Starting phenix.real_space_refine on Sun Mar 24 21:24:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/03_2024/8oxm_17265_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/03_2024/8oxm_17265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/03_2024/8oxm_17265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/03_2024/8oxm_17265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/03_2024/8oxm_17265_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/03_2024/8oxm_17265_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 302 5.16 5 C 28218 2.51 5 N 7504 2.21 5 O 8140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44174 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "A" Number of atoms: 22001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2748, 22001 Classifications: {'peptide': 2748} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 85, 'TRANS': 2662} Chain breaks: 19 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "F" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "B" Number of atoms: 22001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2748, 22001 Classifications: {'peptide': 2748} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 85, 'TRANS': 2662} Chain breaks: 19 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13293 SG CYS A1899 77.976 135.917 101.933 1.00281.63 S ATOM 13299 SG CYS A1900 73.887 134.726 100.613 1.00275.72 S ATOM 35347 SG CYS B1899 35.654 78.857 101.469 1.00249.57 S ATOM 35353 SG CYS B1900 39.930 80.092 100.884 1.00243.90 S Time building chain proxies: 21.78, per 1000 atoms: 0.49 Number of scatterers: 44174 At special positions: 0 Unit cell: (115.64, 215.586, 222.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 302 16.00 P 6 15.00 Mg 2 11.99 O 8140 8.00 N 7504 7.00 C 28218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.97 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3103 " pdb="ZN ZN A3103 " - pdb=" NE2 HIS A1876 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1899 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1900 " pdb=" ZN B3103 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1899 " pdb="ZN ZN B3103 " - pdb=" NE2 HIS B1876 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1900 " 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 292 helices and 6 sheets defined 67.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 18.03 Creating SS restraints... Processing helix chain 'A' and resid 6 through 16 Processing helix chain 'A' and resid 20 through 33 removed outlier: 4.147A pdb=" N LYS A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 57 through 73 Processing helix chain 'A' and resid 88 through 108 removed outlier: 4.126A pdb=" N LYS A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 182 through 201 removed outlier: 3.982A pdb=" N VAL A 185 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 188 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS A 192 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 194 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 195 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS A 198 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 199 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 201 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 removed outlier: 4.236A pdb=" N ASP A 211 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 5.288A pdb=" N VAL A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 267 Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 407 through 422 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 432 through 443 Processing helix chain 'A' and resid 451 through 467 Processing helix chain 'A' and resid 474 through 491 Processing helix chain 'A' and resid 501 through 514 Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.738A pdb=" N LYS A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 521 through 526' Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.774A pdb=" N CYS A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 544 " --> pdb=" O CYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 597 through 600 No H-bonds generated for 'chain 'A' and resid 597 through 600' Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 620 through 628 Processing helix chain 'A' and resid 646 through 656 removed outlier: 3.610A pdb=" N GLU A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 703 Processing helix chain 'A' and resid 713 through 731 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 744 through 765 removed outlier: 3.846A pdb=" N GLU A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER A 759 " --> pdb=" O CYS A 755 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 786 Processing helix chain 'A' and resid 795 through 806 Processing helix chain 'A' and resid 809 through 824 removed outlier: 3.892A pdb=" N SER A 824 " --> pdb=" O LYS A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.409A pdb=" N GLN A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N THR A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 931 removed outlier: 3.569A pdb=" N ILE A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 954 removed outlier: 3.988A pdb=" N GLU A 953 " --> pdb=" O MET A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 980 Proline residue: A 972 - end of helix removed outlier: 5.042A pdb=" N ASN A 975 " --> pdb=" O LYS A 971 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1002 removed outlier: 4.491A pdb=" N HIS A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N VAL A 997 " --> pdb=" O HIS A 993 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 998 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN A1000 " --> pdb=" O HIS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1030 removed outlier: 4.014A pdb=" N VAL A1021 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A1022 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1052 Processing helix chain 'A' and resid 1070 through 1079 removed outlier: 3.532A pdb=" N PHE A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A1078 " --> pdb=" O PHE A1074 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA A1079 " --> pdb=" O THR A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1096 removed outlier: 3.620A pdb=" N LEU A1088 " --> pdb=" O GLN A1084 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN A1094 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG A1095 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU A1096 " --> pdb=" O SER A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1132 Processing helix chain 'A' and resid 1143 through 1164 removed outlier: 3.544A pdb=" N LEU A1162 " --> pdb=" O ILE A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1182 removed outlier: 4.034A pdb=" N LYS A1181 " --> pdb=" O CYS A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1201 Processing helix chain 'A' and resid 1206 through 1211 Processing helix chain 'A' and resid 1214 through 1224 removed outlier: 3.693A pdb=" N LEU A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1238 No H-bonds generated for 'chain 'A' and resid 1236 through 1238' Processing helix chain 'A' and resid 1244 through 1260 removed outlier: 6.277A pdb=" N LYS A1253 " --> pdb=" O ARG A1249 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A1254 " --> pdb=" O SER A1250 " (cutoff:3.500A) Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1265 through 1272 Processing helix chain 'A' and resid 1279 through 1285 Processing helix chain 'A' and resid 1287 through 1298 removed outlier: 3.646A pdb=" N ASN A1293 " --> pdb=" O LYS A1289 " (cutoff:3.500A) Proline residue: A1296 - end of helix Processing helix chain 'A' and resid 1306 through 1322 removed outlier: 4.751A pdb=" N GLN A1311 " --> pdb=" O GLY A1307 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG A1312 " --> pdb=" O MET A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1341 through 1349 removed outlier: 4.050A pdb=" N GLU A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1396 Processing helix chain 'A' and resid 1404 through 1408 Processing helix chain 'A' and resid 1412 through 1428 removed outlier: 3.517A pdb=" N TYR A1415 " --> pdb=" O PRO A1412 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A1417 " --> pdb=" O SER A1414 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A1418 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A1422 " --> pdb=" O LEU A1419 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS A1423 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A1425 " --> pdb=" O ILE A1422 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A1427 " --> pdb=" O GLU A1424 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A1428 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1452 removed outlier: 3.930A pdb=" N ASP A1452 " --> pdb=" O LEU A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1477 removed outlier: 4.238A pdb=" N TRP A1461 " --> pdb=" O GLY A1458 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA A1462 " --> pdb=" O GLY A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1508 Processing helix chain 'A' and resid 1518 through 1523 Processing helix chain 'A' and resid 1525 through 1527 No H-bonds generated for 'chain 'A' and resid 1525 through 1527' Processing helix chain 'A' and resid 1532 through 1547 Processing helix chain 'A' and resid 1553 through 1560 removed outlier: 4.462A pdb=" N ILE A1557 " --> pdb=" O GLU A1553 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR A1558 " --> pdb=" O ASN A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1569 through 1582 removed outlier: 4.683A pdb=" N ASP A1573 " --> pdb=" O VAL A1570 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN A1579 " --> pdb=" O ILE A1576 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS A1580 " --> pdb=" O THR A1577 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A1581 " --> pdb=" O GLN A1578 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A1582 " --> pdb=" O GLN A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1603 Processing helix chain 'A' and resid 1611 through 1623 Processing helix chain 'A' and resid 1625 through 1634 removed outlier: 3.827A pdb=" N VAL A1629 " --> pdb=" O ASP A1626 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP A1630 " --> pdb=" O GLN A1627 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE A1631 " --> pdb=" O MET A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1641 No H-bonds generated for 'chain 'A' and resid 1639 through 1641' Processing helix chain 'A' and resid 1643 through 1660 removed outlier: 4.790A pdb=" N ASN A1660 " --> pdb=" O LYS A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1677 removed outlier: 3.578A pdb=" N GLU A1669 " --> pdb=" O LYS A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1702 Processing helix chain 'A' and resid 1706 through 1723 removed outlier: 4.044A pdb=" N VAL A1723 " --> pdb=" O ASN A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1742 Processing helix chain 'A' and resid 1744 through 1755 