Starting phenix.real_space_refine on Thu Dec 26 13:41:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oxp_17267/12_2024/8oxp_17267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxp_17267/12_2024/8oxp_17267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oxp_17267/12_2024/8oxp_17267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxp_17267/12_2024/8oxp_17267.map" model { file = "/net/cci-nas-00/data/ceres_data/8oxp_17267/12_2024/8oxp_17267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxp_17267/12_2024/8oxp_17267.cif" } resolution = 2.6 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= 0.015 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 306 5.16 5 C 28406 2.51 5 N 7556 2.21 5 O 8182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44460 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 22197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2772, 22197 Classifications: {'peptide': 2772} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2683} Chain breaks: 18 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: "B" Number of atoms: 22197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2772, 22197 Classifications: {'peptide': 2772} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2683} Chain breaks: 18 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 13455 SG CYS A1899 81.657 49.513 122.467 1.00269.33 S ATOM 13461 SG CYS A1900 79.712 51.597 121.450 1.00264.27 S ATOM 35652 SG CYS B1899 98.346 134.009 122.480 1.00269.62 S ATOM 35658 SG CYS B1900 100.286 131.926 121.447 1.00260.90 S Time building chain proxies: 23.71, per 1000 atoms: 0.53 Number of scatterers: 44460 At special positions: 0 Unit cell: (180.894, 184.198, 210.63, 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 306 16.00 P 6 15.00 Mg 2 11.99 O 8182 8.00 N 7556 7.00 C 28406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.03 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3103 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1899 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1900 " pdb="ZN ZN A3103 " - pdb=" ND1 HIS A1876 " pdb=" ZN B3103 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1899 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1900 " pdb="ZN ZN B3103 " - pdb=" ND1 HIS B1876 " 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10664 Finding SS restraints... Secondary structure from input PDB file: 315 helices and 8 sheets defined 76.7% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.78 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 19 through 34 removed outlier: 4.188A pdb=" N LYS A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 57 through 74 removed outlier: 3.749A pdb=" N GLU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 109 removed outlier: 4.206A pdb=" N LYS A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 95 " --> pdb=" O GLN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.764A pdb=" N LEU A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.686A pdb=" N TYR A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.509A pdb=" N THR A 202 " --> pdb=" O CYS A 198 " (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 223 removed outlier: 3.777A pdb=" N PHE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 243 Processing helix chain 'A' and resid 247 through 269 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: 4.382A 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: 4.190A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 423 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 424 through 427 removed outlier: 3.832A 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 451 through 468 Processing helix chain 'A' and resid 473 through 493 removed outlier: 3.843A pdb=" N ARG A 493 " --> pdb=" O CYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 514 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.857A pdb=" N TRP A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 525' Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.504A 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 Processing helix chain 'A' and resid 645 through 656 Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 712 through 732 removed outlier: 3.556A pdb=" N MET A 732 " --> pdb=" O CYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 743 removed outlier: 3.681A pdb=" N LYS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 766 removed outlier: 3.583A pdb=" N SER A 751 " --> pdb=" O GLN A 747 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 759 " --> pdb=" O CYS A 755 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 787 removed outlier: 4.201A pdb=" N GLY A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 775 " --> pdb=" O PHE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 807 Processing helix chain 'A' and resid 808 through 823 removed outlier: 3.604A pdb=" N MET A 812 " --> pdb=" O THR A 808 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 891 through 912 removed outlier: 4.367A pdb=" N GLN A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 931 removed outlier: 3.926A pdb=" N ILE A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 954 removed outlier: 3.530A pdb=" N TYR A 947 " --> pdb=" O HIS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 971 removed outlier: 3.584A pdb=" N VAL A 966 " --> pdb=" O PRO A 962 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 967 " --> pdb=" O MET A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 983 through 995 removed outlier: 3.536A pdb=" N LEU A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1008 through 1031 removed outlier: 3.683A pdb=" N VAL A1021 " --> pdb=" O