Starting phenix.real_space_refine on Sun Jul 28 10:24:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/07_2024/8oxm_17265_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/07_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_17265/07_2024/8oxm_17265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/07_2024/8oxm_17265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/07_2024/8oxm_17265_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxm_17265/07_2024/8oxm_17265_neut.cif" } 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: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 21.94, per 1000 atoms: 0.50 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: 17.19 Conformation dependent library (CDL) restraints added in 7.7 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... Secondary structure from input PDB file: 311 helices and 8 sheets defined 75.6% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 19 through 34 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) removed outlier: 4.085A pdb=" N ILE A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 57 through 74 Processing helix chain 'A' and resid 88 through 109 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 116 through 129 removed outlier: 3.880A pdb=" N LEU A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.871A pdb=" N ILE A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.520A pdb=" N ARG A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.752A pdb=" N PHE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 244 Processing helix chain 'A' and resid 247 through 268 Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 272 through 291 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.987A pdb=" N SER A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 357 Processing helix chain 'A' and resid 392 through 403 removed outlier: 3.952A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 423 Processing helix chain 'A' and resid 424 through 427 removed outlier: 3.700A pdb=" N LEU A 427 " --> pdb=" O PRO A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 427' Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 450 through 468 removed outlier: 4.638A pdb=" N TYR A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 492 removed outlier: 3.787A pdb=" N PHE A 492 " --> pdb=" O TRP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 514 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.097A pdb=" N TRP A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) 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) removed outlier: 4.201A pdb=" N PHE A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 527' Processing helix chain 'A' and resid 535 through 548 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 571 through 581 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 607 through 617 Processing helix chain 'A' and resid 619 through 629 removed outlier: 3.501A pdb=" N SER A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 656 removed outlier: 3.725A pdb=" N GLU A 649 " --> pdb=" O PHE A 645 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 704 Processing helix chain 'A' and resid 712 through 732 Processing helix chain 'A' and resid 736 through 743 Processing helix chain 'A' and resid 743 through 766 removed outlier: 3.525A pdb=" N GLN A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) 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 772 through 787 Processing helix chain 'A' and resid 794 through 807 removed outlier: 3.520A pdb=" N ILE A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 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 886 through 890 removed outlier: 3.781A pdb=" N TYR A 889 " --> pdb=" O ALA A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 912 removed outlier: 4.409A pdb=" N GLN A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 931 removed outlier: 4.007A pdb=" N ILE A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 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 962 through 971 Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.835A pdb=" N VAL A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 995 Processing helix chain 'A' and resid 997 through 1003 removed outlier: 4.199A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1031 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 1035 through 1053 Processing helix chain 'A' and resid 1070 through 1077 removed outlier: 3.532A pdb=" N PHE A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1080 No H-bonds generated for 'chain 'A' and resid 1078 through 1080' Processing helix chain 'A' and resid 1082 through 1093 removed outlier: 4.139A pdb=" N ARG A1086 " --> pdb=" O HIS A1082 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A1087 " --> pdb=" O HIS A1083 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A1088 " --> pdb=" O GLN A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1112 through 1133 Processing helix chain 'A' and resid 1143 through 1165 removed outlier: 3.544A pdb=" N LEU A1162 " --> pdb=" O ILE A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1183 removed outlier: 4.034A pdb=" N LYS A1181 " --> pdb=" O CYS A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1202 Processing helix chain 'A' and resid 1205 through 1212 Processing helix chain 'A' and resid 1213 through 1223 Processing helix chain 'A' and resid 1235 through 1239 Processing helix chain 'A' and resid 1243 through 1261 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 removed outlier: 3.637A pdb=" N ILE A1261 " --> pdb=" O PRO A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1273 Processing helix chain 'A' and resid 1278 through 1286 Processing helix chain 'A' and resid 1286 through 1295 removed outlier: 3.646A pdb=" N ASN A1293 " --> pdb=" O LYS A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1299 Processing helix chain 'A' and resid 1305 through 1323 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 1331 through 1339 removed outlier: 3.528A pdb=" N ASN A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1350 removed outlier: 4.050A pdb=" N GLU A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1397 removed outlier: 3.546A pdb=" N HIS A1397 " --> pdb=" O ILE A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1409 removed outlier: 4.146A pdb=" N ILE A1407 " --> pdb=" O SER A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1429 removed outlier: 3.967A pdb=" N GLN A1416 " --> pdb=" O PRO A1412 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A1418 " --> pdb=" O SER A1414 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1419 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS A1423 " --> pdb=" O LEU A1419 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A1425 " --> pdb=" O ALA A1421 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A1426 " --> pdb=" O ILE A1422 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1451 Processing helix chain 'A' and resid 1457 through 1459 No H-bonds generated for 'chain 'A' and resid 1457 through 1459' Processing helix chain 'A' and resid 1460 through 1478 Processing helix chain 'A' and resid 1491 through 1509 Processing helix chain 'A' and resid 1517 through 1524 removed outlier: 3.759A pdb=" N LEU A1524 " --> pdb=" O ILE A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1528 Processing helix chain 'A' and resid 1531 through 1548 Processing helix chain 'A' and resid 1552 through 1561 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 1568 through 1570 No H-bonds generated for 'chain 'A' and resid 1568 through 1570' Processing helix chain 'A' and resid 1571 through 1577 Processing helix chain 'A' and resid 1578 through 1583 Processing helix chain 'A' and resid 1589 through 1604 Processing helix chain 'A' and resid 1610 through 1624 removed outlier: 3.549A pdb=" N HIS A1624 " --> pdb=" O GLN A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1635 removed outlier: 3.918A pdb=" N ILE A1631 " --> pdb=" O GLN A1627 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET A1632 " --> pdb=" O MET A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1641 Processing helix chain 'A' and resid 1642 through 1659 Processing helix chain 'A' and resid 1663 through 1677 removed outlier: 3.615A pdb=" N VAL A1667 " --> pdb=" O GLY A1663 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A1669 " --> pdb=" O LYS A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1703 Processing helix chain 'A' and resid 1705 through 1722 Processing helix chain 'A' and resid 1726 through 1741 removed outlier: 3.761A pdb=" N ARG A1730 " --> pdb=" O CYS A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1754 Processing helix chain 'A' and resid 1759 through 1765 Processing helix chain 'A' and resid 1791 through 1796 removed outlier: 3.561A pdb=" N TRP A1795 " --> pdb=" O ASP A1791 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A1796 " --> pdb=" O ILE A1792 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1791 through 1796' Processing helix chain 'A' and resid 1801 through 1816 removed outlier: 3.747A pdb=" N SER A1816 " --> pdb=" O ALA A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1827 through 1832 Processing helix chain 'A' and resid 1834 through 1852 removed outlier: 3.617A pdb=" N CYS A1838 " --> pdb=" O LYS A1834 " (cutoff:3.500A) Proline residue: A1843 - end of helix removed outlier: 3.728A pdb=" N GLN A1852 " --> pdb=" O ASP A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1874 removed outlier: 3.911A pdb=" N LEU A1861 " --> pdb=" O SER A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1902 through 1918 removed outlier: 4.073A pdb=" N GLN A1906 " --> pdb=" O ASP A1902 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1926 through 1931 Processing helix chain 'A' and resid 1937 through 1948 removed outlier: 4.053A pdb=" N VAL A1941 " --> pdb=" O ASN A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1974 