removed outlier: 4.866A pdb=" N MET A1755 " --> pdb=" O GLU A1751 " (cutoff:3.500A) Processing helix chain 'A' and resid 1760 through 1765 Processing helix chain 'A' and resid 1792 through 1795 No H-bonds generated for 'chain 'A' and resid 1792 through 1795' Processing helix chain 'A' and resid 1802 through 1815 Processing helix chain 'A' and resid 1828 through 1831 No H-bonds generated for 'chain 'A' and resid 1828 through 1831' Processing helix chain 'A' and resid 1835 through 1851 Proline residue: A1843 - end of helix Processing helix chain 'A' and resid 1857 through 1873 removed outlier: 3.911A pdb=" N LEU A1861 " --> pdb=" O SER A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1903 through 1918 removed outlier: 3.548A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1932 removed outlier: 3.525A pdb=" N PHE A1932 " --> pdb=" O PHE A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1947 Processing helix chain 'A' and resid 1951 through 1973 Processing helix chain 'A' and resid 1986 through 1996 Processing helix chain 'A' and resid 2001 through 2011 Processing helix chain 'A' and resid 2018 through 2021 Processing helix chain 'A' and resid 2029 through 2038 Processing helix chain 'A' and resid 2042 through 2051 removed outlier: 3.630A pdb=" N VAL A2047 " --> pdb=" O GLY A2043 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2070 removed outlier: 3.581A pdb=" N GLN A2061 " --> pdb=" O SER A2057 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA A2062 " --> pdb=" O SER A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2075 through 2087 Processing helix chain 'A' and resid 2093 through 2105 Processing helix chain 'A' and resid 2124 through 2136 Processing helix chain 'A' and resid 2141 through 2160 Processing helix chain 'A' and resid 2167 through 2188 Proline residue: A2171 - end of helix Processing helix chain 'A' and resid 2195 through 2211 Processing helix chain 'A' and resid 2217 through 2236 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2242 through 2265 removed outlier: 3.694A pdb=" N PHE A2265 " --> pdb=" O LEU A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2269 through 2281 Processing helix chain 'A' and resid 2290 through 2301 Processing helix chain 'A' and resid 2305 through 2321 removed outlier: 3.691A pdb=" N ALA A2321 " --> pdb=" O LYS A2317 " (cutoff:3.500A) Processing helix chain 'A' and resid 2328 through 2348 Processing helix chain 'A' and resid 2353 through 2371 removed outlier: 3.829A pdb=" N GLN A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU A2362 " --> pdb=" O GLN A2358 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A2363 " --> pdb=" O THR A2359 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A2371 " --> pdb=" O VAL A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2406 removed outlier: 4.180A pdb=" N GLY A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2408 through 2429 Processing helix chain 'A' and resid 2436 through 2475 Processing helix chain 'A' and resid 2481 through 2491 removed outlier: 3.800A pdb=" N VAL A2484 " --> pdb=" O ASP A2481 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A2485 " --> pdb=" O MET A2482 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2506 Processing helix chain 'A' and resid 2508 through 2510 No H-bonds generated for 'chain 'A' and resid 2508 through 2510' Processing helix chain 'A' and resid 2513 through 2515 No H-bonds generated for 'chain 'A' and resid 2513 through 2515' Processing helix chain 'A' and resid 2520 through 2524 Processing helix chain 'A' and resid 2535 through 2551 Processing helix chain 'A' and resid 2553 through 2555 No H-bonds generated for 'chain 'A' and resid 2553 through 2555' Processing helix chain 'A' and resid 2557 through 2564 Processing helix chain 'A' and resid 2568 through 2572 Processing helix chain 'A' and resid 2593 through 2612 removed outlier: 3.892A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2614 through 2632 Processing helix chain 'A' and resid 2636 through 2638 No H-bonds generated for 'chain 'A' and resid 2636 through 2638' Processing helix chain 'A' and resid 2652 through 2655 No H-bonds generated for 'chain 'A' and resid 2652 through 2655' Processing helix chain 'A' and resid 2723 through 2741 Processing helix chain 'A' and resid 2743 through 2748 removed outlier: 3.624A pdb=" N LYS A2747 " --> pdb=" O THR A2743 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A2748 " --> pdb=" O GLU A2744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2743 through 2748' Processing helix chain 'A' and resid 2776 through 2780 Processing helix chain 'A' and resid 2787 through 2791 Processing helix chain 'A' and resid 2798 through 2808 Processing helix chain 'A' and resid 2813 through 2825 Processing helix chain 'A' and resid 2831 through 2837 removed outlier: 4.533A pdb=" N CYS A2835 " --> pdb=" O ARG A2832 " (cutoff:3.500A) Processing helix chain 'A' and resid 2842 through 2866 Processing helix chain 'A' and resid 2873 through 2875 No H-bonds generated for 'chain 'A' and resid 2873 through 2875' Processing helix chain 'A' and resid 2912 through 2918 Processing helix chain 'A' and resid 2926 through 2940 Processing helix chain 'A' and resid 2942 through 2951 removed outlier: 4.569A pdb=" N VAL A2951 " --> pdb=" O THR A2947 " (cutoff:3.500A) Processing helix chain 'A' and resid 3004 through 3018 Processing helix chain 'A' and resid 3028 through 3040 Processing helix chain 'A' and resid 3042 through 3046 Processing helix chain 'A' and resid 3050 through 3052 No H-bonds generated for 'chain 'A' and resid 3050 through 3052' Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 20 through 33 removed outlier: 4.139A pdb=" N LYS B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 57 through 73 Processing helix chain 'B' and resid 88 through 108 removed outlier: 4.154A pdb=" N LYS B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 135 through 147 Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 182 through 201 removed outlier: 3.989A pdb=" N VAL B 185 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 188 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS B 192 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 194 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 195 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 198 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 199 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN B 201 " --> pdb=" O CYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 removed outlier: 4.282A pdb=" N ASP B 211 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 245 removed outlier: 5.190A pdb=" N VAL B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 267 Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 273 through 290 Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 306 through 323 Processing helix chain 'B' and resid 343 through 356 Processing helix chain 'B' and resid 393 through 402 Processing helix chain 'B' and resid 407 through 422 Proline residue: B 411 - end of helix Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 450 through 467 removed outlier: 4.350A pdb=" N TYR B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 462 " --> pdb=" O CYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 492 removed outlier: 4.291A pdb=" N LYS B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 removed outlier: 5.496A pdb=" N ALA B 502 " --> pdb=" O GLN B 499 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 504 " --> pdb=" O GLN B 501 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 505 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 508 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 509 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 511 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 512 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.795A pdb=" N LYS B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 521 through 526' Processing helix chain 'B' and resid 536 through 547 removed outlier: 3.506A pdb=" N LEU B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 597 through 600 No H-bonds generated for 'chain 'B' and resid 597 through 600' Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 646 through 656 removed outlier: 3.723A pdb=" N GLU B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 703 removed outlier: 3.892A pdb=" N GLU B 688 " --> pdb=" O GLN B 684 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 689 " --> pdb=" O ASN B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 731 Processing helix chain 'B' and resid 737 through 741 Processing helix chain 'B' and resid 744 through 765 removed outlier: 3.510A pdb=" N MET B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU B 758 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER B 759 " --> pdb=" O CYS B 755 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 786 Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 809 through 823 removed outlier: 3.617A pdb=" N LYS B 820 " --> pdb=" O ALA B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 889 No H-bonds generated for 'chain 'B' and resid 887 through 889' Processing helix chain 'B' and resid 892 through 910 Processing helix chain 'B' and resid 920 through 931 removed outlier: 3.574A pdb=" N ILE B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 954 Processing helix chain 'B' and resid 963 through 979 Proline residue: B 972 - end of helix removed outlier: 4.978A pdb=" N ASN B 975 " --> pdb=" O LYS B 971 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 976 " --> pdb=" O PRO B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 996 removed outlier: 3.683A pdb=" N LEU B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N HIS B 996 " --> pdb=" O ASN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1001 No H-bonds generated for 'chain 'B' and resid 998 through 1001' Processing helix chain 'B' and resid 1009 through 1031 Processing helix chain 'B' and resid 1036 through 1052 Processing helix chain 'B' and resid 1070 through 1079 removed outlier: 3.545A pdb=" N PHE B1077 " --> pdb=" O VAL B1073 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B1078 " --> pdb=" O PHE B1074 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA B1079 " --> pdb=" O THR B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1095 removed outlier: 4.507A pdb=" N ASN B1094 " --> pdb=" O ALA B1090 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG B1095 " --> pdb=" O GLU B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1132 Processing helix chain 'B' and resid 1143 through 1164 Processing helix chain 'B' and resid 1169 through 1182 removed outlier: 3.993A pdb=" N LYS B1181 " --> pdb=" O CYS B1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 1187 through 1201 Processing helix chain 'B' and resid 1206 through 1211 Processing helix chain 'B' and resid 1214 through 1224 Processing helix chain 'B' and resid 1231 through 1233 No H-bonds generated for 'chain 'B' and resid 1231 through 