GLN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1053 Processing helix chain 'A' and resid 1070 through 1077 removed outlier: 3.653A pdb=" N THR A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.659A pdb=" N MET A1087 " --> pdb=" O HIS A1083 " (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 Processing helix chain 'A' and resid 1168 through 1182 removed outlier: 4.050A 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 1224 removed outlier: 3.878A pdb=" N PHE A1209 " --> pdb=" O ARG A1205 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS A1213 " --> pdb=" O PHE A1209 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP A1215 " --> pdb=" O ALA A1211 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TYR A1216 " --> pdb=" O SER A1212 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1234 Processing helix chain 'A' and resid 1235 through 1239 Processing helix chain 'A' and resid 1243 through 1262 removed outlier: 6.090A pdb=" N LYS A1253 " --> pdb=" O ARG A1249 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A1254 " --> pdb=" O SER A1250 " (cutoff:3.500A) Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1264 through 1276 removed outlier: 3.551A pdb=" N GLN A1274 " --> pdb=" O SER A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1286 removed outlier: 3.547A pdb=" N CYS A1286 " --> pdb=" O LEU A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1295 removed outlier: 3.896A pdb=" N ASN A1293 " --> pdb=" O LYS A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1305 through 1323 removed outlier: 3.784A pdb=" N GLN A1310 " --> pdb=" O SER A1306 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN A1311 " --> pdb=" O GLY A1307 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A1312 " --> pdb=" O MET A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1330 removed outlier: 4.037A pdb=" N LYS A1330 " --> pdb=" O LEU A1327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1327 through 1330' Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1339 through 1350 removed outlier: 4.455A pdb=" N ILE A1343 " --> pdb=" O ASN A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1397 Processing helix chain 'A' and resid 1403 through 1409 removed outlier: 4.356A pdb=" N ILE A1407 " --> pdb=" O SER A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1429 removed outlier: 3.652A 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 1460 through 1478 Processing helix chain 'A' and resid 1484 through 1509 Processing helix chain 'A' and resid 1512 through 1515 removed outlier: 4.335A pdb=" N ASN A1515 " --> pdb=" O ALA A1512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1512 through 1515' Processing helix chain 'A' and resid 1516 through 1525 Processing helix chain 'A' and resid 1526 through 1529 Processing helix chain 'A' and resid 1531 through 1546 removed outlier: 3.639A pdb=" N GLN A1537 " --> pdb=" O GLU A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 3.545A pdb=" N LYS A1560 " --> pdb=" O TYR A1556 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A1561 " --> pdb=" O ILE A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1583 Processing helix chain 'A' and resid 1589 through 1602 removed outlier: 3.514A pdb=" N VAL A1600 " --> pdb=" O HIS A1596 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A1601 " --> pdb=" O PHE A1597 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A1602 " --> pdb=" O LEU A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1606 through 1609 Processing helix chain 'A' and resid 1610 through 1624 Processing helix chain 'A' and resid 1624 through 1633 removed outlier: 3.811A pdb=" N MET A1628 " --> pdb=" O HIS A1624 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A1629 " --> pdb=" O LYS A1625 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A1630 " --> pdb=" O ASP A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1641 removed outlier: 3.799A pdb=" N ASP A1641 " --> pdb=" O ASN A1638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1638 through 1641' Processing helix chain 'A' and resid 1642 through 1659 Processing helix chain 'A' and resid 1663 through 1678 removed outlier: 4.212A pdb=" N VAL A1667 " --> pdb=" O GLY A1663 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A1678 " --> pdb=" O CYS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1703 removed outlier: 3.882A pdb=" N PHE A1703 " --> pdb=" O ALA A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1721 Processing helix chain 'A' and resid 1722 through 1724 No H-bonds generated for 'chain 'A' and resid 1722 through 1724' Processing helix chain 'A' and resid 1726 through 1743 removed outlier: 3.551A pdb=" N ARG A1730 " --> pdb=" O CYS A1726 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A1743 " --> pdb=" O ASN A1739 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1754 removed outlier: 3.531A pdb=" N GLU A1751 " --> pdb=" O HIS A1747 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A1752 " --> pdb=" O SER A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 4.161A pdb=" N ALA A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1796 Processing helix chain 'A' and resid 1801 through 1816 Processing helix chain 'A' and resid 1821 through 1826 removed outlier: 3.918A pdb=" N GLN A1825 " --> pdb=" O CYS A1821 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1821 through 1826' Processing helix chain 'A' and resid 1827 through 1832 Processing helix chain 'A' and resid 1834 through 1852 removed outlier: 3.681A pdb=" N CYS A1838 " --> pdb=" O LYS A1834 " (cutoff:3.500A) Proline residue: A1843 - end of helix removed outlier: 4.038A pdb=" N GLN A1852 " --> pdb=" O ASP