 4.38: 38091 4.38 - 4.90: 68127 Nonbonded interactions: 164487 Sorted by model distance: nonbonded pdb=" O ASN A 603 " pdb=" OG SER A 607 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR A1426 " pdb=" OD1 ASP A1454 " model vdw 2.317 3.040 nonbonded pdb=" OH TYR A 124 " pdb=" O LEU A 362 " model vdw 2.317 3.040 nonbonded pdb=" O SER A 437 " pdb=" OG SER A 437 " model vdw 2.323 3.040 nonbonded pdb=" O ASP A1293 " pdb=" OH TYR A1324 " model vdw 2.325 3.040 ... (remaining 164482 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 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 0.044 21270 Z= 0.183 Angle : 0.772 15.106 28799 Z= 0.415 Chirality : 0.053 0.471 3191 Planarity : 0.005 0.067 3692 Dihedral : 14.342 89.879 7778 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.04 % Allowed : 0.39 % Favored : 99.57 % 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 aren not related in a simple way. whole: -1.79 (0.15), residues: 2588 helix: -0.57 (0.17), residues: 659 sheet: -0.94 (0.24), residues: 560 loop : -1.60 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 224 TYR 0.024 0.002 TYR C 311 PHE 0.032 0.002 PHE A1217 TRP 0.011 0.001 TRP B 113 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00384 (21268) covalent geometry : angle 0.77219 (28795) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.71261 ( 4) hydrogen bonds : bond 0.18225 ( 727) hydrogen bonds : angle 7.45135 ( 2037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.7633 (tp) cc_final: 0.7239 (tt) REVERT: A 16 ILE cc_start: 0.6795 (pt) cc_final: 0.6388 (mm) REVERT: A 112 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6952 (mt-10) REVERT: A 115 LYS cc_start: 0.8164 (mmpt) cc_final: 0.7733 (pttp) REVERT: A 130 TYR cc_start: 0.7588 (p90) cc_final: 0.7382 (p90) REVERT: A 172 LYS cc_start: 0.6683 (tttm) cc_final: 0.6326 (tptp) REVERT: A 188 TYR cc_start: 0.7320 (t80) cc_final: 0.7102 (t80) REVERT: A 251 LEU cc_start: 0.8347 (mm) cc_final: 0.7960 (mt) REVERT: A 259 LEU cc_start: 0.7807 (mp) cc_final: 0.7562 (mp) REVERT: A 269 ASP cc_start: 0.7706 (m-30) cc_final: 0.7317 (m-30) REVERT: A 310 ARG cc_start: 0.6445 (mmm-85) cc_final: 0.5614 (mtm180) REVERT: A 600 PHE cc_start: 0.7441 (t80) cc_final: 0.7115 (t80) REVERT: A 603 ASN cc_start: 0.4458 (t0) cc_final: 0.4062 (t0) REVERT: A 671 ASP cc_start: 0.6804 (p0) cc_final: 0.6090 (m-30) REVERT: A 675 ASN cc_start: 0.7027 (m110) cc_final: 0.6669 (m110) REVERT: A 881 ASP cc_start: 0.6122 (p0) cc_final: 0.5502 (p0) REVERT: A 1072 ASN cc_start: 0.8148 (t0) cc_final: 0.7908 (t0) REVERT: A 1149 ILE cc_start: 0.8161 (mm) cc_final: 0.7587 (mt) REVERT: A 1289 LYS cc_start: 0.5807 (tptt) cc_final: 0.5360 (tppp) REVERT: A 1294 LYS cc_start: 0.7720 (tppt) cc_final: 0.7278 (mptt) REVERT: A 1375 LYS cc_start: 0.7700 (tptm) cc_final: 0.7207 (ptmt) REVERT: A 1395 ASP cc_start: 0.6764 (t0) cc_final: 0.6218 (t0) REVERT: A 1461 ASN cc_start: 0.8077 (m-40) cc_final: 0.7803 (t0) REVERT: A 1549 GLN cc_start: 0.8054 (mt0) cc_final: 0.7736 (mp10) REVERT: A 1742 GLU cc_start: 0.7076 (tp30) cc_final: 0.6757 (tp30) REVERT: A 1785 ILE cc_start: 0.7856 (tt) cc_final: 0.7655 (pt) REVERT: A 1874 SER cc_start: 0.7474 (t) cc_final: 0.7252 (p) REVERT: A 1968 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7165 (mp10) REVERT: A 1978 ASN cc_start: 0.8239 (t0) cc_final: 0.7873 (t0) REVERT: A 2047 ASN cc_start: 0.6433 (p0) cc_final: 0.6213 (p0) REVERT: A 2056 TYR cc_start: 0.6719 (t80) cc_final: 0.6293 (t80) REVERT: A 2184 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7136 (mm-30) REVERT: B 3 LYS cc_start: 0.7688 (pttp) cc_final: 0.7042 (mmmt) REVERT: B 12 VAL cc_start: 0.7772 (p) cc_final: 0.7464 (t) REVERT: B 34 MET cc_start: 0.8890 (mmt) cc_final: 0.8688 (mmm) REVERT: B 45 LEU cc_start: 0.5353 (mp) cc_final: 0.5089 (mp) REVERT: B 46 GLU cc_start: 0.6655 (mm-30) cc_final: 0.6455 (mm-30) REVERT: B 87 ARG cc_start: 0.7435 (ptp90) cc_final: 0.6964 (ptp-170) REVERT: C 237 ASP cc_start: 0.7822 (m-30) cc_final: 0.6489 (t0) REVERT: C 285 SER cc_start: 0.8417 (t) cc_final: 0.7797 (m) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.1409 time to fit residues: 82.6226 Evaluate side-chains 203 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 138 ASN A 235 HIS A 248 GLN A 256 GLN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 598 ASN A 615 ASN A 655 HIS A 692 ASN A 733 ASN A 945 ASN A1892 GLN A1973 ASN A2123 GLN A2360 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.142391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.115326 