Processing helix chain 'A' and resid 1985 through 1997 Processing helix chain 'A' and resid 2000 through 2012 removed outlier: 3.527A pdb=" N LEU A2004 " --> pdb=" O SER A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2017 through 2022 removed outlier: 3.539A pdb=" N GLY A2020 " --> pdb=" O SER A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2039 Processing helix chain 'A' and resid 2041 through 2052 removed outlier: 3.630A pdb=" N VAL A2047 " --> pdb=" O GLY A2043 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2071 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 2074 through 2088 Processing helix chain 'A' and resid 2092 through 2106 Processing helix chain 'A' and resid 2123 through 2137 Processing helix chain 'A' and resid 2140 through 2161 removed outlier: 4.031A pdb=" N ARG A2161 " --> pdb=" O GLU A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2189 removed outlier: 4.247A pdb=" N THR A2172 " --> pdb=" O SER A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2212 Processing helix chain 'A' and resid 2216 through 2237 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2241 through 2264 removed outlier: 3.562A pdb=" N GLU A2245 " --> pdb=" O ASN A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2282 Processing helix chain 'A' and resid 2289 through 2302 removed outlier: 4.130A pdb=" N LEU A2293 " --> pdb=" O SER A2289 " (cutoff:3.500A) Processing helix chain 'A' and resid 2304 through 2322 removed outlier: 3.691A pdb=" N ALA A2321 " --> pdb=" O LYS A2317 " (cutoff:3.500A) Processing helix chain 'A' and resid 2327 through 2349 Processing helix chain 'A' and resid 2352 through 2371 removed outlier: 3.734A pdb=" N ILE A2356 " --> pdb=" O ASN A2352 " (cutoff:3.500A) 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 2376 through 2407 removed outlier: 4.180A pdb=" N GLY A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2430 Processing helix chain 'A' and resid 2435 through 2476 removed outlier: 4.170A pdb=" N SER A2476 " --> pdb=" O ASN A2472 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2482 No H-bonds generated for 'chain 'A' and resid 2480 through 2482' Processing helix chain 'A' and resid 2483 through 2492 Processing helix chain 'A' and resid 2497 through 2507 removed outlier: 3.609A pdb=" N ASN A2501 " --> pdb=" O VAL A2497 " (cutoff:3.500A) Processing helix chain 'A' and resid 2508 through 2511 Processing helix chain 'A' and resid 2512 through 2516 removed outlier: 3.795A pdb=" N LYS A2515 " --> pdb=" O PRO A2512 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A2516 " --> pdb=" O THR A2513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2512 through 2516' Processing helix chain 'A' and resid 2519 through 2525 Processing helix chain 'A' and resid 2534 through 2552 removed outlier: 3.897A pdb=" N HIS A2538 " --> pdb=" O GLY A2534 " (cutoff:3.500A) Processing helix chain 'A' and resid 2556 through 2565 Processing helix chain 'A' and resid 2567 through 2573 Processing helix chain 'A' and resid 2592 through 2613 removed outlier: 3.892A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2613 through 2633 Processing helix chain 'A' and resid 2635 through 2639 removed outlier: 3.821A pdb=" N LYS A2639 " --> pdb=" O THR A2636 " (cutoff:3.500A) Processing helix chain 'A' and resid 2651 through 2656 removed outlier: 4.116A pdb=" N LYS A2655 " --> pdb=" O GLN A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2722 through 2742 Processing helix chain 'A' and resid 2742 through 2749 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) Processing helix chain 'A' and resid 2776 through 2781 Processing helix chain 'A' and resid 2786 through 2792 Processing helix chain 'A' and resid 2797 through 2809 Processing helix chain 'A' and resid 2812 through 2826 Processing helix chain 'A' and resid 2832 through 2837 removed outlier: 4.412A pdb=" N MET A2836 " --> pdb=" O ARG A2832 " (cutoff:3.500A) Processing helix chain 'A' and resid 2841 through 2867 Processing helix chain 'A' and resid 2872 through 2874 No H-bonds generated for 'chain 'A' and resid 2872 through 2874' Processing helix chain 'A' and resid 2911 through 2919 removed outlier: 3.689A pdb=" N GLY A2919 " --> pdb=" O VAL A2915 " (cutoff:3.500A) Processing helix chain 'A' and resid 2925 through 2941 Processing helix chain 'A' and resid 2941 through 2950 Processing helix chain 'A' and resid 3003 through 3019 Processing helix chain 'A' and resid 3027 through 3041 Processing helix chain 'A' and resid 3041 through 3047 removed outlier: 3.811A pdb=" N ARG A3047 " --> pdb=" O LYS A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3049 through 3053 Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 19 through 34 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) removed outlier: 4.077A pdb=" N ILE B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 57 through 74 Processing helix chain 'B' and resid 88 through 109 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 116 through 129 removed outlier: 3.860A pdb=" N LEU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 148 Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.903A pdb=" N ILE B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.512A pdb=" N ARG B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.711A pdb=" N PHE B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 244 Processing helix chain 'B' and resid 247 through 268 Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 272 through 291 Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 305 through 324 removed outlier: 4.016A pdb=" N SER B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 357 Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.987A pdb=" N ILE B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 423 Processing helix chain 'B' and resid 424 through 427 removed outlier: 3.939A pdb=" N LEU B 427 " --> pdb=" O PRO B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 424 through 427' Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 450 through 468 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 473 through 493 removed outlier: 4.291A pdb=" N LYS B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG B 493 " --> pdb=" O CYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 515 removed outlier: 3.537A pdb=" N LEU B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 removed outlier: 4.059A pdb=" N TRP B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) 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) removed outlier: 4.125A pdb=" N PHE B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 527' Processing helix chain 'B' and resid 535 through 548 removed outlier: 3.506A pdb=" N LEU B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 596 through 601 Processing helix chain 'B' and resid 607 through 616 removed outlier: 3.684A pdb=" N THR B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 628 removed outlier: 3.624A pdb=" N GLN B 628 " --> pdb=" O MET B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 657 removed outlier: 3.821A pdb=" N GLU B 649 " --> pdb=" O PHE B 645 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 704 removed outlier: 3.608A pdb=" N LYS B 687 " --> pdb=" O HIS B 683 " (cutoff:3.500A) 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) removed outlier: 3.565A pdb=" N ASN B 704 " --> pdb=" O GLN B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 732 Processing helix chain 'B' and resid 736 through 742 Processing helix chain 'B' and resid 743 through 766 removed outlier: 3.591A pdb=" N GLN B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) 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 772 through 787 Processing helix chain 'B' and resid 794 through 807 Processing helix chain 'B' and resid 808 through 824 removed outlier: 3.617A pdb=" N LYS B 820 " --> pdb=" O ALA B 816 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 824 " --> pdb=" O LYS B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.855A pdb=" N TYR B 889 " --> pdb=" O ALA B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 911 Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 919 through 931 removed outlier: 3.770A pdb=" N ILE B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 954 Processing helix chain 'B' and resid 962 through 971 Processing helix chain 'B' and resid 972 through 980 removed outlier: 3.850A pdb=" N VAL B 976 " --> pdb=" O PRO B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 995 removed outlier: 3.683A pdb=" N LEU B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1002 Processing helix chain 'B' and resid 1008 through 1031 Processing helix chain 'B' and resid 1035 through 1053 Processing helix chain 'B' and resid 1070 through 1077 removed outlier: 3.545A pdb=" N PHE B1077 " --> pdb=" O VAL B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1080 No H-bonds generated for 'chain 'B' and resid 1078 through 1080' Processing helix chain 'B' and resid 1082 through 1093 Processing helix chain 'B' and resid 1094 through 1096 No H-bonds generated for 'chain 'B' and resid 1094 through 1096' Processing helix chain 'B' and resid 1112 through 1133 Processing helix chain 'B' and resid 1143 through 1165 Processing helix chain 'B' and resid 1168 through 1183 removed outlier: 3.993A pdb=" N LYS B1181 " --> pdb=" O CYS B1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1202 Processing helix chain 'B' and resid 1205 through 1212 Processing helix chain 'B' and resid 1213 through 1225 removed outlier: 3.558A pdb=" N LEU B1217 " --> pdb=" O HIS B1213 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B1225 " --> pdb=" O TRP B1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1234 Processing helix chain 'B' and resid 1235 through 1239 Processing helix chain 'B' and resid 1243 through 1262 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 1264 through 1275 Processing helix chain 'B' and resid 1278 through 1286 