1233' Processing helix chain 'B' and resid 1236 through 1238 No H-bonds generated for 'chain 'B' and resid 1236 through 1238' Processing helix chain 'B' and resid 1244 through 1261 removed outlier: 5.932A pdb=" N LYS B1253 " --> pdb=" O ARG B1249 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B1254 " --> pdb=" O SER B1250 " (cutoff:3.500A) Proline residue: B1257 - end of helix Processing helix chain 'B' and resid 1265 through 1274 Processing helix chain 'B' and resid 1279 through 1285 Processing helix chain 'B' and resid 1287 through 1298 Proline residue: B1296 - end of helix Processing helix chain 'B' and resid 1306 through 1323 removed outlier: 4.687A pdb=" N GLN B1311 " --> pdb=" O GLY B1307 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG B1312 " --> pdb=" O MET B1308 " (cutoff:3.500A) Processing helix chain 'B' and resid 1328 through 1338 removed outlier: 3.834A pdb=" N ILE B1332 " --> pdb=" O GLY B1329 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ASP B1333 " --> pdb=" O LYS B1330 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1335 " --> pdb=" O ILE B1332 " (cutoff:3.500A) Processing helix chain 'B' and resid 1340 through 1349 removed outlier: 3.514A pdb=" N GLU B1346 " --> pdb=" O GLU B1342 " (cutoff:3.500A) Processing helix chain 'B' and resid 1383 through 1396 Processing helix chain 'B' and resid 1404 through 1408 Processing helix chain 'B' and resid 1412 through 1428 removed outlier: 4.369A pdb=" N ILE B1422 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B1428 " --> pdb=" O GLN B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1432 through 1452 removed outlier: 4.029A pdb=" N ASP B1452 " --> pdb=" O LEU B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1464 through 1477 Processing helix chain 'B' and resid 1491 through 1508 Processing helix chain 'B' and resid 1518 through 1523 Processing helix chain 'B' and resid 1525 through 1528 Processing helix chain 'B' and resid 1532 through 1547 Processing helix chain 'B' and resid 1553 through 1560 removed outlier: 4.431A pdb=" N ILE B1557 " --> pdb=" O GLU B1553 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR B1558 " --> pdb=" O ASN B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1569 through 1582 removed outlier: 4.854A pdb=" N ASP B1573 " --> pdb=" O VAL B1570 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS B1580 " --> pdb=" O THR B1577 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE B1581 " --> pdb=" O GLN B1578 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B1582 " --> pdb=" O GLN B1579 " (cutoff:3.500A) Processing helix chain 'B' and resid 1590 through 1603 Processing helix chain 'B' and resid 1611 through 1623 Processing helix chain 'B' and resid 1625 through 1634 removed outlier: 3.836A pdb=" N VAL B1629 " --> pdb=" O ASP B1626 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP B1630 " --> pdb=" O GLN B1627 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE B1631 " --> pdb=" O MET B1628 " (cutoff:3.500A) Processing helix chain 'B' and resid 1639 through 1641 No H-bonds generated for 'chain 'B' and resid 1639 through 1641' Processing helix chain 'B' and resid 1643 through 1660 removed outlier: 4.804A pdb=" N ASN B1660 " --> pdb=" O LYS B1656 " (cutoff:3.500A) Processing helix chain 'B' and resid 1664 through 1677 removed outlier: 3.591A pdb=" N GLU B1669 " --> pdb=" O LYS B1665 " (cutoff:3.500A) Processing helix chain 'B' and resid 1694 through 1702 Processing helix chain 'B' and resid 1706 through 1723 removed outlier: 4.076A pdb=" N VAL B1723 " --> pdb=" O ASN B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1727 through 1742 removed outlier: 3.525A pdb=" N ALA B1742 " --> pdb=" O LYS B1738 " (cutoff:3.500A) Processing helix chain 'B' and resid 1744 through 1755 removed outlier: 4.853A pdb=" N MET B1755 " --> pdb=" O GLU B1751 " (cutoff:3.500A) Processing helix chain 'B' and resid 1760 through 1767 Proline residue: B1766 - end of helix Processing helix chain 'B' and resid 1792 through 1795 No H-bonds generated for 'chain 'B' and resid 1792 through 1795' Processing helix chain 'B' and resid 1802 through 1815 Processing helix chain 'B' and resid 1828 through 1831 No H-bonds generated for 'chain 'B' and resid 1828 through 1831' Processing helix chain 'B' and resid 1835 through 1851 removed outlier: 3.554A pdb=" N GLN B1839 " --> pdb=" O THR B1835 " (cutoff:3.500A) Proline residue: B1843 - end of helix Processing helix chain 'B' and resid 1857 through 1874 removed outlier: 3.844A pdb=" N LEU B1861 " --> pdb=" O SER B1857 " (cutoff:3.500A) Processing helix chain 'B' and resid 1903 through 1918 removed outlier: 3.542A pdb=" N ARG B1918 " --> pdb=" O ASP B1914 " (cutoff:3.500A) Processing helix chain 'B' and resid 1927 through 1932 removed outlier: 3.592A pdb=" N PHE B1932 " --> pdb=" O PHE B1928 " (cutoff:3.500A) Processing helix chain 'B' and resid 1938 through 1947 Processing helix chain 'B' and resid 1951 through 1973 Processing helix chain 'B' and resid 1986 through 1996 Processing helix chain 'B' and resid 2001 through 2011 Processing helix chain 'B' and resid 2019 through 2021 No H-bonds generated for 'chain 'B' and resid 2019 through 2021' Processing helix chain 'B' and resid 2029 through 2038 Processing helix chain 'B' and resid 2042 through 2051 removed outlier: 3.682A pdb=" N VAL B2047 " --> pdb=" O GLY B2043 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2070 removed outlier: 3.613A pdb=" N GLN B2061 " --> pdb=" O SER B2057 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA B2062 " --> pdb=" O SER B2058 " (cutoff:3.500A) Processing helix chain 'B' and resid 2075 through 2087 Processing helix chain 'B' and resid 2093 through 2105 Processing helix chain 'B' and resid 2124 through 2136 Processing helix chain 'B' and resid 2140 through 2160 Processing helix chain 'B' and resid 2167 through 2188 Proline residue: B2171 - end of helix Processing helix chain 'B' and resid 2195 through 2211 Processing helix chain 'B' and resid 2217 through 2236 Proline residue: B2222 - end of helix Processing helix chain 'B' and resid 2242 through 2265 removed outlier: 3.689A pdb=" N PHE B2265 " --> pdb=" O LEU B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2269 through 2281 Processing helix chain 'B' and resid 2291 through 2301 Processing helix chain 'B' and resid 2305 through 2321 removed outlier: 3.727A pdb=" N ALA B2321 " --> pdb=" O LYS B2317 " (cutoff:3.500A) Processing helix chain 'B' and resid 2328 through 2348 Processing helix chain 'B' and resid 2353 through 2371 removed outlier: 3.844A pdb=" N GLN B2358 " --> pdb=" O ALA B2354 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU B2362 " --> pdb=" O GLN B2358 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS B2363 " --> pdb=" O THR B2359 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B2371 " --> pdb=" O VAL B2367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2377 through 2405 removed outlier: 4.195A pdb=" N GLY B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) Processing helix chain 'B' and resid 2408 through 2429 Processing helix chain 'B' and resid 2436 through 2475 Processing helix chain 'B' and resid 2481 through 2490 removed outlier: 3.754A pdb=" N VAL B2484 " --> pdb=" O ASP B2481 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B2485 " --> pdb=" O MET B2482 " (cutoff:3.500A) Processing helix chain 'B' and resid 2498 through 2506 Processing helix chain 'B' and resid 2508 through 2510 No H-bonds generated for 'chain 'B' and resid 2508 through 2510' Processing helix chain 'B' and resid 2513 through 2515 No H-bonds generated for 'chain 'B' and resid 2513 through 2515' Processing helix chain 'B' and resid 2520 through 2525 Processing helix chain 'B' and resid 2535 through 2551 Processing helix chain 'B' and resid 2553 through 2555 No H-bonds generated for 'chain 'B' and resid 2553 through 2555' Processing helix chain 'B' and resid 2557 through 2564 Processing helix chain 'B' and resid 2568 through 2572 Processing helix chain 'B' and resid 2593 through 2612 removed outlier: 3.899A pdb=" N ARG B2612 " --> pdb=" O THR B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2614 through 2632 Processing helix chain 'B' and resid 2636 through 2638 No H-bonds generated for 'chain 'B' and resid 2636 through 2638' Processing helix chain 'B' and resid 2652 through 2655 No H-bonds generated for 'chain 'B' and resid 2652 through 2655' Processing helix chain 'B' and resid 2723 through 2741 Processing helix chain 'B' and resid 2743 through 2748 removed outlier: 3.719A pdb=" N LYS B2747 " --> pdb=" O THR B2743 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B2748 " --> pdb=" O GLU B2744 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2743 through 2748' Processing helix chain 'B' and resid 2776 through 2780 Processing helix chain 'B' and resid 2787 through 2791 Processing helix chain 'B' and resid 2798 through 2808 Processing helix chain 'B' and resid 2813 through 2825 Processing helix chain 'B' and resid 2831 through 2838 removed outlier: 4.327A pdb=" N CYS B2835 " --> pdb=" O ARG B2832 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B2838 " --> pdb=" O CYS B2835 " (cutoff:3.500A) Processing helix chain 'B' and resid 2842 through 2866 Processing helix chain 'B' and resid 2873 through 2875 No H-bonds generated for 'chain 'B' and resid 2873 through 2875' Processing helix chain 'B' and resid 2912 through 2918 Processing helix chain 'B' and resid 2922 through 2924 No H-bonds generated for 'chain 'B' and resid 2922 through 2924' Processing helix chain 'B' and resid 2926 through 2940 Processing helix chain 'B' and resid 2942 through 2951 removed outlier: 4.544A pdb=" N VAL B2951 " --> pdb=" O THR B2947 " (cutoff:3.500A) Processing helix chain 'B' and resid 3004 through 3018 Processing helix chain 'B' and resid 3028 through 3040 Processing helix chain 'B' and resid 3042 through 3046 Processing helix chain 'B' and resid 3050 through 3052 No H-bonds generated for 'chain 'B' and resid 3050 through 3052' Processing sheet with id= A, first strand: chain 'A' and resid 1060 through 1063 Processing sheet with id= B, first strand: chain 'A' and resid 2757 through 2759 removed outlier: 3.596A pdb=" N GLY A2765 " --> pdb=" O LYS A2717 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id= D, first strand: chain 'B' and resid 1060 through 1063 Processing sheet with id= E, first strand: chain 'B' and resid 2757 through 2759 Processing sheet with id= F, first strand: chain 'B' and resid 2773 through 2775 2389 hydrogen bonds defined for protein. 6780 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: 19.26 Time building geometry restraints manager: 18.