restraints weight = 38557.218| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.16 r_work: 0.3496 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21270 Z= 0.162 Angle : 0.582 8.143 28799 Z= 0.314 Chirality : 0.045 0.256 3191 Planarity : 0.004 0.047 3692 Dihedral : 4.976 20.707 2800 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.68 % Allowed : 7.57 % Favored : 90.75 % 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 aren not related in a simple way. whole: -1.06 (0.16), residues: 2588 helix: 0.85 (0.20), residues: 672 sheet: -0.80 (0.23), residues: 576 loop : -1.48 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 667 TYR 0.016 0.002 TYR A1862 PHE 0.021 0.002 PHE A1217 TRP 0.012 0.001 TRP B 113 HIS 0.005 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00370 (21268) covalent geometry : angle 0.58117 (28795) SS BOND : bond 0.00275 ( 2) SS BOND : angle 1.82189 ( 4) hydrogen bonds : bond 0.04177 ( 727) hydrogen bonds : angle 5.25611 ( 2037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7837 (mmpt) cc_final: 0.7498 (tttp) REVERT: A 138 ASN cc_start: 0.7675 (m110) cc_final: 0.7474 (t0) REVERT: A 251 LEU cc_start: 0.8070 (mm) cc_final: 0.7696 (mt) REVERT: A 297 PHE cc_start: 0.6851 (m-10) cc_final: 0.6324 (m-80) REVERT: A 600 PHE cc_start: 0.7483 (t80) cc_final: 0.7163 (t80) REVERT: A 668 LEU cc_start: 0.6706 (mp) cc_final: 0.6385 (mt) REVERT: A 671 ASP cc_start: 0.6703 (p0) cc_final: 0.6186 (m-30) REVERT: A 694 GLU cc_start: 0.6868 (tm-30) cc_final: 0.6404 (tt0) REVERT: A 756 LEU cc_start: 0.8498 (tp) cc_final: 0.8290 (tp) REVERT: A 1149 ILE cc_start: 0.8510 (mm) cc_final: 0.8142 (mt) REVERT: A 1289 LYS cc_start: 0.6676 (tptt) cc_final: 0.6293 (tppp) REVERT: A 1591 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.5198 (m-80) REVERT: A 1656 GLU cc_start: 0.7431 (tt0) cc_final: 0.7179 (tt0) REVERT: A 1758 LYS cc_start: 0.8162 (mptt) cc_final: 0.7762 (mtmt) REVERT: A 1805 GLU cc_start: 0.6239 (tm-30) cc_final: 0.5652 (tm-30) REVERT: A 2056 TYR cc_start: 0.6956 (t80) cc_final: 0.6644 (t80) REVERT: B 3 LYS cc_start: 0.8004 (pttp) cc_final: 0.7495 (mmmt) REVERT: B 12 VAL cc_start: 0.7200 (p) cc_final: 0.6928 (t) REVERT: B 45 LEU cc_start: 0.6521 (mp) cc_final: 0.5925 (mt) REVERT: B 76 LYS cc_start: 0.6657 (pttt) cc_final: 0.6018 (mmtm) REVERT: B 87 ARG cc_start: 0.7553 (ptp90) cc_final: 0.7294 (ptp-170) REVERT: C 285 SER cc_start: 0.8301 (t) cc_final: 0.7928 (m) outliers start: 39 outliers final: 25 residues processed: 247 average time/residue: 0.1544 time to fit residues: 60.1909 Evaluate side-chains 202 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1591 PHE Chi-restraints excluded: chain A residue 1891 MET Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2029 VAL Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 222 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 36 optimal weight: 0.8980 chunk 220 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 243 optimal weight: 0.6980 chunk 231 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN A 615 ASN A 675 ASN A1892 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.142313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.117028 restraints weight = 38575.869| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.16 r_work: 0.3493 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21270 Z= 0.126 Angle : 0.532 11.302 28799 Z= 0.285 Chirality : 0.044 0.258 3191 Planarity : 0.003 0.040 3692 Dihedral : 4.751 21.111 2800 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.94 % Allowed : 10.46 % Favored : 87.61 % 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 aren not related in a simple way. whole: -0.84 (0.17), residues: 2588 helix: 1.27 (0.20), residues: 676 sheet: -0.77 (0.23), residues: 573 loop : -1.43 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 310 TYR 0.016 0.001 TYR A1822 PHE 0.016 0.001 PHE A1217 TRP 0.009 0.001 TRP B 113 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00279 (21268) covalent geometry : angle 0.53193 (28795) SS BOND : bond 0.00440 ( 2) SS BOND : angle 1.06301 ( 4) hydrogen bonds : bond 0.03750 ( 727) hydrogen bonds : angle 4.89055 ( 2037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8102 (mmpt) cc_final: 0.7898 (tttp) REVERT: A 251 LEU cc_start: 0.8028 (mm) cc_final: 0.7565 (mt) REVERT: A 297 PHE cc_start: 0.6891 (m-10) cc_final: 0.5642 (m-10) REVERT: A 394 