Processing helix chain 'B' and resid 1286 through 1295 Processing helix chain 'B' and resid 1296 through 1299 Processing helix chain 'B' and resid 1305 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 1327 through 1330 removed outlier: 4.040A pdb=" N LYS B1330 " --> pdb=" O LEU B1327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1327 through 1330' Processing helix chain 'B' and resid 1331 through 1339 removed outlier: 3.515A pdb=" N ASN B1339 " --> pdb=" O LEU B1335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1339 through 1350 removed outlier: 3.984A pdb=" N ILE B1343 " --> pdb=" O ASN B1339 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B1346 " --> pdb=" O GLU B1342 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1397 Processing helix chain 'B' and resid 1403 through 1409 removed outlier: 4.145A pdb=" N ILE B1407 " --> pdb=" O SER B1403 " (cutoff:3.500A) Processing helix chain 'B' and resid 1412 through 1429 removed outlier: 3.940A pdb=" N GLN B1416 " --> pdb=" O PRO B1412 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS B1423 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR B1429 " --> pdb=" O GLN B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1431 through 1451 Processing helix chain 'B' and resid 1463 through 1478 Processing helix chain 'B' and resid 1491 through 1509 Processing helix chain 'B' and resid 1517 through 1524 removed outlier: 3.921A pdb=" N LEU B1524 " --> pdb=" O ILE B1520 " (cutoff:3.500A) Processing helix chain 'B' and resid 1525 through 1529 removed outlier: 4.037A pdb=" N TYR B1529 " --> pdb=" O PRO B1526 " (cutoff:3.500A) Processing helix chain 'B' and resid 1531 through 1548 Processing helix chain 'B' and resid 1552 through 1561 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 1568 through 1570 No H-bonds generated for 'chain 'B' and resid 1568 through 1570' Processing helix chain 'B' and resid 1571 through 1583 removed outlier: 4.605A pdb=" N ILE B1581 " --> pdb=" O THR B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1589 through 1604 Processing helix chain 'B' and resid 1610 through 1624 Processing helix chain 'B' and resid 1627 through 1635 removed outlier: 3.900A pdb=" N ILE B1631 " --> pdb=" O GLN B1627 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET B1632 " --> pdb=" O MET B1628 " (cutoff:3.500A) Processing helix chain 'B' and resid 1638 through 1641 Processing helix chain 'B' and resid 1642 through 1659 Processing helix chain 'B' and resid 1663 through 1677 removed outlier: 3.628A pdb=" N VAL B1667 " --> pdb=" O GLY B1663 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B1669 " --> pdb=" O LYS B1665 " (cutoff:3.500A) Processing helix chain 'B' and resid 1693 through 1703 Processing helix chain 'B' and resid 1705 through 1722 Processing helix chain 'B' and resid 1726 through 1741 removed outlier: 3.839A pdb=" N ARG B1730 " --> pdb=" O CYS B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1743 through 1754 Processing helix chain 'B' and resid 1759 through 1765 Processing helix chain 'B' and resid 1766 through 1768 No H-bonds generated for 'chain 'B' and resid 1766 through 1768' Processing helix chain 'B' and resid 1791 through 1796 removed outlier: 3.539A pdb=" N ILE B1796 " --> pdb=" O ILE B1792 " (cutoff:3.500A) Processing helix chain 'B' and resid 1801 through 1816 removed outlier: 3.723A pdb=" N SER B1816 " --> pdb=" O ALA B1812 " (cutoff:3.500A) Processing helix chain 'B' and resid 1827 through 1832 Processing helix chain 'B' and resid 1834 through 1852 removed outlier: 3.862A pdb=" N CYS B1838 " --> pdb=" O LYS B1834 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B1839 " --> pdb=" O THR B1835 " (cutoff:3.500A) Proline residue: B1843 - end of helix removed outlier: 3.735A pdb=" N GLN B1852 " --> pdb=" O ASP B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1856 through 1875 removed outlier: 3.844A pdb=" N LEU B1861 " --> pdb=" O SER B1857 " (cutoff:3.500A) Processing helix chain 'B' and resid 1902 through 1918 removed outlier: 4.105A pdb=" N GLN B1906 " --> pdb=" O ASP B1902 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B1918 " --> pdb=" O ASP B1914 " (cutoff:3.500A) Processing helix chain 'B' and resid 1926 through 1931 Processing helix chain 'B' and resid 1937 through 1948 removed outlier: 4.422A pdb=" N VAL B1941 " --> pdb=" O ASN B1937 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1974 Processing helix chain 'B' and resid 1985 through 1997 Processing helix chain 'B' and resid 2000 through 2012 removed outlier: 3.518A pdb=" N LEU B2004 " --> pdb=" O SER B2000 " (cutoff:3.500A) Processing helix chain 'B' and resid 2018 through 2022 Processing helix chain 'B' and resid 2028 through 2039 Processing helix chain 'B' and resid 2041 through 2052 removed outlier: 3.682A pdb=" N VAL B2047 " --> pdb=" O GLY B2043 " (cutoff:3.500A) Processing helix chain 'B' and resid 2056 through 2071 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 2074 through 2088 Processing helix chain 'B' and resid 2092 through 2106 Processing helix chain 'B' and resid 2123 through 2137 Processing helix chain 'B' and resid 2139 through 2161 removed outlier: 4.038A pdb=" N ARG B2161 " --> pdb=" O GLU B2157 " (cutoff:3.500A) Processing helix chain 'B' and resid 2168 through 2189 removed outlier: 4.252A pdb=" N THR B2172 " --> pdb=" O SER B2168 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2212 Processing helix chain 'B' and resid 2216 through 2237 Proline residue: B2222 - end of helix Processing helix chain 'B' and resid 2241 through 2264 removed outlier: 3.559A pdb=" N GLU B2245 " --> pdb=" O ASN B2241 " (cutoff:3.500A) Processing helix chain 'B' and resid 2268 through 2282 Processing helix chain 'B' and resid 2290 through 2302 removed outlier: 3.562A pdb=" N GLU B2294 " --> pdb=" O GLU B2290 " (cutoff:3.500A) Processing helix chain 'B' and resid 2304 through 2322 removed outlier: 3.727A pdb=" N ALA B2321 " --> pdb=" O LYS B2317 " (cutoff:3.500A) Processing helix chain 'B' and resid 2327 through 2349 Processing helix chain 'B' and resid 2352 through 2371 removed outlier: 3.732A pdb=" N ILE B2356 " --> pdb=" O ASN B2352 " (cutoff:3.500A) 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 2376 through 2406 removed outlier: 4.195A pdb=" N GLY B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) Processing helix chain 'B' and resid 2407 through 2430 Processing helix chain 'B' and resid 2435 through 2476 removed outlier: 4.138A pdb=" N SER B2476 " --> pdb=" O ASN B2472 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2482 No H-bonds generated for 'chain 'B' and resid 2480 through 2482' Processing helix chain 'B' and resid 2483 through 2490 Processing helix chain 'B' and resid 2497 through 2507 removed outlier: 3.614A pdb=" N ASN B2501 " --> pdb=" O VAL B2497 " (cutoff:3.500A) Processing helix chain 'B' and resid 2508 through 2511 Processing helix chain 'B' and resid 2512 through 2516 removed outlier: 3.784A pdb=" N LYS B2515 " --> pdb=" O PRO B2512 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B2516 " --> pdb=" O THR B2513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2512 through 2516' Processing helix chain 'B' and resid 2519 through 2525 Processing helix chain 'B' and resid 2534 through 2552 removed outlier: 3.931A pdb=" N HIS B2538 " --> pdb=" O GLY B2534 " (cutoff:3.500A) Processing helix chain 'B' and resid 2556 through 2565 Processing helix chain 'B' and resid 2567 through 2573 Processing helix chain 'B' and resid 2592 through 2611 Processing helix chain 'B' and resid 2613 through 2633 Processing helix chain 'B' and resid 2635 through 2639 removed outlier: 3.823A pdb=" N LYS B2639 " --> pdb=" O THR B2636 " (cutoff:3.500A) Processing helix chain 'B' and resid 2651 through 2656 removed outlier: 4.110A pdb=" N LYS B2655 " --> pdb=" O GLN B2651 " (cutoff:3.500A) Processing helix chain 'B' and resid 2722 through 2742 Processing helix chain 'B' and resid 2742 through 2749 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) Processing helix chain 'B' and resid 2776 through 2781 Processing helix chain 'B' and resid 2786 through 2792 Processing helix chain 'B' and resid 2797 through 2809 Processing helix chain 'B' and resid 2812 through 2826 Processing helix chain 'B' and resid 2830 through 2832 No H-bonds generated for 'chain 'B' and resid 2830 through 2832' Processing helix chain 'B' and resid 2833 through 2839 Processing helix chain 'B' and resid 2841 through 2867 Processing helix chain 'B' and resid 2911 through 2918 Processing helix chain 'B' and resid 2921 through 2924 removed outlier: 3.623A pdb=" N GLU B2924 " --> pdb=" O THR B2921 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2921 through 2924' Processing helix chain 'B' and resid 2925 through 2941 removed outlier: 3.620A pdb=" N ARG B2929 " --> pdb=" O GLY B2925 " (cutoff:3.500A) Processing helix chain 'B' and resid 2941 through 2950 Processing helix chain 'B' and resid 3003 through 3019 Processing helix chain 'B' and resid 3027 through 3041 Processing helix chain 'B' and resid 3041 through 3047 removed outlier: 3.823A pdb=" N ARG B3047 " --> pdb=" O LYS B3043 " (cutoff:3.500A) Processing helix chain 'B' and resid 3049 through 3053 Processing sheet with id=AA1, first strand: chain 'A' and resid 1060 through 1063 Processing sheet with id=AA2, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 6.963A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 6.963A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A2765 " --> pdb=" O LYS A2717 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id=AA5, first strand: chain 'B' and resid 1060 through 1063 Processing sheet with id=AA6, first strand: chain 'B' and resid 2645 through 2646 removed outlier: 6.953A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP B2703 " --> pdb=" O GLU B2689 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2645 through 2646 removed outlier: 6.953A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP B2703 " --> pdb=" O GLU B2689 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2773 through 2775 2778 hydrogen bonds defined for protein. 