A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1875 Processing helix chain 'A' and resid 1902 through 1918 removed outlier: 3.553A pdb=" N GLN A1906 " --> pdb=" O ASP A1902 " (cutoff:3.500A) removed outlier: 3.871A 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: 3.558A 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 1998 Processing helix chain 'A' and resid 2000 through 2013 removed outlier: 3.603A pdb=" N LEU A2006 " --> pdb=" O GLN A2002 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A2007 " --> pdb=" O ASP A2003 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A2008 " --> pdb=" O LEU A2004 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2020 removed outlier: 3.587A pdb=" N LEU A2018 " --> pdb=" O PRO A2015 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2039 Processing helix chain 'A' and resid 2041 through 2052 Processing helix chain 'A' and resid 2056 through 2071 removed outlier: 3.790A pdb=" N ALA A2062 " --> pdb=" O SER A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2073 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 2139 through 2161 removed outlier: 3.527A pdb=" N VAL A2155 " --> pdb=" O ARG A2151 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A2157 " --> pdb=" O LYS A2153 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A2158 " --> pdb=" O GLU A2154 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2167 No H-bonds generated for 'chain 'A' and resid 2165 through 2167' Processing helix chain 'A' and resid 2168 through 2191 removed outlier: 4.592A pdb=" N THR A2172 " --> pdb=" O SER A2168 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A2187 " --> pdb=" O GLU A2183 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A2188 " --> pdb=" O SER A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2211 removed outlier: 3.646A pdb=" N LEU A2211 " --> pdb=" O LYS A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2216 through 2237 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2244 through 2265 Processing helix chain 'A' and resid 2268 through 2282 removed outlier: 3.721A pdb=" N TYR A2281 " --> pdb=" O GLN A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2289 through 2302 removed outlier: 3.814A pdb=" N LEU A2293 " --> pdb=" O SER A2289 " (cutoff:3.500A) Processing helix chain 'A' and resid 2304 through 2323 Processing helix chain 'A' and resid 2327 through 2349 removed outlier: 4.015A pdb=" N LEU A2332 " --> pdb=" O PRO A2328 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A2333 " --> pdb=" O SER A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2360 Processing helix chain 'A' and resid 2360 through 2371 removed outlier: 3.667A pdb=" N TYR A2371 " --> pdb=" O VAL A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2407 Processing helix chain 'A' and resid 2407 through 2422 removed outlier: 3.507A pdb=" N LEU A2417 " --> pdb=" O LYS A2413 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A2422 " --> pdb=" O LYS A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2437 through 2476 removed outlier: 4.130A pdb=" N GLU A2449 " --> pdb=" O LEU A2445 " (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 2494 Processing helix chain 'A' and resid 2497 through 2507 Processing helix chain 'A' and resid 2508 through 2511 Processing helix chain 'A' and resid 2512 through 2517 removed outlier: 3.544A pdb=" N LEU A2517 " --> pdb=" O TYR A2514 " (cutoff:3.500A) Processing helix chain 'A' and resid 2519 through 2526 removed outlier: 3.520A pdb=" N ARG A2526 " --> pdb=" O GLN A2522 " (cutoff:3.500A) Processing helix chain 'A' and resid 2536 through 2552 Processing helix chain 'A' and resid 2552 through 2565 removed outlier: 3.536A pdb=" N THR A2556 " --> pdb=" O HIS A2552 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHE A2558 " --> pdb=" O HIS A2554 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE A2559 " --> pdb=" O HIS A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2567 through 2573 removed outlier: 3.772A pdb=" N PHE A2571 " --> pdb=" O ASN A2567 " (cutoff:3.500A) Processing helix chain 'A' and resid 2592 through 2613 removed outlier: 3.884A pdb=" N GLU A2596 " --> pdb=" O SER A2592 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2613 through 2633 removed outlier: 3.592A pdb=" N VAL A2617 " --> pdb=" O ARG A2613 " (cutoff:3.500A) Processing helix chain 'A' and resid 2636 through 2641 removed outlier: 3.681A pdb=" N LYS A2639 " --> pdb=" O THR A2636 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR A2640 " --> pdb=" O GLN A2637 " (cutoff:3.500A) Processing helix chain 'A' and resid 2722 through 2742 removed outlier: 3.532A pdb=" N VAL A2731 " --> pdb=" O VAL A2727 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A2742 " --> pdb=" O LEU A2738 " (cutoff:3.500A) Processing helix chain 'A' and resid 2742 through 2749 removed outlier: 3.956A 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 2808 Processing helix chain 'A' and resid 2812 through 2826 Processing helix chain 'A' and resid 2832 through 2839 removed outlier: 4.064A pdb=" N MET A2836 " --> pdb=" O ARG A2832 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A2838 " --> pdb=" O PHE A2834 " (cutoff:3.500A) Processing helix chain 'A' and resid 2841 through 2866 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 2917 Processing helix chain 'A' and resid 2925 through 2941 Processing helix chain 'A' and resid 2941 through 2954 Processing helix chain 'A' and resid 2963 through 2971 Processing helix chain 'A' and resid 3002 through 3018 Processing helix chain 'A' and resid 3027 through 3041 Processing helix chain 'A' and resid 3041 through 3048 removed outlier: 3.624A pdb=" N ARG A3047 " --> pdb=" O LYS A3043 