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14287 1.34 - 1.46: 7558 1.46 - 1.58: 22691 1.58 - 1.69: 10 1.69 - 1.81: 446 Bond restraints: 44992 Sorted by residual: bond pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" O3A ANP B3101 " pdb=" PB ANP B3101 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O5' ANP B3101 " pdb=" PA ANP B3101 " ideal model delta sigma weight residual 1.655 1.583 0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 44987 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.06: 680 105.06 - 112.31: 23102 112.31 - 119.56: 15215 119.56 - 126.81: 21242 126.81 - 134.06: 559 Bond angle restraints: 60798 Sorted by residual: angle pdb=" PB ANP B3101 " pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 126.95 109.84 17.11 3.00e+00 1.11e-01 3.25e+01 angle pdb=" PB ANP A3101 " pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 126.95 109.88 17.07 3.00e+00 1.11e-01 3.24e+01 angle pdb=" N GLU B1195 " pdb=" CA GLU B1195 " pdb=" CB GLU B1195 " ideal model delta sigma weight residual 110.16 116.85 -6.69 1.48e+00 4.57e-01 2.05e+01 angle pdb=" C LEU B1194 " pdb=" N GLU B1195 " pdb=" CA GLU B1195 " ideal model delta sigma weight residual 120.29 114.47 5.82 1.42e+00 4.96e-01 1.68e+01 angle pdb=" O1B ANP A3101 " pdb=" PB ANP A3101 " pdb=" O2B ANP A3101 " ideal model delta sigma weight residual 120.08 109.44 10.64 3.00e+00 1.11e-01 1.26e+01 ... (remaining 60793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 24887 17.94 - 35.88: 2100 35.88 - 53.82: 322 53.82 - 71.76: 88 71.76 - 89.70: 59 Dihedral angle restraints: 27456 sinusoidal: 11216 harmonic: 16240 Sorted by residual: dihedral pdb=" CA MET A 949 " pdb=" C MET A 949 " pdb=" N LEU A 950 " pdb=" CA LEU A 950 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP A2003 " pdb=" CB ASP A2003 " pdb=" CG ASP A2003 " pdb=" OD1 ASP A2003 " ideal model delta sinusoidal sigma weight residual -30.00 -88.23 58.23 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP B2003 " pdb=" CB ASP B2003 " pdb=" CG ASP B2003 " pdb=" OD1 ASP B2003 " ideal model delta sinusoidal sigma weight residual -30.00 -88.13 58.13 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 27453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 6108 0.054 - 0.109: 814 0.109 - 0.163: 56 0.163 - 0.218: 0 0.218 - 0.272: 2 Chirality restraints: 6980 Sorted by residual: chirality pdb=" C3' ANP A3101 " pdb=" C2' ANP A3101 " pdb=" C4' ANP A3101 " pdb=" O3' ANP A3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' ANP B3101 " pdb=" C2' ANP B3101 " pdb=" C4' ANP B3101 " pdb=" O3' ANP B3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA LEU B1194 " pdb=" N LEU B1194 " pdb=" C LEU B1194 " pdb=" CB LEU B1194 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 6977 not shown) Planarity restraints: 7648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B1463 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C PHE B1463 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE B1463 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B1464 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A2092 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A2093 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A2093 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2093 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B2092 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO B2093 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B2093 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B2093 " 0.027 5.00e-02 4.00e+02 ... (remaining 7645 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 490 2.66 - 3.22: 43442 3.22 - 3.78: 71762 3.78 - 4.34: 91581 4.34 - 4.90: 149180 Nonbonded interactions: 356455 Sorted by model distance: nonbonded pdb=" O1A ANP B3101 " pdb="MG MG B3102 " model vdw 2.097 2.170 nonbonded pdb=" OD2 ASP B2889 " pdb="MG MG B3102 " model vdw 2.118 2.170 nonbonded pdb=" OD2 ASP A2889 " pdb="MG MG A3102 " model vdw 2.187 2.170 nonbonded pdb=" O VAL A1519 " pdb=" OG1 THR A1523 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR A1753 " pdb=" OD2 ASP A1758 " model vdw 2.234 2.440 ... (remaining 356450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 15.970 Check model and map are aligned: 0.610 Set scattering table: 0.340 Process input model: 118.980 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.002 0.142 44992 Z= 0.149 Angle : 0.504 17.110 60798 Z= 0.241 Chirality : 0.036 0.272 6980 Planarity : 0.003 0.048 7648 Dihedral : 14.092 89.699 16864 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.12), residues: 5426 helix: 1.95 (0.09), residues: 3782 sheet: 0.81 (0.81), residues: 38 loop : 0.00 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 488 HIS 0.005 0.000 HIS B1443 PHE 0.016 0.001 PHE B2143 TYR 0.016 0.001 TYR B2049 ARG 0.003 0.000 ARG A1095 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 921 time to evaluate : 4.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 LEU cc_start: 0.7821 (mt) cc_final: 0.7506 (tp) REVERT: A 1248 TYR cc_start: 0.5469 (m-10) cc_final: 0.4805 (m-80) REVERT: A 1295 LEU cc_start: 0.7390 (mm) cc_final: 0.7114 (mm) REVERT: A 1397 HIS cc_start: 0.6543 (t-90) cc_final: 0.6241 (t70) REVERT: A 1444 LEU cc_start: 0.9271 (tt) cc_final: 0.9071 (mm) REVERT: A 1539 LEU cc_start: 0.8877 (mm) cc_final: 0.8641 (mm) REVERT: A 1572 LYS cc_start: 0.9360 (mtpt) cc_final: 0.9104 (tppt) REVERT: A 1590 LEU cc_start: 0.8171 (tp) cc_final: 0.7957 (tt) REVERT: A 1629 VAL cc_start: 0.8390 (t) cc_final: 0.8081 (m) REVERT: A 1741 LEU cc_start: 0.9396 (mm) cc_final: 0.8990 (mt) REVERT: A 1807 LYS cc_start: 0.9435 (tmmt) cc_final: 0.9017 (mmtm) REVERT: A 1995 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8316 (pt0) REVERT: A 2051 LEU cc_start: 0.7817 (tt) cc_final: 0.7577 (tt) REVERT: A 2154 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7909 (tp30) REVERT: A 2341 CYS cc_start: 0.8275 (t) cc_final: 0.7865 (t) REVERT: A 2370 ASN cc_start: 0.8062 (m-40) cc_final: 0.7726 (m-40) REVERT: A 2399 GLN cc_start: 0.8612 (mt0) cc_final: 0.8313 (mt0) REVERT: A 2448 ASP cc_start: 0.8816 (m-30) cc_final: 0.8505 (m-30) REVERT: A 2506 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7315 (ptp-110) REVERT: A 2667 MET cc_start: 0.7708 (ttp) cc_final: 0.7471 (ptm) REVERT: A 2877 LEU cc_start: 0.8278 (mt) cc_final: 0.8044 (mt) REVERT: A 2888 ILE cc_start: 0.7659 (pt) cc_final: 0.7147 (pt) REVERT: A 3011 MET cc_start: 0.8537 (tmm) cc_final: 0.8150 (tmm) REVERT: B 542 LEU cc_start: 0.9132 (tp) cc_final: 0.8875 (mt) REVERT: B 731 TYR cc_start: 0.7241 (t80) cc_final: 0.6784 (t80) REVERT: B 949 MET cc_start: 0.7485 (mmp) cc_final: 0.6835 (ttp) REVERT: B 1018 PHE cc_start: 0.8534 (t80) cc_final: 0.8184 (t80) REVERT: B 1022 ILE cc_start: 0.9144 (mm) cc_final: 0.8837 (pt) REVERT: B 1064 MET cc_start: 0.4494 (pmm) cc_final: 0.1346 (ttp) REVERT: B 1495 CYS cc_start: 0.9249 (m) cc_final: 0.8824 (t) REVERT: B 1514 GLU cc_start: 0.8224 (pt0) cc_final: 0.7927 (tp30) REVERT: B 1516 HIS cc_start: 0.7966 (p90) cc_final: 0.7732 (p90) REVERT: B 1539 LEU cc_start: 0.8813 (mm) cc_final: 0.8583 (mm) REVERT: B 1590 LEU cc_start: 0.8144 (tp) cc_final: 0.7919 (tt) REVERT: B 1629 VAL cc_start: 0.8449 (t) cc_final: 0.8191 (m) REVERT: B 1813 PHE cc_start: 0.9093 (m-80) cc_final: 0.8579 (m-80) REVERT: B 1836 ASP cc_start: 0.9267 (m-30) cc_final: 0.8900 (p0) REVERT: B 1907 ARG cc_start: 0.7805 (ptp-170) cc_final: 0.7437 (mtt90) REVERT: B 2051 LEU cc_start: 0.7892 (tt) cc_final: 0.7605 (tt) REVERT: B 2107 MET cc_start: 0.9085 (mtp) cc_final: 0.8543 (mtp) REVERT: B 2154 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7932 (tp30) REVERT: B 2334 TYR cc_start: 0.8197 (t80) cc_final: 0.7982 (t80) REVERT: B 2341 CYS cc_start: 0.8277 (t) cc_final: 0.7922 (t) REVERT: B 2399 GLN cc_start: 0.8648 (mt0) cc_final: 0.8377 (mt0) REVERT: B 2448 ASP cc_start: 0.8762 (m-30) cc_final: 0.8462 (m-30) REVERT: B 2847 GLU cc_start: 0.7895 (tt0) cc_final: 0.7612 (tt0) REVERT: B 2877 LEU cc_start: 0.8251 (mt) cc_final: 0.8007 (mt) REVERT: B 3011 MET cc_start: 0.8504 (tmm) cc_final: 0.8098 (tmm) outliers start: 0 outliers final: 0 residues processed: 921 average time/residue: 0.5922 time to fit residues: 902.2277 Evaluate side-chains 536 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 5.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 463 optimal weight: 3.9990 chunk 416 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 222 optimal weight: 0.8980 chunk 430 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 320 optimal weight: 6.9990 chunk 498 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1098 GLN A1149 ASN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1443 HIS ** A1516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1537 GLN A2070 ASN A2101 GLN A2206 GLN A2433 GLN A2542 ASN A2565 ASN ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 GLN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1258 HIS B1478 GLN B1537 GLN ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2070 ASN B2101 GLN B2206 GLN B2494 ASN B2542 ASN ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 44992 Z= 0.172 Angle : 0.550 12.081 60798 Z= 0.267 Chirality : 0.038 0.285 6980 Planarity : 0.004 0.053 7648 Dihedral : 5.005 81.201 5968 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.45 % Allowed : 8.30 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.12), residues: 5426 helix: 1.87 (0.09), residues: 3782 sheet: 0.97 (0.66), residues: 58 loop : -0.01 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1461 HIS 0.008 0.001 HIS A 291 PHE 0.020 0.001 PHE B1236 TYR 0.022 0.001 TYR A 731 ARG 0.007 0.000 ARG A2598 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 536 time to evaluate : 4.