8214 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: 21.04 Time building geometry restraints manager: 18.71 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: 484 2.66 - 3.22: 43160 3.22 - 3.78: 71518 3.78 - 4.34: 90720 4.34 - 4.90: 149049 Nonbonded interactions: 354931 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 354926 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.820 Check model and map are aligned: 0.310 Set scattering table: 0.420 Process input model: 123.700 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.830 ------------------------------------------------------------------------------- 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= 0.148 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 : 4.984 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: 0.5692 time to fit residues: 861.3926 Evaluate side-chains 536 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 5.214 ------------------------------------------------------------------------------- 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: 5.9990 chunk 416 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 280 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 430 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 320 optimal weight: 0.0170 chunk 498 optimal weight: 1.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- 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** ** A 399 HIS ** 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** A2809 GLN B 476 GLN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1183 ASN ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1431 ASN B1478 GLN B1537 GLN ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2070 ASN B2101 GLN B2206 GLN B2494 ASN B2542 ASN B2565 ASN ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2809 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1853 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= 0.178 Angle : 0.569 12.707 60798 Z= 0.279 Chirality : 0.038 0.276 6980 Planarity : 0.004 0.054 7648 Dihedral : 5.077 80.417 5968 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.47 % Allowed : 8.26 % Favored : 90.27 % 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: 2.11 (0.12), residues: 5426 helix: 2.01 (0.09), residues: 3802 sheet: 0.99 (0.66), residues: 58 loop : -0.04 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1461 HIS 0.010 0.001 HIS A 291 PHE 0.022 0.001 PHE B1236 TYR 0.021 0.001 TYR B1717 ARG 0.005 0.000 ARG B1619 *********************** 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 611 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 539 time to evaluate : 4.943 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: A 615 LEU cc_start: 0.7675 (mt) cc_final: 0.7449 (tp) REVERT: A 624 MET cc_start: 0.6345 (mmm) cc_final: 0.5790 (mmm) REVERT: A 660 MET cc_start: 0.6113 (mmp) cc_final: 0.5597 (mmp) REVERT: A 1087 MET cc_start: 0.8029 (mmm) cc_final: 0.7542 (mmp) REVERT: A 1210 MET cc_start: 0.6913 (mmm) cc_final: 0.6341 (ptp) REVERT: A 1248 TYR cc_start: 0.5346 (m-10) cc_final: 0.5102 (m-80) REVERT: A 1295 LEU cc_start: 0.7305 (mm) cc_final: 0.7001 (mm) REVERT: A 1539 LEU cc_start: 0.9039 (mm) cc_final: 0.8800 (mm) REVERT: A 1556 TYR cc_start: 0.7813 (m-80) cc_final: 0.7513 (m-80) REVERT: A 1572 LYS cc_start: 0.9352 (mtpt) cc_final: 0.9078 (tptp) REVERT: A 1807 LYS cc_start: 0.9448 (tmmt) cc_final: 0.9077 (mmtm) REVERT: A 1813 PHE cc_start: 0.9113 (m-80) cc_final: 0.8568 (m-80) REVERT: A 1995 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8314 (pt0) REVERT: A 2097 GLU cc_start: 0.8653 (pt0) cc_final: 0.8347 (pt0) REVERT: A 2156 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7803 (tm-30) REVERT: A 2294 GLU cc_start: 0.8337 (tp30) cc_final: 0.8072 (tp30) REVERT: A 2448 ASP cc_start: 0.8876 (m-30) cc_final: 0.8642 (m-30) REVERT: A 2506 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7374 (ptp-110) REVERT: A 3011 MET cc_start: 0.8618 (tmm) cc_final: 0.8215 (tmm) REVERT: B 96 GLU cc_start: 0.4765 (OUTLIER) cc_final: 0.4431 (mt-10) REVERT: B 542 LEU cc_start: 0.9118 (tp) cc_final: 0.8859 (mt) REVERT: B 626 PHE cc_start: 0.7693 (t80) cc_final: 0.7432 (t80) REVERT: B 731 TYR cc_start: 0.7125 (t80) cc_final: 0.6441 (t80) REVERT: B 732 MET cc_start: 0.8082 (mmp) cc_final: 0.7568 (tpp) REVERT: B 949 MET cc_start: 0.7499 (mmp) cc_final: 0.6799 (ttp) REVERT: B 1018 PHE cc_start: 0.8470 (t80) cc_final: 0.8090 (t80) REVERT: B 1022 ILE cc_start: 0.9122 (mm) cc_final: 0.8806 (pt) REVERT: B 1064 MET cc_start: 0.4461 (pmm) cc_final: 0.1674 (mmm) REVERT: B 1199 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8327 (mm-30) REVERT: B 1210 MET cc_start: 0.8899 (mmp) cc_final: 0.8645 (mmp) REVERT: B 1454 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8326 (tptp) REVERT: B 1495 CYS cc_start: 0.9288 (m) cc_final: 0.8951 (t) REVERT: B 1514 GLU cc_start: 0.8301 (pt0) cc_final: 0.8068 (tp30) REVERT: B 1539 LEU cc_start: 0.8965 (mm) cc_final: 0.8610 (mm) REVERT: B 1556 TYR cc_start: 0.8578 (t80) cc_final: 0.8030 (m-80) REVERT: B 1907 ARG cc_start: 0.7981 (ptp-170) cc_final: 0.7634 (mtt90) REVERT: B 1995 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B 2156 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 2282 ASN cc_start: 0.8560 (m-40) cc_final: 0.8356 (m-40) REVERT: B 2384 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8105 (mtp) REVERT: B 2395 ASP cc_start: 0.8052 (t0) cc_final: 0.7338 (t0) REVERT: B 2411 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7942 (pp20) REVERT: B 2448 ASP cc_start: 0.8834 (m-30) cc_final: 0.8593 (m-30) REVERT: B 2962 MET cc_start: 0.6260 (ptp) cc_final: 0.5954 (mmm) REVERT: B 3011 MET cc_start: 0.8580 (tmm) cc_final: 0.8162 (tmm) outliers start: 72 outliers final: 44 residues processed: 587 average time/residue: 0.5296 time to fit residues: 533.2052 Evaluate side-chains 493 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 445 time to evaluate : 5.222 ------------------------------------------------------------------------------- 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 1932 PHE Chi-restraints excluded: chain A residue 2016 ASP Chi-restraints excluded: chain A residue 2101 GLN 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 2411 GLU Chi-restraints excluded: chain A residue 2429 GLU 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 291 HIS Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1199 GLU 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 2211 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 2556 THR Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2860 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 277 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 414 optimal weight: 0.3980 chunk 339 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 499 optimal weight: 5.9990 chunk 539 optimal weight: 2.9990 chunk 444 optimal weight: 4.9990 chunk 495 optimal weight: 0.1980 chunk 170 optimal weight: 1.9990 chunk 400 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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** A 399 HIS ** 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** A1443 HIS A2565 ASN ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS B1017 GLN ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 ASN ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1225 GLN ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2565 ASN ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44992 Z= 0.186 Angle : 0.565 10.904 60798 Z= 0.273 Chirality : 0.038 0.286 6980 Planarity : 0.004 0.058 7648 Dihedral : 4.435 76.430 5968 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.61 % Allowed : 10.24 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.10 (0.12), residues: 5426 helix: 1.98 (0.09), residues: 3818 sheet: 0.92 (0.64), residues: 58 loop : 0.00 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1221 HIS 0.020 0.001 HIS A1443 PHE 0.017 0.001 PHE B2143 TYR 0.021 0.001 TYR A 731 ARG 0.005 0.000 ARG A1633 *********************** 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 555 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 476 time to evaluate : 5.067 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: 0.6902 (mmm) cc_final: 0.6441 (mmm) REVERT: A 731 TYR cc_start: 0.6632 (t80) cc_final: 0.6416 (t80) REVERT: A 1209 PHE cc_start: 0.5411 (t80) cc_final: 0.4945 (t80) REVERT: A 1210 MET cc_start: 0.7199 (mmm) cc_final: 0.6776 (ptp) REVERT: A 1248 TYR cc_start: 0.5244 (m-10) cc_final: 0.5025 (m-80) REVERT: A 1295 LEU cc_start: 0.7374 (mm) cc_final: 0.6966 (mm) REVERT: A 1308 MET cc_start: 0.4928 (ppp) cc_final: 0.4726 (ppp) REVERT: A 1539 LEU cc_start: 0.9084 (mm) cc_final: 0.8841 (mm) REVERT: A 1556 TYR cc_start: 0.7880 (m-80) cc_final: 0.7541 (m-80) REVERT: A 1572 LYS cc_start: 0.9363 (mtpt) cc_final: 0.9029 (tppt) REVERT: A 1755 MET cc_start: 0.9056 (mpp) cc_final: 0.8817 (pmm) REVERT: A 1807 LYS cc_start: 0.9473 (tmmt) cc_final: 0.9097 (mmtm) REVERT: A 1813 PHE cc_start: 0.9124 (m-80) cc_final: 0.8613 (m-80) REVERT: A 1995 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8403 (pt0) REVERT: A 2156 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7831 (tm-30) REVERT: A 2294 GLU cc_start: 0.8512 (tp30) cc_final: 0.8278 (tp30) REVERT: A 2506 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7459 (ptp-110) REVERT: A 3011 MET cc_start: 0.8640 (tmm) cc_final: 0.8238 (tmm) REVERT: B 96 GLU cc_start: 0.4787 (OUTLIER) cc_final: 0.4438 (mt-10) REVERT: B 617 MET cc_start: 0.8289 (tpp) cc_final: 0.7990 (tpp) REVERT: B 626 PHE cc_start: 0.7862 (t80) cc_final: 0.7650 (t80) REVERT: B 731 TYR cc_start: 0.7243 (t80) cc_final: 0.6655 (t80) REVERT: B 732 MET cc_start: 0.8235 (mmp) cc_final: 