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8060 (tt) REVERT: A 600 PHE cc_start: 0.7500 (t80) cc_final: 0.7186 (t80) REVERT: A 671 ASP cc_start: 0.6664 (p0) cc_final: 0.6276 (m-30) REVERT: A 694 GLU cc_start: 0.6750 (tm-30) cc_final: 0.6303 (tt0) REVERT: A 722 MET cc_start: 0.6059 (ppp) cc_final: 0.5691 (ppp) REVERT: A 756 LEU cc_start: 0.8409 (tp) cc_final: 0.8179 (tp) REVERT: A 795 ASN cc_start: 0.7125 (t0) cc_final: 0.6911 (t0) REVERT: A 1050 LEU cc_start: 0.7122 (mt) cc_final: 0.6712 (tt) REVERT: A 1149 ILE cc_start: 0.8451 (mm) cc_final: 0.8101 (mt) REVERT: A 1388 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6297 (mt0) REVERT: A 1591 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.5198 (m-80) REVERT: A 1656 GLU cc_start: 0.7417 (tt0) cc_final: 0.7138 (tt0) REVERT: A 1758 LYS cc_start: 0.8139 (mptt) cc_final: 0.7869 (ptmt) REVERT: A 1805 GLU cc_start: 0.6424 (tm-30) cc_final: 0.6032 (tm-30) REVERT: A 2184 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6218 (pm20) REVERT: B 3 LYS cc_start: 0.8095 (pttp) cc_final: 0.7579 (mmmt) REVERT: B 12 VAL cc_start: 0.7155 (p) cc_final: 0.6921 (t) REVERT: B 45 LEU cc_start: 0.6724 (mp) cc_final: 0.6442 (mt) REVERT: B 76 LYS cc_start: 0.6731 (pttt) cc_final: 0.6033 (mmtm) REVERT: B 87 ARG cc_start: 0.7555 (ptp90) cc_final: 0.7302 (ptp-170) REVERT: C 285 SER cc_start: 0.8321 (t) cc_final: 0.7995 (m) outliers start: 45 outliers final: 30 residues processed: 224 average time/residue: 0.1419 time to fit residues: 51.7734 Evaluate side-chains 204 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1388 GLN Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1591 PHE Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2330 THR Chi-restraints excluded: chain A residue 2360 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 222 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 165 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 196 optimal weight: 0.4980 chunk 30 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 114 optimal weight: 0.0670 chunk 98 optimal weight: 5.9990 overall best weight: 1.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 422 ASN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 615 ASN A 675 ASN A1388 GLN A1491 ASN B 39 GLN C 258 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.140776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.113284 restraints weight = 38753.094| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.14 r_work: 0.3472 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21270 Z= 0.133 Angle : 0.535 10.522 28799 Z= 0.288 Chirality : 0.044 0.255 3191 Planarity : 0.003 0.038 3692 Dihedral : 4.753 22.558 2800 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.54 % Allowed : 11.57 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.17), residues: 2588 helix: 1.48 (0.20), residues: 675 sheet: -0.82 (0.23), residues: 573 loop : -1.44 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 310 TYR 0.019 0.001 TYR A 254 PHE 0.019 0.001 PHE A1217 TRP 0.008 0.001 TRP B 113 HIS 0.005 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00302 (21268) covalent geometry : angle 0.53506 (28795) SS BOND : bond 0.00425 ( 2) SS BOND : angle 1.14019 ( 4) hydrogen bonds : bond 0.03754 ( 727) hydrogen bonds : angle 4.73726 ( 2037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 251 LEU cc_start: 0.7969 (mm) cc_final: 0.7451 (mt) REVERT: A 297 PHE cc_start: 0.6934 (m-10) cc_final: 0.5575 (m-10) REVERT: A 600 PHE cc_start: 0.7484 (t80) cc_final: 0.7175 (t80) REVERT: A 603 ASN cc_start: 0.4663 (t0) cc_final: 0.4020 (m-40) REVERT: A 671 ASP cc_start: 0.6630 (p0) cc_final: 0.6179 (m-30) REVERT: A 694 GLU cc_start: 0.6763 (tm-30) cc_final: 0.6304 (tt0) REVERT: A 722 MET cc_start: 0.5946 (ppp) cc_final: 0.5465 (ppp) REVERT: A 756 LEU cc_start: 0.8355 (tp) cc_final: 0.8124 (tp) REVERT: A 1050 LEU cc_start: 0.7164 (mt) cc_final: 0.6788 (tt) REVERT: A 1149 ILE cc_start: 0.8485 (mm) cc_final: 0.8132 (mt) REVERT: A 1498 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7548 (p0) REVERT: A 1758 LYS cc_start: 0.8271 (mptt) cc_final: 0.7904 (ptmt) REVERT: A 1805 GLU cc_start: 0.6483 (tm-30) cc_final: 0.6122 (tm-30) REVERT: A 2184 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6232 (pm20) REVERT: B 3 LYS cc_start: 0.7994 (pttp) cc_final: 0.7484 (mmmt) REVERT: B 12 VAL cc_start: 0.7303 (p) cc_final: 0.7059 (t) REVERT: B 45 LEU cc_start: 0.6790 (mp) cc_final: 0.6571 (mt) REVERT: B 76 LYS cc_start: 0.6742 (pttt) cc_final: 0.6121 (mmtm) REVERT: B 87 ARG cc_start: 0.7607 (ptp90) cc_final: 0.7372 (ptp-170) REVERT: C 285 SER cc_start: 0.8369 (t) cc_final: 0.8024 (m) outliers start: 59 outliers final: 39 residues processed: 228 average time/residue: 0.1357 time to fit residues: 50.9113 Evaluate side-chains 209 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1388 GLN Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1591 PHE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 2006 PHE Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2029 VAL Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2330 THR Chi-restraints excluded: chain A residue 2360 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 273 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 250 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 256 GLN A 422 ASN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN A 675 ASN A1388 GLN ** A1914 ASN ** 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 = 0.3978 r_free = 0.3978 target = 0.138662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.110318 restraints weight = 38457.852| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.10 r_work: 0.3440 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21270 Z= 0.215 Angle : 0.624 9.151 28799 Z= 0.337 Chirality : 0.047 0.290 3191 Planarity : 0.004 0.039 3692 Dihedral : 5.235 22.951 2800 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.01 % Allowed : 12.52 % Favored : 84.47 % 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 aren not related in a simple way. whole: -1.03 (0.16), residues: 2588 helix: 1.22 (0.20), residues: 677 sheet: -0.95 (0.22), residues: 571 loop : -1.59 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 72 TYR 0.026 0.002 TYR A 254 PHE 0.025 0.002 PHE A1217 TRP 0.014 0.002 TRP B 113 HIS 0.007 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00504 (21268) covalent geometry : angle 0.62384 (28795) SS BOND : bond 0.00589 ( 2) SS BOND : angle 1.52846 ( 4) hydrogen bonds : bond 0.04554 ( 727) hydrogen bonds : angle 4.98385 ( 2037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 187 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7368 (mp) REVERT: A 251 LEU cc_start: 0.8043 (mm) cc_final: 0.7586 (mm) REVERT: A 297 PHE cc_start: 0.6961 (m-10) cc_final: 0.6036 (m-10) REVERT: A 603 ASN cc_start: 0.5013 (t0) cc_final: 0.4217 (m-40) REVERT: A 671 ASP cc_start: 0.6520 (p0) cc_final: 0.6157 (m-30) REVERT: A 756 LEU cc_start: 0.8374 (tp) cc_final: 0.8152 (tp) REVERT: A 1050 LEU cc_start: 0.7328 (mt) cc_final: 0.6959 (tt) REVERT: A 1149 ILE cc_start: 0.8635 (mm) cc_final: 0.8380 (mt) REVERT: A 1368 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7262 (mm) REVERT: A 1498 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7555 (p0) REVERT: A 1620 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: A 1758 LYS cc_start: 0.8447 (mptt) cc_final: 0.8031 (ptmt) REVERT: A 1805 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6285 (tm-30) REVERT: A 1968 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.6276 (tp40) REVERT: B 12 VAL cc_start: 0.7209 (p) cc_final: 0.6944 (t) REVERT: B 76 LYS cc_start: 0.6927 (pttt) cc_final: 0.6198 (mmtm) REVERT: B 86 LEU cc_start: 0.7759 (mp) cc_final: 0.7547 (mt) REVERT: B 87 ARG cc_start: 0.7619 (ptp90) cc_final: 0.7377 (ptp-170) REVERT: C 301 GLU cc_start: 0.7798 (pm20) cc_final: 0.7434 (pm20) outliers start: 70 outliers final: 46 residues processed: 244 average time/residue: 0.1347 time to fit residues: 53.7035 Evaluate side-chains 223 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1591 PHE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1741 THR Chi-restraints excluded: chain A residue 1818 ASN Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 1968 GLN Chi-restraints excluded: chain A residue 2006 PHE Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2068 TYR Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2360 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 313 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 75 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A1522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.137230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109132 restraints weight = 38655.606| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.15 r_work: 0.3408 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 21270 Z= 0.255 Angle : 0.681 13.617 28799 Z= 0.366 Chirality : 0.048 0.308 