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 MET cc_start: 0.8285 (mmt) cc_final: 0.7814 (mmm) REVERT: A 624 MET cc_start: 0.6371 (mmm) cc_final: 0.5834 (mmm) REVERT: A 660 MET cc_start: 0.6115 (mmp) cc_final: 0.5602 (mmp) REVERT: A 732 MET cc_start: 0.4937 (tpp) cc_final: 0.1771 (ptt) REVERT: A 1087 MET cc_start: 0.8032 (mmm) cc_final: 0.7550 (mmp) REVERT: A 1295 LEU cc_start: 0.7304 (mm) cc_final: 0.7036 (mm) REVERT: A 1539 LEU cc_start: 0.9040 (mm) cc_final: 0.8805 (mm) REVERT: A 1556 TYR cc_start: 0.7835 (m-80) cc_final: 0.7514 (m-80) REVERT: A 1572 LYS cc_start: 0.9375 (mtpt) cc_final: 0.9088 (tppt) REVERT: A 1741 LEU cc_start: 0.9325 (mm) cc_final: 0.9043 (mt) REVERT: A 1807 LYS cc_start: 0.9446 (tmmt) cc_final: 0.9071 (mmtm) REVERT: A 1813 PHE cc_start: 0.9118 (m-80) cc_final: 0.8575 (m-80) REVERT: A 1995 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8296 (tm-30) REVERT: A 2294 GLU cc_start: 0.8376 (tp30) cc_final: 0.8109 (tp30) REVERT: A 2448 ASP cc_start: 0.8891 (m-30) cc_final: 0.8674 (m-30) REVERT: A 2506 ARG cc_start: 0.7865 (ttm110) cc_final: 0.7295 (ptp-110) REVERT: A 3011 MET cc_start: 0.8621 (tmm) cc_final: 0.8216 (tmm) REVERT: B 96 GLU cc_start: 0.4780 (OUTLIER) cc_final: 0.4436 (mt-10) REVERT: B 542 LEU cc_start: 0.9110 (tp) cc_final: 0.8849 (mt) REVERT: B 617 MET cc_start: 0.8414 (tpp) cc_final: 0.8145 (tpp) REVERT: B 626 PHE cc_start: 0.7708 (t80) cc_final: 0.7481 (t80) REVERT: B 731 TYR cc_start: 0.7193 (t80) cc_final: 0.6599 (t80) REVERT: B 732 MET cc_start: 0.8077 (mmp) cc_final: 0.7473 (tpp) REVERT: B 949 MET cc_start: 0.7481 (mmp) cc_final: 0.6779 (ttp) REVERT: B 1018 PHE cc_start: 0.8473 (t80) cc_final: 0.8087 (t80) REVERT: B 1022 ILE cc_start: 0.9116 (mm) cc_final: 0.8802 (pt) REVERT: B 1064 MET cc_start: 0.4465 (pmm) cc_final: 0.1636 (mmm) REVERT: B 1199 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8324 (mm-30) REVERT: B 1210 MET cc_start: 0.8907 (mmp) cc_final: 0.8677 (mmp) REVERT: B 1454 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8352 (tptp) REVERT: B 1495 CYS cc_start: 0.9289 (m) cc_final: 0.8956 (t) REVERT: B 1514 GLU cc_start: 0.8312 (pt0) cc_final: 0.8063 (tp30) REVERT: B 1539 LEU cc_start: 0.8963 (mm) cc_final: 0.8642 (mm) REVERT: B 1556 TYR cc_start: 0.8570 (t80) cc_final: 0.7999 (m-80) REVERT: B 1907 ARG cc_start: 0.8022 (ptp-170) cc_final: 0.7662 (mtt90) REVERT: B 1995 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8302 (tm-30) REVERT: B 2156 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 2282 ASN cc_start: 0.8386 (m-40) cc_final: 0.7971 (m-40) REVERT: B 2384 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8112 (mtt) REVERT: B 2395 ASP cc_start: 0.8088 (t0) cc_final: 0.7420 (t0) REVERT: B 2411 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7911 (pp20) REVERT: B 2448 ASP cc_start: 0.8834 (m-30) cc_final: 0.8592 (m-30) REVERT: B 2962 MET cc_start: 0.6274 (ptp) cc_final: 0.5979 (mmm) REVERT: B 3011 MET cc_start: 0.8595 (tmm) cc_final: 0.8173 (tmm) outliers start: 71 outliers final: 41 residues processed: 583 average time/residue: 0.5148 time to fit residues: 514.7997 Evaluate side-chains 495 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 450 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1336 PHE Chi-restraints excluded: chain A residue 1443 HIS Chi-restraints excluded: chain A residue 1681 ILE Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 2016 ASP Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2214 ASP Chi-restraints excluded: chain A residue 2261 LEU Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2556 THR Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1199 GLU Chi-restraints excluded: chain B residue 1238 LEU Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1681 ILE Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1764 LEU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1794 LEU Chi-restraints excluded: chain B residue 1814 LEU Chi-restraints excluded: chain B residue 2016 ASP Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2261 LEU Chi-restraints excluded: chain B residue 2293 LEU Chi-restraints excluded: chain B residue 2384 MET Chi-restraints excluded: chain B residue 2411 GLU Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2556 THR Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2636 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 277 optimal weight: 40.0000 chunk 154 optimal weight: 6.9990 chunk 414 optimal weight: 0.5980 chunk 339 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 499 optimal weight: 5.9990 chunk 539 optimal weight: 2.9990 chunk 444 optimal weight: 5.9990 chunk 495 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 400 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1690 HIS A1839 GLN A2197 GLN ** A2208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2788 HIS ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 GLN B 996 HIS ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 GLN ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 ASN ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1225 GLN ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1334 HIS B1431 ASN ** B1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1535 GLN B1839 GLN ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2542 ASN B2565 ASN ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2788 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 44992 Z= 0.307 Angle : 0.635 11.536 60798 Z= 0.319 Chirality : 0.041 0.316 6980 Planarity : 0.004 0.061 7648 Dihedral : 4.609 74.335 5968 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 2.08 % Allowed : 10.61 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.12), residues: 5426 helix: 1.52 (0.09), residues: 3796 sheet: 0.75 (0.66), residues: 58 loop : -0.12 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 488 HIS 0.039 0.002 HIS A1443 PHE 0.020 0.002 PHE A1952 TYR 0.020 0.002 TYR B1470 ARG 0.005 0.001 ARG B1730 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 448 time to evaluate : 4.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 TYR cc_start: 0.5468 (m-80) cc_final: 0.5247 (m-80) REVERT: A 615 LEU cc_start: 0.7714 (mt) cc_final: 0.7507 (tp) REVERT: A 624 MET cc_start: 0.7226 (mmm) cc_final: 0.6852 (mmm) REVERT: A 660 MET cc_start: 0.5978 (mmp) cc_final: 0.5502 (mmp) REVERT: A 1295 LEU cc_start: 0.7361 (mm) cc_final: 0.6958 (mm) REVERT: A 1539 LEU cc_start: 0.9102 (mm) cc_final: 0.8710 (mm) REVERT: A 1556 TYR cc_start: 0.7898 (m-80) cc_final: 0.7571 (m-80) REVERT: A 1572 LYS cc_start: 0.9447 (mtpt) cc_final: 0.9144 (tppt) REVERT: A 1813 PHE cc_start: 0.9155 (m-80) cc_final: 0.8598 (m-80) REVERT: A 1836 ASP cc_start: 0.9218 (m-30) cc_final: 0.8794 (p0) REVERT: A 1935 ASP cc_start: 0.9072 (t0) cc_final: 0.8859 (t70) REVERT: A 2097 GLU cc_start: 0.8802 (pt0) cc_final: 0.8573 (pt0) REVERT: A 2156 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 96 GLU cc_start: 0.4578 (OUTLIER) cc_final: 0.4220 (mt-10) REVERT: B 348 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5764 (mt) REVERT: B 511 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6140 (pt) REVERT: B 617 MET cc_start: 0.8472 (tpp) cc_final: 0.8180 (tpp) REVERT: B 949 MET cc_start: 0.7431 (mmp) cc_final: 0.6692 (ttp) REVERT: B 1018 PHE cc_start: 0.8552 (t80) cc_final: 0.8166 (t80) REVERT: B 1022 ILE cc_start: 0.9163 (mm) cc_final: 0.8866 (pt) REVERT: B 1322 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6185 (mm) REVERT: B 1454 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8284 (tptp) REVERT: B 1495 CYS cc_start: 0.9344 (m) cc_final: 0.8883 (t) REVERT: B 1539 LEU cc_start: 0.9080 (mm) cc_final: 0.8805 (mm) REVERT: B 1633 ARG cc_start: 0.8616 (ttp-110) cc_final: 0.8290 (ttp-110) REVERT: B 1935 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8393 (m-30) REVERT: B 2097 GLU cc_start: 0.8788 (pt0) cc_final: 0.8572 (pt0) REVERT: B 2156 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7999 (tm-30) REVERT: B 2239 MET cc_start: 0.6428 (ppp) cc_final: 0.6225 (ppp) REVERT: B 2384 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8409 (mtp) REVERT: B 2404 TYR cc_start: 0.8826 (t80) cc_final: 0.8530 (t80) REVERT: B 2962 MET cc_start: 0.6352 (ptp) cc_final: 0.6064 (mmm) outliers start: 102 outliers final: 60 residues processed: 519 average time/residue: 0.5146 time to fit residues: 460.3151 Evaluate side-chains 435 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 369 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1446 VAL Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1626 ASP Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1710 TRP Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1826 LEU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 2489 SER Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2751 THR Chi-restraints excluded: chain A residue 2783 ASN Chi-restraints excluded: chain A residue 2860 SER Chi-restraints excluded: chain A residue 2873 VAL Chi-restraints excluded: chain A residue 2886 VAL Chi-restraints excluded: chain A residue 2936 GLU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1238 LEU Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1452 ASP Chi-restraints excluded: chain B residue 1517 LEU Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1576 ILE Chi-restraints excluded: chain B residue 1626 ASP Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1756 THR Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1794 LEU Chi-restraints excluded: chain B residue 1814 LEU Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2384 MET Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2489 SER Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2556 THR Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2783 ASN Chi-restraints excluded: chain B residue 2860 SER Chi-restraints excluded: chain B residue 2873 VAL Chi-restraints excluded: chain B residue 2936 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 493 optimal weight: 3.9990 chunk 375 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 335 optimal weight: 50.0000 chunk 501 optimal weight: 0.8980 chunk 530 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 475 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 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 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 ASN A1839 GLN ** A2208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2565 ASN ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2809 GLN B 201 GLN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2565 ASN ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2809 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44992 Z= 0.164 Angle : 0.552 11.338 60798 Z= 0.265 Chirality : 0.037 0.278 6980 Planarity : 0.004 0.057 7648 Dihedral : 4.413 78.328 5968 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.65 % Allowed : 12.36 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.12), residues: 5426 helix: 1.76 (0.09), residues: 3790 sheet: 0.25 (0.64), residues: 62 loop : -0.06 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B1221 HIS 0.010 0.001 HIS A1443 PHE 0.017 0.001 PHE B1247 TYR 0.016 0.001 TYR B2371 ARG 0.006 0.000 ARG A1205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 421 time to evaluate : 5.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 MET cc_start: 0.7341 (mmm) cc_final: 0.6945 (mmm) REVERT: A 660 MET cc_start: 0.5805 (mmp) cc_final: 0.5400 (mmp) REVERT: A 1295 LEU cc_start: 0.7383 (mm) cc_final: 0.7098 (mm) REVERT: A 1308 MET cc_start: 0.4920 (ppp) cc_final: 0.4691 (ppp) REVERT: A 1539 LEU cc_start: 0.9017 (mm) cc_final: 0.8724 (mm) REVERT: A 1556 TYR cc_start: 0.7949 (m-80) cc_final: 0.7573 (m-80) REVERT: A 1572 LYS cc_start: 0.9444 (mtpt) cc_final: 0.9119 (tppt) REVERT: A 1767 PHE cc_start: 0.7771 (m-80) cc_final: 0.7442 (m-80) REVERT: A 1813 PHE cc_start: 0.9098 (m-80) cc_final: 0.8528 (m-80) REVERT: A 1836 ASP cc_start: 0.9194 (m-30) cc_final: 0.8830 (p0) REVERT: A 1906 GLN cc_start: 0.8920 (mp10) cc_final: 0.8627 (mp10) REVERT: A 1916 MET cc_start: 0.9276 (mmm) cc_final: 0.8894 (mmm) REVERT: A 1935 ASP cc_start: 0.9083 (t0) cc_final: 0.8819 (t70) REVERT: A 2156 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 2294 GLU cc_start: 0.8562 (tp30) cc_final: 0.8108 (tp30) REVERT: A 2503 MET cc_start: 0.8836 (tmm) cc_final: 0.8194 (ttp) REVERT: A 2506 ARG cc_start: 0.8433 (ttm110) cc_final: 0.8182 (ptp-110) REVERT: A 2520 MET cc_start: 0.8836 (tpp) cc_final: 0.8596 (tpp) REVERT: A 2667 MET cc_start: 0.8468 (ptt) cc_final: 0.8149 (ptt) REVERT: B 96 GLU cc_start: 0.4589 (OUTLIER) cc_final: 0.4237 (mt-10) REVERT: B 732 MET cc_start: 0.7670 (mmp) cc_final: 0.7460 (tpp) REVERT: B 806 LEU cc_start: 0.6083 (mm) cc_final: 0.5493 (mt) REVERT: B 949 MET cc_start: 0.7394 (mmp) cc_final: 0.6625 (ttp) REVERT: B 1018 PHE cc_start: 0.8525 (t80) cc_final: 0.8147 (t80) REVERT: B 1022 ILE cc_start: 0.9167 (mm) cc_final: 0.8854 (pt) REVERT: B 1064 MET cc_start: 0.4245 (pmm) cc_final: 0.4013 (pmm) REVERT: B 1454 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8283 (tptp) REVERT: B 1475 TYR cc_start: 0.8912 (m-80) cc_final: 0.8467 (m-80) REVERT: B 1539 LEU cc_start: 0.9110 (mm) cc_final: 0.8830 (mm) REVERT: B 1755 MET cc_start: 0.9177 (mpp) cc_final: 0.8910 (pmm) REVERT: B 1907 ARG cc_start: 0.8522 (ptp-170) cc_final: 0.8236 (mtt90) REVERT: B 1916 MET cc_start: 0.9259 (mmm) cc_final: 0.8879 (mmm) REVERT: B 1935 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8375 (m-30) REVERT: B 2156 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 2404 TYR cc_start: 0.8755 (t80) cc_final: 0.8551 (t80) REVERT: B 2503 MET cc_start: 0.8693 (tmm) cc_final: 0.8249 (ttp) outliers start: 81 outliers final: 52 residues processed: 470 average time/residue: 0.5034 time to fit residues: 411.8951 Evaluate side-chains 443 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 389 time to evaluate : 5.