0.7754 (tpp) REVERT: B 949 MET cc_start: 0.7463 (mmp) cc_final: 0.6745 (ttp) REVERT: B 1018 PHE cc_start: 0.8506 (t80) cc_final: 0.8120 (t80) REVERT: B 1022 ILE cc_start: 0.9155 (mm) cc_final: 0.8851 (pt) REVERT: B 1454 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8359 (tptp) REVERT: B 1495 CYS cc_start: 0.9320 (m) cc_final: 0.8863 (t) REVERT: B 1514 GLU cc_start: 0.8361 (pt0) cc_final: 0.8086 (tp30) REVERT: B 1539 LEU cc_start: 0.9027 (mm) cc_final: 0.8727 (mm) REVERT: B 1556 TYR cc_start: 0.8649 (t80) cc_final: 0.8046 (m-80) REVERT: B 1590 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7760 (tt) REVERT: B 1755 MET cc_start: 0.9115 (mpp) cc_final: 0.8804 (pmm) REVERT: B 1907 ARG cc_start: 0.8176 (ptp-170) cc_final: 0.7814 (mtt90) REVERT: B 1935 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: B 2156 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7896 (tm-30) REVERT: B 2411 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8049 (pp20) REVERT: B 2962 MET cc_start: 0.6368 (ptp) cc_final: 0.6077 (mmm) outliers start: 79 outliers final: 43 residues processed: 526 average time/residue: 0.5268 time to fit residues: 480.7162 Evaluate side-chains 461 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 414 time to evaluate : 5.081 ------------------------------------------------------------------------------- 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 1336 PHE 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 1989 LEU Chi-restraints excluded: chain A residue 2016 ASP 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 2429 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2860 SER Chi-restraints excluded: chain A residue 2873 VAL 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 997 VAL Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1678 VAL 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 1935 ASP Chi-restraints excluded: chain B residue 1989 LEU Chi-restraints excluded: chain B residue 2016 ASP Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2261 LEU Chi-restraints excluded: chain B residue 2293 LEU Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2356 ILE 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 2557 LEU Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2860 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 493 optimal weight: 0.1980 chunk 375 optimal weight: 7.9990 chunk 259 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 501 optimal weight: 0.0770 chunk 530 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 475 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 GLN A1116 GLN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2197 GLN A2542 ASN A2565 ASN ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 GLN ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1578 GLN ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2542 ASN ** B2565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 44992 Z= 0.145 Angle : 0.545 11.141 60798 Z= 0.261 Chirality : 0.037 0.206 6980 Planarity : 0.004 0.063 7648 Dihedral : 4.272 79.482 5968 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.77 % Allowed : 11.67 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.14 (0.12), residues: 5426 helix: 2.02 (0.09), residues: 3814 sheet: 0.87 (0.63), residues: 58 loop : 0.00 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1221 HIS 0.006 0.001 HIS A 291 PHE 0.018 0.001 PHE B1247 TYR 0.017 0.001 TYR A2371 ARG 0.012 0.000 ARG A 309 *********************** 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 540 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 453 time to evaluate : 5.163 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 624 MET cc_start: 0.6985 (mmm) cc_final: 0.6532 (mmm) REVERT: A 660 MET cc_start: 0.5825 (OUTLIER) cc_final: 0.5472 (mmp) REVERT: A 731 TYR cc_start: 0.6632 (t80) cc_final: 0.6409 (t80) REVERT: A 753 MET cc_start: 0.7904 (tpp) cc_final: 0.7691 (tpp) REVERT: A 1295 LEU cc_start: 0.7273 (mm) cc_final: 0.6952 (mm) REVERT: A 1539 LEU cc_start: 0.9078 (mm) cc_final: 0.8798 (mm) REVERT: A 1556 TYR cc_start: 0.7931 (m-80) cc_final: 0.7555 (m-80) REVERT: A 1572 LYS cc_start: 0.9311 (mtpt) cc_final: 0.8971 (tppt) REVERT: A 1693 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.6848 (p0) REVERT: A 1755 MET cc_start: 0.9091 (mpp) cc_final: 0.8831 (pmm) REVERT: A 1807 LYS cc_start: 0.9469 (tmmt) cc_final: 0.9106 (mmtp) REVERT: A 1823 ILE cc_start: 0.8987 (mp) cc_final: 0.8627 (tt) REVERT: A 1836 ASP cc_start: 0.9141 (m-30) cc_final: 0.8809 (p0) REVERT: A 1995 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8414 (pt0) REVERT: A 2156 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 2294 GLU cc_start: 0.8501 (tp30) cc_final: 0.8255 (tp30) REVERT: A 2506 ARG cc_start: 0.8042 (ttm110) cc_final: 0.7477 (ptp-110) REVERT: A 2945 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8725 (mp) REVERT: B 96 GLU cc_start: 0.4790 (OUTLIER) cc_final: 0.4448 (mt-10) REVERT: B 626 PHE cc_start: 0.7863 (t80) cc_final: 0.7645 (t80) REVERT: B 731 TYR cc_start: 0.7267 (t80) cc_final: 0.6728 (t80) REVERT: B 732 MET cc_start: 0.8232 (mmp) cc_final: 0.7785 (tpp) REVERT: B 949 MET cc_start: 0.7427 (mmp) cc_final: 0.6686 (ttp) REVERT: B 1018 PHE cc_start: 0.8506 (t80) cc_final: 0.8124 (t80) REVERT: B 1022 ILE cc_start: 0.9143 (mm) cc_final: 0.8838 (pt) REVERT: B 1210 MET cc_start: 0.8861 (mmp) cc_final: 0.8620 (mmp) REVERT: B 1322 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5679 (mm) REVERT: B 1454 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8364 (tptp) REVERT: B 1514 GLU cc_start: 0.8389 (pt0) cc_final: 0.8109 (tp30) REVERT: B 1539 LEU cc_start: 0.9064 (mm) cc_final: 0.8768 (mm) REVERT: B 1556 TYR cc_start: 0.8642 (t80) cc_final: 0.8048 (m-80) REVERT: B 1590 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7890 (tt) REVERT: B 1693 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.6773 (p0) REVERT: B 1755 MET cc_start: 0.9124 (mpp) cc_final: 0.8817 (pmm) REVERT: B 1814 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9093 (mt) REVERT: B 1907 ARG cc_start: 0.8172 (ptp-170) cc_final: 0.7887 (mtt90) REVERT: B 1916 MET cc_start: 0.9086 (mmm) cc_final: 0.8629 (mmm) REVERT: B 1935 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8245 (m-30) REVERT: B 2156 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7913 (tm-30) REVERT: B 2411 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8046 (pp20) REVERT: B 2962 MET cc_start: 0.6211 (ptp) cc_final: 0.5914 (mmm) outliers start: 87 outliers final: 52 residues processed: 507 average time/residue: 0.5226 time to fit residues: 458.0452 Evaluate side-chains 476 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 414 time to evaluate : 5.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1336 PHE 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 1678 VAL Chi-restraints excluded: chain A residue 1681 ILE Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1989 LEU Chi-restraints excluded: chain A residue 2016 ASP Chi-restraints excluded: chain A residue 2084 LEU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE 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 2557 LEU Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2945 LEU 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 781 GLN Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1478 GLN Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1756 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 1935 ASP Chi-restraints excluded: chain B residue 1989 LEU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2211 LEU Chi-restraints excluded: chain B residue 2214 ASP Chi-restraints excluded: chain B residue 2261 LEU Chi-restraints excluded: chain B residue 2293 LEU Chi-restraints excluded: chain B residue 2332 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 2557 LEU Chi-restraints excluded: chain B residue 2624 CYS Chi-restraints excluded: chain B residue 2636 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: 2.9990 chunk 301 optimal weight: 30.0000 chunk 7 optimal weight: 8.9990 chunk 395 optimal weight: 30.0000 chunk 218 optimal weight: 0.0070 chunk 452 optimal weight: 0.8980 chunk 366 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 476 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 GLN A1116 GLN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** 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** B 781 GLN ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2565 ASN ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.003 0.101 44992 Z= 0.199 Angle : 0.569 13.985 60798 Z= 0.274 Chirality : 0.037 0.170 6980 Planarity : 0.004 0.063 7648 Dihedral : 4.280 78.186 5968 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.96 % Allowed : 12.46 % Favored : 85.58 % 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: 2.10 (0.12), residues: 5426 helix: 1.99 (0.09), residues: 3838 sheet: 0.22 (0.64), residues: 62 loop : -0.03 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1221 HIS 0.008 0.001 HIS A 291 PHE 0.019 0.001 PHE B1247 TYR 0.025 0.001 TYR A 313 ARG 0.009 0.000 ARG B1012 *********************** 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 520 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 424 time to evaluate : 4.