3191 Planarity : 0.004 0.041 3692 Dihedral : 5.508 23.383 2800 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.18 % Allowed : 13.73 % Favored : 83.09 % 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 aren not related in a simple way. whole: -1.28 (0.16), residues: 2588 helix: 0.99 (0.20), residues: 670 sheet: -1.08 (0.23), residues: 561 loop : -1.73 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 72 TYR 0.032 0.002 TYR A 254 PHE 0.026 0.002 PHE A1217 TRP 0.018 0.002 TRP B 113 HIS 0.008 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00602 (21268) covalent geometry : angle 0.68062 (28795) SS BOND : bond 0.00742 ( 2) SS BOND : angle 1.69899 ( 4) hydrogen bonds : bond 0.04948 ( 727) hydrogen bonds : angle 5.11659 ( 2037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 176 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7524 (mp) REVERT: A 189 TYR cc_start: 0.7813 (t80) cc_final: 0.7459 (t80) REVERT: A 297 PHE cc_start: 0.7094 (m-10) cc_final: 0.6756 (m-80) REVERT: A 603 ASN cc_start: 0.5197 (t0) cc_final: 0.4330 (m-40) REVERT: A 722 MET cc_start: 0.5883 (ppp) cc_final: 0.5574 (ppp) REVERT: A 756 LEU cc_start: 0.8396 (tp) cc_final: 0.8175 (tp) REVERT: A 945 ASN cc_start: 0.7085 (m110) cc_final: 0.6657 (m110) REVERT: A 1003 ILE cc_start: 0.7635 (mm) cc_final: 0.7131 (mp) REVERT: A 1093 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6470 (mp) REVERT: A 1149 ILE cc_start: 0.8705 (mm) cc_final: 0.8416 (mt) REVERT: A 1157 ILE cc_start: 0.6707 (tt) cc_final: 0.6377 (mt) REVERT: A 1368 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7543 (mm) REVERT: A 1498 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7721 (p0) REVERT: A 1620 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: A 1758 LYS cc_start: 0.8457 (mptt) cc_final: 0.8042 (ptmt) REVERT: A 1805 GLU cc_start: 0.6710 (tm-30) cc_final: 0.6416 (tm-30) REVERT: A 1806 LEU cc_start: 0.7699 (tt) cc_final: 0.7295 (tp) REVERT: A 2184 GLU cc_start: 0.7339 (mm-30) cc_final: 0.5863 (pm20) REVERT: B 60 TYR cc_start: 0.8423 (m-80) cc_final: 0.8127 (m-80) REVERT: B 76 LYS cc_start: 0.6918 (pttt) cc_final: 0.6202 (mmtm) REVERT: B 87 ARG cc_start: 0.7567 (ptp90) cc_final: 0.7341 (ptp-170) REVERT: C 301 GLU cc_start: 0.7777 (pm20) cc_final: 0.7399 (pm20) outliers start: 74 outliers final: 55 residues processed: 237 average time/residue: 0.1421 time to fit residues: 55.2360 Evaluate side-chains 228 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1093 ILE Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1538 ILE Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1591 PHE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1659 TYR Chi-restraints excluded: chain A residue 1741 THR Chi-restraints excluded: chain A residue 1818 ASN Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 2006 PHE Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2068 TYR Chi-restraints excluded: chain A residue 2094 THR Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2360 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 313 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 73 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 215 optimal weight: 0.0980 chunk 150 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 195 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 328 ASN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A1914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.140884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115449 restraints weight = 38751.800| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.98 r_work: 0.3488 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21270 Z= 0.115 Angle : 0.542 12.155 28799 Z= 0.289 Chirality : 0.044 0.277 3191 Planarity : 0.003 0.040 3692 Dihedral : 4.889 21.124 2800 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.50 % Allowed : 14.41 % Favored : 83.09 % 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 aren not related in a simple way. whole: -0.97 (0.17), residues: 2588 helix: 1.39 (0.21), residues: 678 sheet: -0.99 (0.23), residues: 570 loop : -1.59 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 637 TYR 0.025 0.001 TYR A 188 PHE 0.018 0.001 PHE A1094 TRP 0.009 0.001 TRP A1636 HIS 0.003 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00254 (21268) covalent geometry : angle 0.54180 (28795) SS BOND : bond 0.00481 ( 2) SS BOND : angle 0.81045 ( 4) hydrogen bonds : bond 0.03680 ( 727) hydrogen bonds : angle 4.68337 ( 