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1213 HIS Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1336 PHE Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1710 TRP Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 2098 LEU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2341 CYS Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2751 THR Chi-restraints excluded: chain A residue 3011 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1517 LEU Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1576 ILE Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1681 ILE Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1764 LEU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1794 LEU Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2098 LEU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2293 LEU Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2341 CYS Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2751 THR Chi-restraints excluded: chain B residue 3011 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 441 optimal weight: 0.9990 chunk 301 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 395 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 452 optimal weight: 0.0670 chunk 366 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 270 optimal weight: 4.9990 chunk 476 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 overall best weight: 2.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN A1230 ASN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2632 ASN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1690 HIS ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 44992 Z= 0.256 Angle : 0.607 12.708 60798 Z= 0.297 Chirality : 0.039 0.214 6980 Planarity : 0.004 0.064 7648 Dihedral : 4.520 76.768 5968 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.06 % Allowed : 13.20 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.12), residues: 5426 helix: 1.60 (0.09), residues: 3798 sheet: 0.61 (0.60), residues: 62 loop : -0.15 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1221 HIS 0.008 0.001 HIS A 291 PHE 0.022 0.002 PHE A 657 TYR 0.035 0.002 TYR A 731 ARG 0.007 0.001 ARG A1619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 417 time to evaluate : 4.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 MET cc_start: 0.7555 (mmm) cc_final: 0.7084 (mmm) REVERT: A 732 MET cc_start: 0.5105 (tpp) cc_final: 0.4686 (mmp) REVERT: A 1221 TRP cc_start: 0.2368 (t-100) cc_final: 0.1991 (t-100) REVERT: A 1295 LEU cc_start: 0.7367 (mm) cc_final: 0.7071 (mm) REVERT: A 1539 LEU cc_start: 0.9058 (mm) cc_final: 0.8786 (mm) REVERT: A 1556 TYR cc_start: 0.8066 (m-80) cc_final: 0.7656 (m-80) REVERT: A 1813 PHE cc_start: 0.9152 (m-80) cc_final: 0.8532 (m-80) REVERT: A 1916 MET cc_start: 0.9360 (mmm) cc_final: 0.9141 (mmm) REVERT: A 2156 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 2292 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8558 (mt0) REVERT: A 2293 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8963 (tp) REVERT: A 2294 GLU cc_start: 0.8832 (tp30) cc_final: 0.8451 (tp30) REVERT: A 2939 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8482 (mtt180) REVERT: A 3008 ARG cc_start: 0.9018 (ttt-90) cc_final: 0.8663 (ttm-80) REVERT: B 96 GLU cc_start: 0.4601 (OUTLIER) cc_final: 0.4252 (mt-10) REVERT: B 949 MET cc_start: 0.7351 (mmp) cc_final: 0.6584 (ttp) REVERT: B 1018 PHE cc_start: 0.8536 (t80) cc_final: 0.8244 (t80) REVERT: B 1454 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8209 (tptp) REVERT: B 1539 LEU cc_start: 0.9208 (mm) cc_final: 0.8959 (mm) REVERT: B 1755 MET cc_start: 0.9236 (mpp) cc_final: 0.8941 (pmm) REVERT: B 1916 MET cc_start: 0.9348 (mmm) cc_final: 0.9134 (mmm) REVERT: B 1935 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8378 (m-30) REVERT: B 2156 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8081 (tm-30) REVERT: B 2294 GLU cc_start: 0.8528 (tp30) cc_final: 0.8319 (tp30) REVERT: B 2448 ASP cc_start: 0.9057 (m-30) cc_final: 0.8276 (m-30) REVERT: B 2939 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8542 (mtt180) REVERT: B 2962 MET cc_start: 0.6520 (ptp) cc_final: 0.6183 (mmm) outliers start: 101 outliers final: 63 residues processed: 495 average time/residue: 0.5176 time to fit residues: 444.8835 Evaluate side-chains 436 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 367 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1213 HIS Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1471 THR Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1626 ASP Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1681 ILE Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1807 LYS Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 2092 CYS Chi-restraints excluded: chain A residue 2098 LEU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2292 GLN Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2341 CYS Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2751 THR Chi-restraints excluded: chain A residue 2860 SER Chi-restraints excluded: chain A residue 2886 VAL Chi-restraints excluded: chain A residue 2936 GLU Chi-restraints excluded: chain A residue 2939 ARG Chi-restraints excluded: chain A residue 3010 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1517 LEU Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1576 ILE Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1628 MET Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1681 ILE Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1794 LEU Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2092 CYS Chi-restraints excluded: chain B residue 2098 LEU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2341 CYS Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2751 THR Chi-restraints excluded: chain B residue 2860 SER Chi-restraints excluded: chain B residue 2936 GLU Chi-restraints excluded: chain B residue 2939 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 178 optimal weight: 0.9980 chunk 477 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 531 optimal weight: 2.9990 chunk 440 optimal weight: 1.9990 chunk 245 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 278 optimal weight: 30.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 ASN ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44992 Z= 0.196 Angle : 0.576 13.169 60798 Z= 0.277 Chirality : 0.038 0.285 6980 Planarity : 0.004 0.048 7648 Dihedral : 4.425 78.954 5968 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.98 % Allowed : 14.63 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.12), residues: 5426 helix: 1.66 (0.09), residues: 3794 sheet: 0.17 (0.60), residues: 66 loop : -0.11 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2104 HIS 0.008 0.001 HIS B1443 PHE 0.023 0.001 PHE B 626 TYR 0.020 0.001 TYR A 313 ARG 0.007 0.000 ARG B1618 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 393 time to evaluate : 4.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 MET cc_start: 0.7716 (mmm) cc_final: 0.7266 (mmm) REVERT: A 660 MET cc_start: 0.6069 (mmp) cc_final: 0.5682 (mmp) REVERT: A 1221 TRP cc_start: 0.2396 (t-100) cc_final: 0.2062 (t-100) REVERT: A 1295 LEU cc_start: 0.7368 (mm) cc_final: 0.7060 (mm) REVERT: A 1308 MET cc_start: 0.4914 (ppp) cc_final: 0.4666 (ppp) REVERT: A 1539 LEU cc_start: 0.9085 (mm) cc_final: 0.8823 (mm) REVERT: A 1556 TYR cc_start: 0.8097 (m-80) cc_final: 0.7658 (m-80) REVERT: A 1755 MET cc_start: 0.9184 (mpp) cc_final: 0.8954 (pmm) REVERT: A 1767 PHE cc_start: 0.7882 (m-80) cc_final: 0.7476 (m-80) REVERT: A 1813 PHE cc_start: 0.9099 (m-80) cc_final: 0.8472 (m-80) REVERT: A 1906 GLN cc_start: 0.9095 (mp10) cc_final: 0.8750 (mp10) REVERT: A 1916 MET cc_start: 0.9320 (mmm) cc_final: 0.9095 (mmm) REVERT: A 2026 MET cc_start: 0.8298 (ttm) cc_final: 0.8082 (ttm) REVERT: A 2156 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8192 (tm-30) REVERT: A 2293 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9029 (tp) REVERT: A 2294 GLU cc_start: 0.8741 (tp30) cc_final: 0.8337 (tp30) REVERT: A 2667 MET cc_start: 0.8730 (ptt) cc_final: 0.8420 (ptt) REVERT: A 3008 ARG cc_start: 0.8975 (ttt-90) cc_final: 0.8626 (ttm-80) REVERT: B 96 GLU cc_start: 0.4571 (OUTLIER) cc_final: 0.4204 (mt-10) REVERT: B 949 MET cc_start: 0.7337 (mmp) cc_final: 0.6575 (ttp) REVERT: B 1018 PHE cc_start: 0.8548 (t80) cc_final: 0.8340 (t80) REVERT: B 1094 ASN cc_start: 0.9209 (p0) cc_final: 0.8830 (p0) REVERT: B 1454 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8216 (tptp) REVERT: B 1475 TYR cc_start: 0.8919 (m-80) cc_final: 0.8433 (m-80) REVERT: B 1539 LEU cc_start: 0.9209 (mm) cc_final: 0.8969 (mm) REVERT: B 1714 MET cc_start: 0.8811 (mmm) cc_final: 0.8605 (mmm) REVERT: B 1755 MET cc_start: 0.9176 (mpp) cc_final: 0.8894 (pmm) REVERT: B 1916 MET cc_start: 0.9310 (mmm) cc_final: 0.9064 (mmm) REVERT: B 1935 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8397 (m-30) REVERT: B 2156 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 2448 ASP cc_start: 0.8983 (m-30) cc_final: 0.8131 (m-30) REVERT: B 2962 MET cc_start: 0.6531 (ptp) cc_final: 0.6247 (mmm) outliers start: 97 outliers final: 68 residues processed: 464 average time/residue: 0.5225 time to fit residues: 422.1862 Evaluate side-chains 446 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 375 time to evaluate : 4.