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 MET cc_start: 0.7219 (mmm) cc_final: 0.6805 (mmm) REVERT: A 660 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5585 (mmp) REVERT: A 732 MET cc_start: 0.5594 (tpp) cc_final: 0.3676 (ptm) REVERT: A 1199 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: A 1295 LEU cc_start: 0.7302 (mm) cc_final: 0.6968 (mm) REVERT: A 1308 MET cc_start: 0.4828 (ppp) cc_final: 0.4624 (ppp) REVERT: A 1539 LEU cc_start: 0.9106 (mm) cc_final: 0.8797 (mm) REVERT: A 1556 TYR cc_start: 0.7941 (m-80) cc_final: 0.7552 (m-80) REVERT: A 1572 LYS cc_start: 0.9381 (mtpt) cc_final: 0.9034 (tppt) REVERT: A 1693 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7164 (p0) REVERT: A 1807 LYS cc_start: 0.9492 (tmmt) cc_final: 0.9144 (mmtp) REVERT: A 1823 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8773 (tt) REVERT: A 1836 ASP cc_start: 0.9090 (m-30) cc_final: 0.8819 (p0) REVERT: A 2097 GLU cc_start: 0.8765 (pt0) cc_final: 0.8561 (pt0) REVERT: A 2156 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 2667 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8126 (ptt) REVERT: B 96 GLU cc_start: 0.4798 (OUTLIER) cc_final: 0.4455 (mt-10) REVERT: B 542 LEU cc_start: 0.8987 (tp) cc_final: 0.8652 (mt) REVERT: B 732 MET cc_start: 0.8201 (mmp) cc_final: 0.7881 (tpp) REVERT: B 748 LYS cc_start: 0.8385 (tptp) cc_final: 0.7969 (mttt) REVERT: B 949 MET cc_start: 0.7368 (mmp) cc_final: 0.6608 (ttp) REVERT: B 1018 PHE cc_start: 0.8491 (t80) cc_final: 0.8219 (t80) REVERT: B 1454 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8344 (tptp) REVERT: B 1539 LEU cc_start: 0.9108 (mm) cc_final: 0.8821 (mm) REVERT: B 1556 TYR cc_start: 0.8706 (t80) cc_final: 0.8066 (m-80) REVERT: B 1590 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8310 (tt) REVERT: B 1693 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7110 (p0) REVERT: B 1714 MET cc_start: 0.8612 (mmm) cc_final: 0.8381 (mmm) REVERT: B 1755 MET cc_start: 0.9157 (mpp) cc_final: 0.8867 (pmm) REVERT: B 1907 ARG cc_start: 0.8427 (ptp-170) cc_final: 0.8121 (mtt90) REVERT: B 1916 MET cc_start: 0.9212 (mmm) cc_final: 0.8983 (mmm) REVERT: B 1935 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: B 2097 GLU cc_start: 0.8741 (pt0) cc_final: 0.8532 (pt0) REVERT: B 2156 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 2411 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8136 (pp20) REVERT: B 2962 MET cc_start: 0.6290 (ptp) cc_final: 0.5961 (mmm) outliers start: 96 outliers final: 59 residues processed: 482 average time/residue: 0.5292 time to fit residues: 436.8194 Evaluate side-chains 447 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 378 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1336 PHE 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 1628 MET Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2092 CYS 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 2261 LEU 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 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 A residue 2667 MET Chi-restraints excluded: chain A residue 2873 VAL Chi-restraints excluded: chain A residue 2936 GLU 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 291 HIS Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1478 GLN 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 1590 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1711 THR Chi-restraints excluded: chain B residue 1756 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 2016 ASP Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 CYS Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2261 LEU Chi-restraints excluded: chain B residue 2293 LEU Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2356 ILE 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 2557 LEU Chi-restraints excluded: chain B residue 2624 CYS Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2873 VAL Chi-restraints excluded: chain B residue 2936 GLU Chi-restraints excluded: chain B residue 3011 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 178 optimal weight: 1.9990 chunk 477 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 311 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 531 optimal weight: 0.9980 chunk 440 optimal weight: 7.9990 chunk 245 optimal weight: 0.0040 chunk 44 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 278 optimal weight: 0.4980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN ** A1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2565 ASN ** 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 ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1395 ASN ** 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: 0.8086 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 44992 Z= 0.146 Angle : 0.564 14.517 60798 Z= 0.266 Chirality : 0.037 0.244 6980 Planarity : 0.003 0.053 7648 Dihedral : 4.210 79.611 5968 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.69 % Allowed : 13.59 % Favored : 84.72 % 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: 2.17 (0.12), residues: 5426 helix: 2.04 (0.09), residues: 3830 sheet: 0.18 (0.63), residues: 62 loop : 0.00 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B2491 HIS 0.009 0.001 HIS A1443 PHE 0.023 0.001 PHE B 505 TYR 0.031 0.001 TYR A 313 ARG 0.007 0.000 ARG B3008 *********************** 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 502 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 419 time to evaluate : 5.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 MET cc_start: 0.7374 (mmm) cc_final: 0.6991 (mmm) REVERT: A 660 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5588 (mmp) REVERT: A 732 MET cc_start: 0.5782 (tpp) cc_final: 0.3475 (ptm) REVERT: A 1199 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: A 1209 PHE cc_start: 0.5460 (t80) cc_final: 0.4917 (t80) REVERT: A 1210 MET cc_start: 0.7323 (mmm) cc_final: 0.6601 (ptp) REVERT: A 1295 LEU cc_start: 0.7451 (mm) cc_final: 0.7118 (mm) REVERT: A 1539 LEU cc_start: 0.9133 (mm) cc_final: 0.8826 (mm) REVERT: A 1556 TYR cc_start: 0.7962 (m-80) cc_final: 0.7567 (m-80) REVERT: A 1572 LYS cc_start: 0.9367 (mtpt) cc_final: 0.9019 (tppt) REVERT: A 1661 HIS cc_start: 0.7454 (m-70) cc_final: 0.7204 (m-70) REVERT: A 1693 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7171 (p0) REVERT: A 1767 PHE cc_start: 0.7620 (m-80) cc_final: 0.7331 (m-80) REVERT: A 1807 LYS cc_start: 0.9501 (tmmt) cc_final: 0.9139 (mmtm) REVERT: A 1823 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8813 (tt) REVERT: A 1836 ASP cc_start: 0.9084 (m-30) cc_final: 0.8833 (p0) REVERT: A 1906 GLN cc_start: 0.8857 (mp10) cc_final: 0.8587 (mp10) REVERT: A 2097 GLU cc_start: 0.8726 (pt0) cc_final: 0.8515 (pt0) REVERT: A 2156 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7901 (tm-30) REVERT: A 2667 MET cc_start: 0.8509 (ptt) cc_final: 0.8186 (ptt) REVERT: B 96 GLU cc_start: 0.4787 (OUTLIER) cc_final: 0.4443 (mt-10) REVERT: B 732 MET cc_start: 0.8150 (mmp) cc_final: 0.7888 (tpp) REVERT: B 748 LYS cc_start: 0.8396 (tptp) cc_final: 0.7924 (mttt) REVERT: B 806 LEU cc_start: 0.5941 (mm) cc_final: 0.5410 (mt) REVERT: B 949 MET cc_start: 0.7355 (mmp) cc_final: 0.6592 (ttp) REVERT: B 1454 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8341 (tptp) REVERT: B 1539 LEU cc_start: 0.9133 (mm) cc_final: 0.8857 (mm) REVERT: B 1556 TYR cc_start: 0.8700 (t80) cc_final: 0.8073 (m-80) REVERT: B 1590 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8303 (tt) REVERT: B 1661 HIS cc_start: 0.7437 (m-70) cc_final: 0.7191 (m-70) REVERT: B 1693 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7128 (p0) REVERT: B 1830 MET cc_start: 0.8853 (tmm) cc_final: 0.8327 (tmm) REVERT: B 1907 ARG cc_start: 0.8434 (ptp-170) cc_final: 0.8139 (mtt90) REVERT: B 1916 MET cc_start: 0.9154 (mmm) cc_final: 0.8712 (mmm) REVERT: B 1935 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: B 2052 GLU cc_start: 0.8646 (tp30) cc_final: 0.8435 (tp30) REVERT: B 2156 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 2411 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8125 (pp20) outliers start: 83 outliers final: 53 residues processed: 471 average time/residue: 0.5260 time to fit residues: 428.0917 Evaluate side-chains 440 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 378 time to evaluate : 5.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1336 PHE Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1628 MET Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2084 LEU Chi-restraints excluded: chain A residue 2092 CYS Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE 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 2356 ILE Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2873 VAL Chi-restraints excluded: chain A residue 2936 GLU 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 291 HIS Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1478 GLN 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 1590 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1693 ASP 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 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 2261 LEU Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2356 ILE 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 2557 LEU Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2936 GLU Chi-restraints excluded: chain B residue 3011 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 512 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 302 optimal weight: 40.0000 chunk 387 optimal weight: 9.9990 chunk 300 optimal weight: 30.0000 chunk 447 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 chunk 529 optimal weight: 2.9990 chunk 331 optimal weight: 0.4980 chunk 322 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN A 605 HIS ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN A1230 ASN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1690 HIS A1839 GLN A2101 GLN ** A2208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2494 ASN A2542 ASN ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2788 HIS B 201 GLN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1690 HIS B1839 GLN ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2565 ASN ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2788 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 44992 Z= 0.428 Angle : 0.769 15.698 60798 Z= 0.386 Chirality : 0.044 0.223 6980 Planarity : 0.005 0.061 7648 Dihedral : 4.801 73.861 5968 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.78 % Favored : 97.20 % Rotamer: Outliers : 2.04 % Allowed : 14.18 % Favored : 83.78 % 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: 1.22 (0.11), residues: 5426 helix: 1.32 (0.08), residues: 3880 sheet: -0.01 (0.58), residues: 66 loop : -0.38 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1710 HIS 0.012 0.002 HIS B2111 PHE 0.032 0.003 PHE A2846 TYR 0.024 0.002 TYR B1753 ARG 0.030 0.001 ARG B1466 *********************** 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 490 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 390 time to evaluate : 5.029 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 624 MET cc_start: 0.7886 (mmm) cc_final: 0.7408 (mmm) REVERT: A 1209 PHE cc_start: 0.5292 (t80) cc_final: 0.4862 (t80) REVERT: A 1210 MET cc_start: 0.7622 (mmm) cc_final: 0.6972 (ptp) REVERT: A 1221 TRP cc_start: 0.3066 (t-100) cc_final: 0.2597 (t-100) REVERT: A 1295 LEU cc_start: 0.7454 (mm) cc_final: 0.7134 (mm) REVERT: A 1410 LYS cc_start: 0.8899 (mmtp) cc_final: 0.8601 (mttt) REVERT: A 1565 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: A 1693 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7587 (p0) REVERT: A 1916 MET cc_start: 0.9312 (mmm) cc_final: 0.8991 (mmm) REVERT: A 2156 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 2294 GLU cc_start: 0.8964 (tp30) cc_final: 0.8735 (tp30) REVERT: B 96 GLU cc_start: 0.4661 (OUTLIER) cc_final: 0.4289 (mt-10) REVERT: B 542 LEU cc_start: 0.8942 (tp) cc_final: 0.8573 (mt) REVERT: B 732 MET cc_start: 0.8037 (mmp) cc_final: 0.7774 (tpp) REVERT: B 949 MET cc_start: 0.7387 (mmp) cc_final: 0.6708 (ttt) REVERT: B 1022 ILE cc_start: 0.8976 (mm) cc_final: 0.8696 (pt) REVERT: B 1308 MET cc_start: 0.5740 (tmm) cc_final: 0.5488 (tmm) REVERT: B 1454 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8251 (tmtt) REVERT: B 1470 TYR cc_start: 0.9363 (m-80) cc_final: 0.9131 (m-80) REVERT: B 1539 LEU cc_start: 0.9271 (mm) cc_final: 0.9057 (mm) REVERT: B 1693 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7560 (p0) REVERT: B 1839 GLN cc_start: 0.9172 (mt0) cc_final: 0.8893 (mt0) REVERT: B 1916 MET cc_start: 0.9388 (mmm) cc_final: 0.9066 (mmm) REVERT: B 1935 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8555 (m-30) REVERT: B 2156 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 2962 MET cc_start: 0.6896 (ptp) cc_final: 0.6593 (mmm) outliers start: 100 outliers final: 53 residues processed: 464 average time/residue: 0.5216 time to fit residues: 417.0426 Evaluate side-chains 402 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 344 time to evaluate : 4.363 ------------------------------------------------------------------------------- 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 1336 PHE 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 1628 MET Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 2092 CYS Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2204 LYS 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 2557 LEU Chi-restraints excluded: chain A residue 2636 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 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 997 VAL Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1452 ASP Chi-restraints excluded: chain B residue 1461 TRP 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 1637 ASP Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1693 ASP 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 1822 GLU Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2092 CYS Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2204 LYS Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2860 SER Chi-restraints excluded: chain B residue 2886 VAL Chi-restraints excluded: chain B residue 2936 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 327 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 316 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 336 optimal weight: 6.9990 chunk 360 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 415 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 HIS ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 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** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1867 GLN ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3038 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 44992 Z= 0.162 Angle : 0.627 17.746 60798 Z= 0.297 Chirality : 0.039 0.243 6980 Planarity : 0.004 0.074 7648 Dihedral : 4.421 78.960 5968 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.33 % Allowed : 15.36 % Favored : 83.31 % 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: 1.78 (0.12), residues: 5426 helix: 1.73 (0.09), residues: 3858 sheet: 0.18 (0.59), residues: 66 loop : -0.14 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B2104 HIS 0.009 0.001 HIS B1443 PHE 0.029 0.001 PHE B 626 TYR 0.028 0.001 TYR A 313 ARG 0.008 0.000 ARG B1466 *********************** 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 478 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 413 time to evaluate : 5.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 MET cc_start: 0.7763 (mmm) cc_final: 0.7337 (mmm) REVERT: A 1209 PHE cc_start: 0.5289 (t80) cc_final: 0.4877 (t80) REVERT: A 1210 MET cc_start: 0.7766 (mmm) cc_final: 0.7119 (ptp) REVERT: A 1295 LEU cc_start: 0.7489 (mm) cc_final: 0.7170 (mm) REVERT: A 1410 LYS cc_start: 0.8837 (mmtp) cc_final: 0.8530 (mttt) REVERT: A 1556 TYR cc_start: 0.8772 (t80) cc_final: 0.8300 (m-10) REVERT: A 1565 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: A 1572 LYS cc_start: 0.9339 (ptpp) cc_final: 0.9008 (tppt) REVERT: A 1693 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7252 (p0) REVERT: A 1767 PHE cc_start: 0.7513 (m-80) cc_final: 0.6737 (m-80) REVERT: A 1906 GLN cc_start: 0.9151 (mp10) cc_final: 0.8743 (mp10) REVERT: A 1915 TYR cc_start: 0.9068 (t80) cc_final: 0.8652 (t80) REVERT: A 1916 MET cc_start: 0.9221 (mmm) cc_final: 0.8955 (mmm) REVERT: A 2156 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8006 (tm-30) REVERT: A 2235 MET cc_start: 0.8872 (mmt) cc_final: 0.8536 (mmm) REVERT: A 2520 MET cc_start: 0.8893 (mmm) cc_final: 0.8619 (tpp) REVERT: A 2532 MET cc_start: 0.5789 (mtt) cc_final: 0.5174 (ppp) REVERT: A 2616 MET cc_start: 0.8654 (tpp) cc_final: 0.8447 (tpp) REVERT: A 2667 MET cc_start: 0.8707 (ptt) cc_final: 0.8448 (ptt) REVERT: A 2762 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 2939 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8256 (mtt180) REVERT: B 96 GLU cc_start: 0.4680 (OUTLIER) cc_final: 0.4307 (mt-10) REVERT: B 732 MET cc_start: 0.8083 (mmp) cc_final: 0.7873 (tpp) REVERT: B 806 LEU cc_start: 0.6023 (mm) cc_final: 0.5593 (mt) REVERT: B 949 MET cc_start: 0.7376 (mmp) cc_final: 0.6619 (ttp) REVERT: B 1094 ASN cc_start: 0.9185 (p0) cc_final: 0.8792 (p0) REVERT: B 1210 MET cc_start: 0.8949 (mmp) cc_final: 0.7751 (ptp) REVERT: B 1308 MET cc_start: 0.5665 (tmm) cc_final: 0.5428 (tmm) REVERT: B 1454 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8229 (tptp) REVERT: B 1475 TYR cc_start: 0.8968 (m-80) cc_final: 0.8424 (m-10) REVERT: B 1539 LEU cc_start: 0.9255 (mm) cc_final: 0.9028 (mm) REVERT: B 1693 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7188 (p0) REVERT: B 1916 MET cc_start: 0.9289 (mmm) cc_final: 0.8973 (mmm) REVERT: B 1935 ASP cc_start: 0.8977 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: B 2156 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8102 (tm-30) REVERT: B 2235 MET cc_start: 0.8900 (mmt) cc_final: 0.8557 (mmm) REVERT: B 2962 MET cc_start: 0.6785 (ptp) cc_final: 0.6417 (mmm) outliers start: 65 outliers final: 41 residues processed: 454 average time/residue: 0.5315 time to fit residues: 415.5228 Evaluate side-chains 418 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 371 time to evaluate : 5.145 ------------------------------------------------------------------------------- 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 1519 VAL 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 1693 ASP Chi-restraints excluded: chain A residue 2084 LEU Chi-restraints excluded: chain A residue 2092 CYS 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 2519 LEU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2936 GLU Chi-restraints excluded: chain A residue 2939 ARG Chi-restraints excluded: chain A residue 3011 MET 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 1018 PHE Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1755 MET 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 1935 ASP Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 CYS Chi-restraints excluded: chain B residue 2157 GLU 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 2429 GLU Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2936 GLU Chi-restraints excluded: chain B residue 3011 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 549 random chunks: chunk 481 optimal weight: 2.9990 chunk 506 optimal weight: 9.9990 chunk 462 optimal weight: 0.5980 chunk 493 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 387 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 445 optimal weight: 4.9990 chunk 466 optimal weight: 0.9980 chunk 491 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 HIS ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 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** ** B1477 ASN ** 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: 0.8217 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 44992 Z= 0.162 Angle : 0.622 16.780 60798 Z= 0.293 Chirality : 0.038 0.270 6980 Planarity : 0.004 0.057 7648 Dihedral : 4.215 73.487 5968 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.08 % Allowed : 15.79 % Favored : 83.13 % 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: 1.87 (0.12), residues: 5426 helix: 1.83 (0.09), residues: 3854 sheet: 0.19 (0.59), residues: 66 loop : -0.15 (0.17), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1221 HIS 0.010 0.001 HIS A 993 