2037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 173 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8385 (ttm) REVERT: A 97 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7520 (mp) REVERT: A 251 LEU cc_start: 0.8049 (mm) cc_final: 0.7721 (mm) REVERT: A 297 PHE cc_start: 0.6886 (m-10) cc_final: 0.5982 (m-10) REVERT: A 603 ASN cc_start: 0.4884 (t0) cc_final: 0.4262 (m-40) REVERT: A 671 ASP cc_start: 0.6387 (p0) cc_final: 0.5829 (m-30) REVERT: A 722 MET cc_start: 0.6102 (ppp) cc_final: 0.5750 (ppp) REVERT: A 756 LEU cc_start: 0.8330 (tp) cc_final: 0.8090 (tp) REVERT: A 795 ASN cc_start: 0.7083 (t0) cc_final: 0.6854 (t0) REVERT: A 1003 ILE cc_start: 0.7608 (mm) cc_final: 0.7153 (mp) REVERT: A 1149 ILE cc_start: 0.8576 (mm) cc_final: 0.8284 (mt) REVERT: A 1368 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7267 (mm) REVERT: A 1498 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7624 (p0) REVERT: A 1594 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.8002 (tp) REVERT: A 1620 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: A 1758 LYS cc_start: 0.8385 (mptt) cc_final: 0.8122 (ptmt) REVERT: A 2184 GLU cc_start: 0.7275 (mm-30) cc_final: 0.5895 (pm20) REVERT: B 60 TYR cc_start: 0.8493 (m-80) cc_final: 0.8268 (m-80) REVERT: B 76 LYS cc_start: 0.6834 (pttt) cc_final: 0.6159 (mmtm) outliers start: 58 outliers final: 42 residues processed: 219 average time/residue: 0.1413 time to fit residues: 51.2807 Evaluate side-chains 212 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1538 ILE Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1591 PHE Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1659 TYR Chi-restraints excluded: chain A residue 1741 THR Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 1890 VAL Chi-restraints excluded: chain A residue 2006 PHE Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2029 VAL Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2068 TYR Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2360 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 309 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 170 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1968 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.139155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.115824 restraints weight = 38663.034| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.27 r_work: 0.3407 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21270 Z= 0.171 Angle : 0.593 11.623 28799 Z= 0.316 Chirality : 0.045 0.281 3191 Planarity : 0.003 0.040 3692 Dihedral : 5.055 21.487 2800 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.80 % Allowed : 14.80 % Favored : 82.40 % 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 aren not related in a simple way. whole: -1.02 (0.17), residues: 2588 helix: 1.38 (0.20), residues: 670 sheet: -1.03 (0.23), residues: 568 loop : -1.62 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1808 TYR 0.025 0.002 TYR A 254 PHE 0.017 0.002 PHE A 550 TRP 0.011 0.001 TRP B 113 HIS 0.005 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00400 (21268) covalent geometry : angle 0.59242 (28795) SS BOND : bond 0.00527 ( 2) SS BOND : angle 1.20591 ( 4) hydrogen bonds : bond 0.04148 ( 727) hydrogen bonds : angle 4.78590 ( 2037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 166 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8319 (ttm) REVERT: A 97 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7480 (mp) REVERT: A 228 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7918 (tt) REVERT: A 251 LEU cc_start: 0.7989 (mm) cc_final: 0.7598 (mm) REVERT: A 297 PHE cc_start: 0.6892 (m-10) cc_final: 0.6064 (m-10) REVERT: A 320 MET cc_start: 0.6138 (mtt) cc_final: 0.5843 (mtt) REVERT: A 603 ASN cc_start: 0.4906 (t0) cc_final: 0.4273 (m-40) REVERT: A 721 ILE cc_start: 0.6489 (mm) cc_final: 0.6100 (mm) REVERT: A 722 MET cc_start: 0.6043 (ppp) cc_final: 0.5529 (ppp) REVERT: A 756 LEU cc_start: 0.8286 (tp) cc_final: 0.8065 (tp) REVERT: A 795 ASN cc_start: 0.7195 (t0) cc_final: 0.6982 (t0) REVERT: A 844 GLU cc_start: 0.7576 (pm20) cc_final: 0.6827 (pm20) REVERT: A 1003 ILE cc_start: 0.7643 (mm) cc_final: 0.7166 (mp) REVERT: A 1149 ILE cc_start: 0.8605 (mm) cc_final: 0.8327 (mt) REVERT: A 1157 ILE cc_start: 0.6508 (tt) cc_final: 0.6243 (mt) REVERT: A 1368 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7346 (mm) REVERT: A 1498 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7564 (p0) REVERT: A 1620 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: A 1758 LYS cc_start: 0.8300 (mptt) cc_final: 0.8099 (ptmt) REVERT: A 1805 GLU cc_start: 0.6393 (tm-30) cc_final: 0.6121 (tm-30) REVERT: A 2184 GLU cc_start: 0.7265 (mm-30) cc_final: 0.5935 (pm20) REVERT: B 60 TYR cc_start: 0.8467 (m-80) cc_final: 0.8211 (m-80) REVERT: B 76 LYS cc_start: 0.6774 (pttt) cc_final: 0.6168 (mmtm) outliers start: 65 outliers final: 49 residues processed: 220 average time/residue: 0.1360 time to fit residues: 49.7401 Evaluate side-chains 215 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1538 ILE Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1591 PHE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1659 TYR Chi-restraints excluded: chain A residue 1741 THR Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 1890 VAL Chi-restraints excluded: chain A residue 1891 MET Chi-restraints excluded: chain A residue 2006 PHE Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2068 TYR Chi-restraints excluded: chain A residue 2094 THR Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2360 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 309 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 243 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 217 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1957 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.141896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.116471 restraints weight = 38468.661| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.02 r_work: 0.3505 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21270 Z= 0.107 Angle : 0.531 10.997 28799 Z= 0.283 Chirality : 0.044 0.266 3191 Planarity : 0.003 0.041 3692 Dihedral : 4.689 20.684 2800 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.19 % Allowed : 15.23 % Favored : 82.57 % 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 aren not related in a simple way. whole: -0.83 (0.17), residues: 2588 helix: 1.55 (0.21), residues: 681 sheet: -0.91 (0.23), residues: 568 loop : -1.54 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 637 TYR 0.029 0.001 TYR A 188 PHE 0.018 0.001 PHE A1094 TRP 0.009 0.001 TRP A1636 HIS 0.002 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00235 (21268) covalent geometry : angle 0.53114 (28795) SS BOND : bond 0.00393 ( 2) SS BOND : angle 0.73046 ( 4) hydrogen bonds : bond 0.03489 ( 727) hydrogen bonds : angle 4.55879 ( 2037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8391 (ttm) REVERT: A 97 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7518 (mp) REVERT: A 228 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7913 (tt) REVERT: A 251 LEU cc_start: 0.8058 (mm) cc_final: 0.7646 (mt) REVERT: A 320 MET cc_start: 0.6559 (mtt) cc_final: 0.6179 (mtt) REVERT: A 600 PHE cc_start: 0.6964 (t80) cc_final: 0.6661 (t80) REVERT: A 603 ASN cc_start: 0.4595 (t0) cc_final: 0.4042 (m-40) REVERT: A 721 ILE cc_start: 0.6269 (mm) cc_final: 0.5987 (mm) REVERT: A 722 MET cc_start: 0.6114 (ppp) cc_final: 0.5607 (ppp) REVERT: A 756 LEU cc_start: 0.8268 (tp) cc_final: 0.8022 (tp) REVERT: A 1003 ILE cc_start: 0.7590 (mm) cc_final: 0.7142 (mp) REVERT: A 1149 ILE cc_start: 0.8549 (mm) cc_final: 0.8212 (mt) REVERT: A 1157 ILE cc_start: 0.6480 (tt) cc_final: 0.6216 (mt) REVERT: A 1368 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7103 (mm) REVERT: A 1498 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7545 (p0) REVERT: A 1758 LYS cc_start: 0.8369 (mptt) cc_final: 0.8063 (ptmt) REVERT: A 2184 GLU cc_start: 0.7250 (mm-30) cc_final: 0.5971 (pm20) REVERT: B 60 TYR cc_start: 0.8488 (m-80) cc_final: 0.8238 (m-80) REVERT: B 76 LYS cc_start: 0.6880 (pttt) cc_final: 0.6239 (mmtm) outliers start: 51 outliers final: 40 residues processed: 211 average time/residue: 0.1483 time to fit residues: 51.4360 Evaluate side-chains 204 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1538 ILE Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1591 PHE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1659 TYR Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 2006 PHE Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2068 TYR Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2360 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 309 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 236 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 224 optimal weight: 0.4980 chunk 95 