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1213 HIS Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1470 TYR Chi-restraints excluded: chain A residue 1471 THR Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1710 TRP Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1807 LYS Chi-restraints excluded: chain A residue 2084 LEU Chi-restraints excluded: chain A residue 2092 CYS Chi-restraints excluded: chain A residue 2098 LEU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2214 ASP Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2341 CYS Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2751 THR Chi-restraints excluded: chain A residue 2860 SER Chi-restraints excluded: chain A residue 2886 VAL Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 963 MET Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1238 LEU Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1517 LEU Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1576 ILE Chi-restraints excluded: chain B residue 1628 MET Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1681 ILE Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1764 LEU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1794 LEU Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 CYS Chi-restraints excluded: chain B residue 2098 LEU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2341 CYS Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2545 ILE Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2860 SER Chi-restraints excluded: chain B residue 2924 GLU Chi-restraints excluded: chain B residue 2936 GLU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 512 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 302 optimal weight: 6.9990 chunk 387 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 chunk 447 optimal weight: 0.8980 chunk 296 optimal weight: 7.9990 chunk 529 optimal weight: 1.9990 chunk 331 optimal weight: 9.9990 chunk 322 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2542 ASN ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2632 ASN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44992 Z= 0.222 Angle : 0.591 15.685 60798 Z= 0.285 Chirality : 0.038 0.243 6980 Planarity : 0.004 0.067 7648 Dihedral : 4.387 77.851 5968 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.94 % Allowed : 15.46 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.12), residues: 5426 helix: 1.64 (0.09), residues: 3798 sheet: 0.13 (0.59), residues: 66 loop : -0.17 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2104 HIS 0.007 0.001 HIS B1443 PHE 0.027 0.001 PHE B 626 TYR 0.017 0.001 TYR A 313 ARG 0.006 0.000 ARG B1633 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 381 time to evaluate : 4.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 MET cc_start: 0.7823 (mmm) cc_final: 0.7403 (mmm) REVERT: A 660 MET cc_start: 0.5907 (mmp) cc_final: 0.5601 (mmp) REVERT: A 732 MET cc_start: 0.3687 (mmp) cc_final: 0.3220 (tpp) REVERT: A 1221 TRP cc_start: 0.2285 (t-100) cc_final: 0.1940 (t-100) REVERT: A 1295 LEU cc_start: 0.7425 (mm) cc_final: 0.7127 (mm) REVERT: A 1410 LYS cc_start: 0.8892 (mmtp) cc_final: 0.8617 (mttt) REVERT: A 1477 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.8004 (p0) REVERT: A 1539 LEU cc_start: 0.9100 (mm) cc_final: 0.8847 (mm) REVERT: A 1813 PHE cc_start: 0.9098 (m-80) cc_final: 0.8452 (m-80) REVERT: A 1916 MET cc_start: 0.9320 (mmm) cc_final: 0.9045 (mmm) REVERT: A 2156 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8178 (tm-30) REVERT: A 2532 MET cc_start: 0.5751 (mtt) cc_final: 0.5224 (ppp) REVERT: A 2667 MET cc_start: 0.8783 (ptt) cc_final: 0.8487 (ptt) REVERT: A 2939 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8443 (mtt180) REVERT: A 3008 ARG cc_start: 0.8973 (ttt-90) cc_final: 0.8649 (ttm-80) REVERT: B 96 GLU cc_start: 0.4581 (OUTLIER) cc_final: 0.4213 (mt-10) REVERT: B 949 MET cc_start: 0.7378 (mmp) cc_final: 0.6612 (ttp) REVERT: B 1094 ASN cc_start: 0.9230 (p0) cc_final: 0.8872 (p0) REVERT: B 1454 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8225 (tptp) REVERT: B 1539 LEU cc_start: 0.9241 (mm) cc_final: 0.9013 (mm) REVERT: B 1755 MET cc_start: 0.9149 (mpp) cc_final: 0.8928 (pmm) REVERT: B 1827 LEU cc_start: 0.9449 (mt) cc_final: 0.9243 (mt) REVERT: B 1916 MET cc_start: 0.9307 (mmm) cc_final: 0.9012 (mmm) REVERT: B 1935 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: B 2156 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 2448 ASP cc_start: 0.9014 (m-30) cc_final: 0.8162 (m-30) REVERT: B 2939 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8412 (mtt180) REVERT: B 2962 MET cc_start: 0.6621 (ptp) cc_final: 0.6400 (mmm) outliers start: 95 outliers final: 67 residues processed: 453 average time/residue: 0.5202 time to fit residues: 407.4257 Evaluate side-chains 431 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 359 time to evaluate : 4.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1213 HIS Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1470 TYR Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1807 LYS Chi-restraints excluded: chain A residue 2084 LEU Chi-restraints excluded: chain A residue 2092 CYS Chi-restraints excluded: chain A residue 2098 LEU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2341 CYS Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 2545 ILE Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2751 THR Chi-restraints excluded: chain A residue 2860 SER Chi-restraints excluded: chain A residue 2886 VAL Chi-restraints excluded: chain A residue 2936 GLU Chi-restraints excluded: chain A residue 2939 ARG Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 963 MET Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1238 LEU Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1517 LEU Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1626 ASP Chi-restraints excluded: chain B residue 1628 MET Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1681 ILE Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1794 LEU Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 CYS Chi-restraints excluded: chain B residue 2098 LEU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2341 CYS Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2545 ILE Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2860 SER Chi-restraints excluded: chain B residue 2924 GLU Chi-restraints excluded: chain B residue 2936 GLU Chi-restraints excluded: chain B residue 2939 ARG Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 327 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 316 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 336 optimal weight: 8.9990 chunk 360 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 415 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 GLN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1474 HIS A1839 GLN ** A2208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 GLN ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 44992 Z= 0.251 Angle : 0.616 14.176 60798 Z= 0.296 Chirality : 0.038 0.237 6980 Planarity : 0.004 0.066 7648 Dihedral : 4.409 76.736 5968 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.73 % Allowed : 16.08 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.12), residues: 5426 helix: 1.58 (0.09), residues: 3802 sheet: 0.14 (0.58), residues: 66 loop : -0.20 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B1710 HIS 0.008 0.001 HIS B1443 PHE 0.029 0.001 PHE B 626 TYR 0.026 0.001 TYR A 313 ARG 0.012 0.000 ARG A1633 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 380 time to evaluate : 5.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1221 TRP cc_start: 0.2294 (t-100) cc_final: 0.1962 (t-100) REVERT: A 1295 LEU cc_start: 0.7443 (mm) cc_final: 0.7133 (mm) REVERT: A 1308 MET cc_start: 0.4853 (ppp) cc_final: 0.4607 (ppp) REVERT: A 1397 HIS cc_start: 0.6159 (t70) cc_final: 0.5693 (t70) REVERT: A 1410 LYS cc_start: 0.8912 (mmtp) cc_final: 0.8646 (mttt) REVERT: A 1477 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7935 (p0) REVERT: A 1539 LEU cc_start: 0.9110 (mm) cc_final: 0.8872 (mm) REVERT: A 1565 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: A 1813 PHE cc_start: 0.9140 (m-80) cc_final: 0.8933 (m-80) REVERT: A 1916 MET cc_start: 0.9332 (mmm) cc_final: 0.9046 (mmm) REVERT: A 2156 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 2294 GLU cc_start: 0.8643 (tp30) cc_final: 0.8292 (tp30) REVERT: A 2532 MET cc_start: 0.5945 (mtt) cc_final: 0.5414 (ppp) REVERT: A 2616 MET cc_start: 0.8844 (tpp) cc_final: 0.8585 (tpp) REVERT: A 2667 MET cc_start: 0.8790 (ptt) cc_final: 0.8566 (ptt) REVERT: A 2821 MET cc_start: 0.9238 (mmm) cc_final: 0.9030 (mmm) REVERT: A 2939 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8462 (mtt180) REVERT: A 3008 ARG cc_start: 0.8987 (ttt-90) cc_final: 0.8690 (ttm-80) REVERT: B 96 GLU cc_start: 0.4512 (OUTLIER) cc_final: 0.4123 (mt-10) REVERT: B 542 LEU cc_start: 0.8963 (tt) cc_final: 0.8706 (pp) REVERT: B 617 MET cc_start: 0.8557 (tpp) cc_final: 0.8351 (tpp) REVERT: B 949 MET cc_start: 0.7368 (mmp) cc_final: 0.6608 (ttp) REVERT: B 1094 ASN cc_start: 0.9247 (p0) cc_final: 0.8899 (p0) REVERT: B 1454 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8218 (tptp) REVERT: B 1475 TYR cc_start: 0.8910 (m-80) cc_final: 0.8377 (m-10) REVERT: B 1539 LEU cc_start: 0.9261 (mm) cc_final: 0.9042 (mm) REVERT: B 1827 LEU cc_start: 0.9468 (mt) cc_final: 0.9216 (mt) REVERT: B 1916 MET cc_start: 0.9327 (mmm) cc_final: 0.9002 (mmm) REVERT: B 1935 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: B 2026 MET cc_start: 0.8314 (ttm) cc_final: 0.8111 (ttm) REVERT: B 2156 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 2158 MET cc_start: 0.9231 (ttm) cc_final: 0.9014 (ttt) REVERT: B 2448 ASP cc_start: 0.9040 (m-30) cc_final: 0.8392 (m-30) REVERT: B 2821 MET cc_start: 0.9269 (mmm) cc_final: 0.9055 (mmm) REVERT: B 2939 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8433 (mtt180) REVERT: B 2962 MET cc_start: 0.6690 (ptp) cc_final: 0.6443 (mmm) outliers start: 85 outliers final: 72 residues processed: 445 average time/residue: 0.5106 time to fit residues: 394.3460 Evaluate side-chains 441 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 363 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1213 HIS Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1667 VAL Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1807 LYS Chi-restraints excluded: chain A residue 2084 LEU Chi-restraints excluded: chain A residue 2092 CYS Chi-restraints excluded: chain A residue 2098 LEU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2341 CYS Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 2545 ILE Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2751 THR Chi-restraints excluded: chain A residue 2773 THR Chi-restraints excluded: chain A residue 2860 SER Chi-restraints excluded: chain A residue 2886 VAL Chi-restraints excluded: chain A residue 2936 GLU Chi-restraints excluded: chain A residue 2939 ARG Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 963 MET Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1238 LEU Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1517 LEU Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1626 ASP Chi-restraints excluded: chain B residue 1628 MET Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1794 LEU Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 CYS