PHE 0.031 0.001 PHE B 626 TYR 0.031 0.001 TYR A 313 ARG 0.011 0.000 ARG A2618 *********************** 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 438 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 385 time to evaluate : 5.058 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 624 MET cc_start: 0.7759 (mmm) cc_final: 0.7327 (mmm) REVERT: A 660 MET cc_start: 0.6426 (mmp) cc_final: 0.6213 (mmp) REVERT: A 732 MET cc_start: 0.4995 (mmm) cc_final: 0.4265 (tpp) REVERT: A 1209 PHE cc_start: 0.5315 (t80) cc_final: 0.4912 (t80) REVERT: A 1210 MET cc_start: 0.7807 (mmm) cc_final: 0.7158 (ptp) REVERT: A 1295 LEU cc_start: 0.7452 (mm) cc_final: 0.7134 (mm) REVERT: A 1308 MET cc_start: 0.5134 (ppp) cc_final: 0.4926 (ppp) REVERT: A 1397 HIS cc_start: 0.6058 (t70) cc_final: 0.5636 (t70) REVERT: A 1410 LYS cc_start: 0.8836 (mmtp) cc_final: 0.8521 (mttt) REVERT: A 1556 TYR cc_start: 0.8772 (t80) cc_final: 0.8274 (m-10) REVERT: A 1565 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: A 1572 LYS cc_start: 0.9343 (ptpp) cc_final: 0.9017 (tppt) REVERT: A 1693 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7215 (p0) REVERT: A 1767 PHE cc_start: 0.7553 (m-80) cc_final: 0.6775 (m-80) REVERT: A 2200 GLU cc_start: 0.9173 (pt0) cc_final: 0.8926 (pp20) REVERT: A 2235 MET cc_start: 0.8914 (mmt) cc_final: 0.8618 (mmm) REVERT: A 2520 MET cc_start: 0.8822 (mmm) cc_final: 0.8599 (tpp) REVERT: A 2532 MET cc_start: 0.5898 (mtt) cc_final: 0.5246 (ppp) REVERT: A 2667 MET cc_start: 0.8720 (ptt) cc_final: 0.8458 (ptt) REVERT: A 2821 MET cc_start: 0.9249 (mmm) cc_final: 0.9030 (mmm) REVERT: B 96 GLU cc_start: 0.4861 (OUTLIER) cc_final: 0.4498 (mt-10) REVERT: B 732 MET cc_start: 0.8131 (mmp) cc_final: 0.7929 (tpp) REVERT: B 806 LEU cc_start: 0.6019 (mm) cc_final: 0.5547 (mt) REVERT: B 949 MET cc_start: 0.7384 (mmp) cc_final: 0.6636 (ttp) REVERT: B 1094 ASN cc_start: 0.9189 (p0) cc_final: 0.8805 (p0) REVERT: B 1308 MET cc_start: 0.5641 (tmm) cc_final: 0.5400 (tmm) REVERT: B 1443 HIS cc_start: 0.9210 (t-90) cc_final: 0.8845 (t-90) REVERT: B 1454 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8299 (tptp) REVERT: B 1539 LEU cc_start: 0.9239 (mm) cc_final: 0.9017 (mm) REVERT: B 1693 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7427 (p0) REVERT: B 1830 MET cc_start: 0.9011 (tmm) cc_final: 0.8614 (tmm) REVERT: B 1916 MET cc_start: 0.9254 (mmm) cc_final: 0.8887 (mmm) REVERT: B 1935 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8320 (m-30) REVERT: B 2156 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8070 (tm-30) REVERT: B 2235 MET cc_start: 0.8903 (mmt) cc_final: 0.8585 (mmm) REVERT: B 2450 LEU cc_start: 0.9545 (tt) cc_final: 0.9027 (mm) REVERT: B 2962 MET cc_start: 0.6709 (ptp) cc_final: 0.6385 (mmm) outliers start: 53 outliers final: 41 residues processed: 422 average time/residue: 0.5183 time to fit residues: 378.1139 Evaluate side-chains 420 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 374 time to evaluate : 4.874 ------------------------------------------------------------------------------- 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 1332 ILE 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 1678 VAL Chi-restraints excluded: chain A residue 1693 ASP 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 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 2519 LEU Chi-restraints excluded: chain A residue 2557 LEU 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 291 HIS 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 1295 LEU Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1693 ASP 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 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2429 GLU Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2557 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: 8.9990 chunk 521 optimal weight: 0.7980 chunk 318 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 362 optimal weight: 0.0670 chunk 546 optimal weight: 0.2980 chunk 503 optimal weight: 7.9990 chunk 435 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 336 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** 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: 0.8208 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 44992 Z= 0.158 Angle : 0.628 16.615 60798 Z= 0.293 Chirality : 0.038 0.319 6980 Planarity : 0.004 0.086 7648 Dihedral : 4.118 71.788 5968 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.06 % Allowed : 15.81 % Favored : 83.13 % 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: 1.95 (0.12), residues: 5426 helix: 1.89 (0.09), residues: 3832 sheet: 0.21 (0.60), residues: 66 loop : -0.12 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A1221 HIS 0.010 0.001 HIS A 993 PHE 0.031 0.001 PHE B 626 TYR 0.032 0.001 TYR A 313 ARG 0.010 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 440 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 388 time to evaluate : 4.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 MET cc_start: 0.7744 (mmm) cc_final: 0.7307 (mmm) REVERT: A 1209 PHE cc_start: 0.5319 (t80) cc_final: 0.4922 (t80) REVERT: A 1210 MET cc_start: 0.7870 (mmm) cc_final: 0.7221 (ptp) REVERT: A 1295 LEU cc_start: 0.7475 (mm) cc_final: 0.7149 (mm) REVERT: A 1397 HIS cc_start: 0.5939 (t70) cc_final: 0.5523 (t70) REVERT: A 1410 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8514 (mttt) REVERT: A 1556 TYR cc_start: 0.8770 (t80) cc_final: 0.8224 (m-10) REVERT: A 1565 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: A 1572 LYS cc_start: 0.9343 (ptpp) cc_final: 0.9026 (tppt) REVERT: A 1693 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7257 (p0) REVERT: A 1767 PHE cc_start: 0.7585 (m-80) cc_final: 0.6842 (m-80) REVERT: A 2160 LYS cc_start: 0.9316 (mtmt) cc_final: 0.9052 (mmmt) REVERT: A 2200 GLU cc_start: 0.9168 (pt0) cc_final: 0.8927 (pp20) REVERT: A 2294 GLU cc_start: 0.8452 (tp30) cc_final: 0.8226 (tp30) REVERT: A 2532 MET cc_start: 0.5826 (mtt) cc_final: 0.5247 (ppp) REVERT: A 2667 MET cc_start: 0.8690 (ptt) cc_final: 0.8430 (ptt) REVERT: A 2821 MET cc_start: 0.9226 (mmm) cc_final: 0.8987 (mmm) REVERT: B 96 GLU cc_start: 0.4853 (OUTLIER) cc_final: 0.4487 (mt-10) REVERT: B 732 MET cc_start: 0.8147 (mmp) cc_final: 0.7936 (tpp) REVERT: B 806 LEU cc_start: 0.6002 (mm) cc_final: 0.5536 (mt) REVERT: B 949 MET cc_start: 0.7382 (mmp) cc_final: 0.6621 (ttp) REVERT: B 1094 ASN cc_start: 0.9180 (p0) cc_final: 0.8792 (p0) REVERT: B 1210 MET cc_start: 0.8933 (mmp) cc_final: 0.7792 (ptp) REVERT: B 1308 MET cc_start: 0.5555 (tmm) cc_final: 0.5330 (tmm) REVERT: B 1443 HIS cc_start: 0.9210 (t-90) cc_final: 0.8896 (t-90) REVERT: B 1454 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8295 (tptp) REVERT: B 1539 LEU cc_start: 0.9233 (mm) cc_final: 0.8997 (mt) REVERT: B 1693 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7442 (p0) REVERT: B 1916 MET cc_start: 0.9202 (mmm) cc_final: 0.8852 (mmm) REVERT: B 1935 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: B 2156 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 2235 MET cc_start: 0.8881 (mmt) cc_final: 0.8582 (mmm) REVERT: B 2450 LEU cc_start: 0.9546 (tt) cc_final: 0.9025 (mm) REVERT: B 2520 MET cc_start: 0.8827 (mmm) cc_final: 0.8583 (tpp) REVERT: B 2762 GLN cc_start: 0.8750 (mt0) cc_final: 0.8546 (mp10) outliers start: 52 outliers final: 42 residues processed: 423 average time/residue: 0.5151 time to fit residues: 378.4274 Evaluate side-chains 428 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 381 time to evaluate : 5.029 ------------------------------------------------------------------------------- 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 1332 ILE 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 1678 VAL Chi-restraints excluded: chain A residue 1681 ILE Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 2084 LEU Chi-restraints excluded: chain A residue 2092 CYS 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 2519 LEU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2557 LEU 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 291 HIS 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 1295 LEU Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1755 MET 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 2163 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2546 SER Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2936 GLU Chi-restraints excluded: chain B residue 3011 MET 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: 5.9990 chunk 463 optimal weight: 3.9990 chunk 133 optimal weight: 0.0050 chunk 401 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 436 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 447 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN A1230 ASN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2430 HIS ** 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** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2430 HIS ** B2603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.141428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.091856 restraints weight = 132854.334| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 5.18 r_work: 0.3295 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 44992 Z= 0.159 Angle : 0.624 17.168 60798 Z= 0.290 Chirality : 0.038 0.297 6980 Planarity : 0.004 0.053 7648 Dihedral : 4.041 68.004 5968 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.94 % Allowed : 16.24 % Favored : 82.82 % 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: 1.97 (0.12), residues: 5426 helix: 1.91 (0.09), residues: 3850 sheet: 0.21 (0.61), residues: 66 loop : -0.13 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1933 HIS 0.010 0.001 HIS A 993 PHE 0.032 0.001 PHE B 626 TYR 0.032 0.001 TYR A 313 ARG 0.010 0.000 ARG A2618 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12580.35 seconds wall clock time: 226 minutes 11.92 seconds (13571.92 seconds total)