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.141289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116088 restraints weight = 38771.792| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.98 r_work: 0.3487 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21270 Z= 0.122 Angle : 0.544 10.902 28799 Z= 0.290 Chirality : 0.044 0.257 3191 Planarity : 0.003 0.042 3692 Dihedral : 4.707 20.504 2800 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.28 % Allowed : 15.32 % Favored : 82.40 % 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 aren not related in a simple way. whole: -0.79 (0.17), residues: 2588 helix: 1.63 (0.21), residues: 673 sheet: -0.92 (0.23), residues: 570 loop : -1.50 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 637 TYR 0.030 0.001 TYR A 254 PHE 0.029 0.001 PHE A 185 TRP 0.007 0.001 TRP A1636 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00277 (21268) covalent geometry : angle 0.54406 (28795) SS BOND : bond 0.00431 ( 2) SS BOND : angle 0.95356 ( 4) hydrogen bonds : bond 0.03615 ( 727) hydrogen bonds : angle 4.56691 ( 2037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8354 (ttm) REVERT: A 97 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7439 (mp) REVERT: A 160 ILE cc_start: 0.7850 (mt) cc_final: 0.7630 (mt) REVERT: A 228 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7914 (tt) REVERT: A 251 LEU cc_start: 0.8035 (mm) cc_final: 0.7528 (mt) REVERT: A 320 MET cc_start: 0.6826 (mtt) cc_final: 0.6544 (mtt) REVERT: A 498 ILE cc_start: 0.7597 (pt) cc_final: 0.7187 (pt) REVERT: A 600 PHE cc_start: 0.7015 (t80) cc_final: 0.6665 (t80) REVERT: A 603 ASN cc_start: 0.4582 (t0) cc_final: 0.4047 (m-40) REVERT: A 721 ILE cc_start: 0.6384 (mm) cc_final: 0.6116 (mm) REVERT: A 722 MET cc_start: 0.6121 (ppp) cc_final: 0.5589 (ppp) REVERT: A 756 LEU cc_start: 0.8276 (tp) cc_final: 0.8067 (tp) REVERT: A 1003 ILE cc_start: 0.7594 (mm) cc_final: 0.7141 (mp) REVERT: A 1149 ILE cc_start: 0.8540 (mm) cc_final: 0.8227 (mt) REVERT: A 1157 ILE cc_start: 0.6468 (tt) cc_final: 0.6213 (mt) REVERT: A 1368 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7075 (mm) REVERT: A 1498 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7558 (p0) REVERT: A 1620 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: A 1758 LYS cc_start: 0.8377 (mptt) cc_final: 0.8068 (ptmt) REVERT: A 2184 GLU cc_start: 0.7202 (mm-30) cc_final: 0.5926 (pm20) REVERT: B 60 TYR cc_start: 0.8475 (m-80) cc_final: 0.8215 (m-80) REVERT: B 76 LYS cc_start: 0.6851 (pttt) cc_final: 0.6207 (mmtm) outliers start: 53 outliers final: 44 residues processed: 207 average time/residue: 0.1387 time to fit residues: 47.2630 Evaluate side-chains 210 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1226 ASN Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1538 ILE Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1591 PHE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1659 TYR Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 1890 VAL Chi-restraints excluded: chain A residue 2006 PHE Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2068 TYR Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2360 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 309 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 167 optimal weight: 0.4980 chunk 38 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.141303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.115892 restraints weight = 38565.818| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.01 r_work: 0.3488 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21270 Z= 0.124 Angle : 0.543 11.049 28799 Z= 0.289 Chirality : 0.044 0.264 3191 Planarity : 0.003 0.041 3692 Dihedral : 4.695 20.665 2800 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.37 % Allowed : 15.28 % Favored : 82.36 % 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 aren not related in a simple way. whole: -0.77 (0.17), residues: 2588 helix: 1.64 (0.21), residues: 673 sheet: -0.90 (0.23), residues: 570 loop : -1.50 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.030 0.001 TYR A 254 PHE 0.021 0.001 PHE A1094 TRP 0.007 0.001 TRP A 101 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00280 (21268) covalent geometry : angle 0.54289 (28795) SS BOND : bond 0.00450 ( 2) SS BOND : angle 0.97711 ( 4) hydrogen bonds : bond 0.03617 ( 727) hydrogen bonds : angle 4.55774 ( 2037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7642.05 seconds wall clock time: 131 minutes 4.50 seconds (7864.50 seconds total)