Chi-restraints excluded: chain B residue 2098 LEU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2341 CYS Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2362 GLU Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2492 LEU Chi-restraints excluded: chain B residue 2545 ILE Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2751 THR Chi-restraints excluded: chain B residue 2773 THR Chi-restraints excluded: chain B residue 2860 SER Chi-restraints excluded: chain B residue 2936 GLU Chi-restraints excluded: chain B residue 2939 ARG Chi-restraints excluded: chain B residue 3011 MET Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 481 optimal weight: 0.7980 chunk 506 optimal weight: 5.9990 chunk 462 optimal weight: 0.9980 chunk 493 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 387 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 445 optimal weight: 0.9990 chunk 466 optimal weight: 0.9980 chunk 491 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 ASN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1839 GLN ** A2208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3038 GLN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 44992 Z= 0.158 Angle : 0.598 15.564 60798 Z= 0.282 Chirality : 0.037 0.267 6980 Planarity : 0.004 0.081 7648 Dihedral : 4.281 75.787 5968 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.47 % Allowed : 16.54 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.12), residues: 5426 helix: 1.69 (0.09), residues: 3790 sheet: 0.20 (0.59), residues: 66 loop : -0.17 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B1710 HIS 0.008 0.001 HIS B1443 PHE 0.029 0.001 PHE B 626 TYR 0.025 0.001 TYR A 313 ARG 0.012 0.000 ARG B1633 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 386 time to evaluate : 5.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1221 TRP cc_start: 0.2304 (t-100) cc_final: 0.1945 (t-100) REVERT: A 1295 LEU cc_start: 0.7522 (mm) cc_final: 0.7221 (mm) REVERT: A 1349 MET cc_start: 0.8295 (ppp) cc_final: 0.8062 (ppp) REVERT: A 1410 LYS cc_start: 0.8899 (mmtp) cc_final: 0.8634 (mttt) REVERT: A 1477 ASN cc_start: 0.8139 (m110) cc_final: 0.7860 (p0) REVERT: A 1539 LEU cc_start: 0.9119 (mm) cc_final: 0.8883 (mm) REVERT: A 1565 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: A 1767 PHE cc_start: 0.7889 (m-80) cc_final: 0.7430 (m-80) REVERT: A 1916 MET cc_start: 0.9259 (mmm) cc_final: 0.8998 (mmm) REVERT: A 2156 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 2294 GLU cc_start: 0.8614 (tp30) cc_final: 0.8261 (tp30) REVERT: A 2532 MET cc_start: 0.5908 (mtt) cc_final: 0.5410 (ppp) REVERT: A 2667 MET cc_start: 0.8762 (ptt) cc_final: 0.8550 (ptt) REVERT: A 3008 ARG cc_start: 0.8940 (ttt-90) cc_final: 0.8641 (ttm-80) REVERT: B 96 GLU cc_start: 0.4430 (OUTLIER) cc_final: 0.4045 (mt-10) REVERT: B 542 LEU cc_start: 0.8957 (tt) cc_final: 0.8707 (pp) REVERT: B 949 MET cc_start: 0.7359 (mmp) cc_final: 0.6606 (ttp) REVERT: B 1094 ASN cc_start: 0.9214 (p0) cc_final: 0.8848 (p0) REVERT: B 1210 MET cc_start: 0.8748 (mmp) cc_final: 0.7670 (ptp) REVERT: B 1443 HIS cc_start: 0.9266 (t-90) cc_final: 0.8875 (t70) REVERT: B 1454 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8252 (tptp) REVERT: B 1475 TYR cc_start: 0.8871 (m-80) cc_final: 0.8349 (m-10) REVERT: B 1539 LEU cc_start: 0.9254 (mm) cc_final: 0.9036 (mm) REVERT: B 1827 LEU cc_start: 0.9400 (mt) cc_final: 0.9164 (mt) REVERT: B 1916 MET cc_start: 0.9260 (mmm) cc_final: 0.8981 (mmm) REVERT: B 1935 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: B 2156 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 2158 MET cc_start: 0.9216 (ttm) cc_final: 0.9006 (ttt) REVERT: B 2448 ASP cc_start: 0.9040 (m-30) cc_final: 0.8502 (m-30) REVERT: B 2667 MET cc_start: 0.8138 (ptt) cc_final: 0.7864 (ptp) REVERT: B 2962 MET cc_start: 0.6599 (ptp) cc_final: 0.6293 (mmm) outliers start: 72 outliers final: 58 residues processed: 436 average time/residue: 0.5202 time to fit residues: 391.0400 Evaluate side-chains 427 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 366 time to evaluate : 5.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1213 HIS Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1470 TYR Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1626 ASP Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 2084 LEU Chi-restraints excluded: chain A residue 2092 CYS Chi-restraints excluded: chain A residue 2098 LEU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2860 SER Chi-restraints excluded: chain A residue 2936 GLU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 963 MET Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1238 LEU Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1517 LEU Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1628 MET Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1755 MET Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1794 LEU Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 CYS Chi-restraints excluded: chain B residue 2098 LEU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2249 ASP Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2362 GLU Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2492 LEU Chi-restraints excluded: chain B residue 2936 GLU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 323 optimal weight: 10.0000 chunk 521 optimal weight: 0.4980 chunk 318 optimal weight: 0.0570 chunk 247 optimal weight: 0.1980 chunk 362 optimal weight: 9.9990 chunk 546 optimal weight: 5.9990 chunk 503 optimal weight: 1.9990 chunk 435 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 336 optimal weight: 7.9990 chunk 267 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 44992 Z= 0.141 Angle : 0.606 16.066 60798 Z= 0.283 Chirality : 0.037 0.313 6980 Planarity : 0.003 0.053 7648 Dihedral : 4.147 73.006 5968 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.08 % Allowed : 16.79 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.12), residues: 5426 helix: 1.75 (0.09), residues: 3772 sheet: 0.18 (0.60), residues: 66 loop : -0.11 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.001 TRP A1710 HIS 0.012 0.001 HIS A 993 PHE 0.032 0.001 PHE B 626 TYR 0.027 0.001 TYR A1475 ARG 0.009 0.000 ARG B2618 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 400 time to evaluate : 5.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1221 TRP cc_start: 0.2270 (t-100) cc_final: 0.1987 (t-100) REVERT: A 1295 LEU cc_start: 0.7550 (mm) cc_final: 0.7281 (mm) REVERT: A 1397 HIS cc_start: 0.5897 (t70) cc_final: 0.5540 (t70) REVERT: A 1410 LYS cc_start: 0.8884 (mmtp) cc_final: 0.8639 (mtmt) REVERT: A 1477 ASN cc_start: 0.8135 (m110) cc_final: 0.7851 (p0) REVERT: A 1539 LEU cc_start: 0.9111 (mm) cc_final: 0.8873 (mm) REVERT: A 1767 PHE cc_start: 0.7885 (m-80) cc_final: 0.7452 (m-80) REVERT: A 1916 MET cc_start: 0.9166 (mmm) cc_final: 0.8942 (mmm) REVERT: A 2160 LYS cc_start: 0.9213 (mtmt) cc_final: 0.8902 (mmmt) REVERT: A 2294 GLU cc_start: 0.8569 (tp30) cc_final: 0.8215 (tp30) REVERT: A 2532 MET cc_start: 0.5850 (mtt) cc_final: 0.5396 (ppp) REVERT: A 2667 MET cc_start: 0.8777 (ptt) cc_final: 0.8532 (ptt) REVERT: A 3008 ARG cc_start: 0.8922 (ttt-90) cc_final: 0.8633 (ttm-80) REVERT: B 96 GLU cc_start: 0.4450 (OUTLIER) cc_final: 0.4064 (mt-10) REVERT: B 542 LEU cc_start: 0.8968 (tt) cc_final: 0.8725 (pp) REVERT: B 617 MET cc_start: 0.8485 (tpp) cc_final: 0.8212 (tpp) REVERT: B 949 MET cc_start: 0.7404 (mmp) cc_final: 0.6621 (ttp) REVERT: B 1094 ASN cc_start: 0.9190 (p0) cc_final: 0.8820 (p0) REVERT: B 1210 MET cc_start: 0.8773 (mmp) cc_final: 0.7657 (ptp) REVERT: B 1443 HIS cc_start: 0.9240 (t-90) cc_final: 0.8986 (t70) REVERT: B 1454 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8242 (tptp) REVERT: B 1475 TYR cc_start: 0.8835 (m-80) cc_final: 0.8319 (m-10) REVERT: B 1539 LEU cc_start: 0.9242 (mm) cc_final: 0.9026 (mm) REVERT: B 1916 MET cc_start: 0.9179 (mmm) cc_final: 0.8911 (mmm) REVERT: B 1935 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8453 (m-30) REVERT: B 2156 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 2158 MET cc_start: 0.9235 (ttm) cc_final: 0.9017 (ttt) REVERT: B 2160 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8710 (mmmt) REVERT: B 2448 ASP cc_start: 0.9028 (m-30) cc_final: 0.8530 (m-30) REVERT: B 2449 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8460 (mm-30) REVERT: B 2667 MET cc_start: 0.8129 (ptt) cc_final: 0.7852 (ptp) REVERT: B 2962 MET cc_start: 0.6557 (ptp) cc_final: 0.6245 (mmm) outliers start: 53 outliers final: 46 residues processed: 434 average time/residue: 0.4978 time to fit residues: 378.4158 Evaluate side-chains 428 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 380 time to evaluate : 4.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 946 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1213 HIS Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2084 LEU Chi-restraints excluded: chain A residue 2092 CYS Chi-restraints excluded: chain A residue 2098 LEU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 963 MET Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1238 LEU Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1517 LEU Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1794 LEU Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 CYS Chi-restraints excluded: chain B residue 2098 LEU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2362 GLU Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2751 THR Chi-restraints excluded: chain B residue 2936 GLU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 345 optimal weight: 4.9990 chunk 463 optimal weight: 7.9990 chunk 133 optimal weight: 0.0010 chunk 401 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 436 optimal weight: 0.0170 chunk 182 optimal weight: 0.9980 chunk 447 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 80 optimal weight: 0.0070 overall best weight: 0.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 HIS ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2002 GLN ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3038 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.141573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.091581 restraints weight = 131405.429| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.77 r_work: 0.3290 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 44992 Z= 0.138 Angle : 0.612 16.001 60798 Z= 0.283 Chirality : 0.037 0.309 6980 Planarity : 0.004 0.086 7648 Dihedral : 4.020 69.974 5968 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.04 % Allowed : 17.05 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.12), residues: 5426 helix: 1.77 (0.09), residues: 3772 sheet: 0.22 (0.60), residues: 66 loop : -0.07 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP A1710 HIS 0.010 0.001 HIS A 993 PHE 0.032 0.001 PHE B 626 TYR 0.023 0.001 TYR A 313 ARG 0.015 0.000 ARG A1633 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11446.61 seconds wall clock time: 207 minutes 2.48 seconds (12422.48 seconds total)