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A3048 " --> pdb=" O ASN A3044 " (cutoff:3.500A) Processing helix chain 'A' and resid 3049 through 3053 Processing helix chain 'B' and resid 6 through 18 Processing helix chain 'B' and resid 19 through 34 removed outlier: 4.189A pdb=" N LYS B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 57 through 74 removed outlier: 3.750A pdb=" N GLU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 109 removed outlier: 4.206A pdb=" N LYS B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.766A pdb=" N LEU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 148 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 160 through 177 removed outlier: 3.697A pdb=" N TYR B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.509A pdb=" N THR B 202 " --> pdb=" O CYS B 198 " (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 223 removed outlier: 3.778A pdb=" N PHE B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 222 " --> pdb=" O GLN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 269 Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 272 through 291 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 305 through 324 removed outlier: 4.382A 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: 4.189A pdb=" N ILE B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 423 Proline residue: B 411 - end of helix Processing helix chain 'B' and resid 424 through 427 removed outlier: 3.831A 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 451 through 468 Processing helix chain 'B' and resid 473 through 493 removed outlier: 3.841A pdb=" N ARG B 493 " --> pdb=" O CYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 514 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.823A pdb=" N TRP B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 525' Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 535 through 549 removed outlier: 3.544A pdb=" N LEU B 544 " --> pdb=" O CYS B 540 " (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 617 Processing helix chain 'B' and resid 619 through 630 removed outlier: 3.597A pdb=" N ALA B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 630 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 656 Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 712 through 732 removed outlier: 3.542A pdb=" N MET B 732 " --> pdb=" O CYS B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 743 removed outlier: 3.680A pdb=" N LYS B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 766 removed outlier: 3.584A pdb=" N SER B 751 " --> pdb=" O GLN B 747 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 758 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER B 759 " --> pdb=" O CYS B 755 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 787 removed outlier: 4.208A pdb=" N GLY B 774 " --> pdb=" O GLU B 770 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B 775 " --> pdb=" O PHE B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 807 Processing helix chain 'B' and resid 808 through 823 removed outlier: 3.604A pdb=" N MET B 812 " --> pdb=" O THR B 808 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.543A pdb=" N TYR B 889 " --> pdb=" O ALA B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 912 removed outlier: 4.363A pdb=" N GLN B 912 " --> pdb=" O VAL B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 931 removed outlier: 3.936A pdb=" N ILE B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) removed outlier: 3.879A 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 removed outlier: 3.591A pdb=" N VAL B 966 " --> pdb=" O PRO B 962 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 967 " --> pdb=" O MET B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 983 through 995 removed outlier: 3.538A 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 removed outlier: 3.685A pdb=" N VAL B1021 " --> pdb=" O GLN B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1053 Processing helix chain 'B' and resid 1070 through 1077 removed outlier: 3.655A pdb=" N THR B1075 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B1076 " --> pdb=" O GLU B1072 " (cutoff:3.500A) removed outlier: 3.975A 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 1097 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 1182 removed outlier: 4.050A 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 1224 removed outlier: 3.875A pdb=" N PHE B1209 " --> pdb=" O ARG B1205 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS B1213 " --> pdb=" O PHE B1209 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP B1215 " --> pdb=" O ALA B1211 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR B1216 " --> pdb=" O SER B1212 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B1224 " --> pdb=" O GLU B1220 " (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: 6.081A pdb=" N LYS B1253 " --> pdb=" O ARG B1249 " (cutoff:3.500A) removed outlier: 6.380A 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 1276 Processing helix chain 'B' and resid 1278 through 1286 removed outlier: 3.529A pdb=" N CYS B1286 " --> pdb=" O LEU B1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 1286 through 1295 removed outlier: 3.906A pdb=" N ASN B1293 " --> pdb=" O LYS B1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1298 No H-bonds generated for 'chain 'B' and resid 1296 through 1298' Processing helix chain 'B' and resid 1305 through 1323 removed outlier: 3.784A pdb=" N GLN B1310 " --> pdb=" O SER B1306 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN B1311 " --> pdb=" O GLY B1307 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B1312 " --> pdb=" O MET B1308 " (cutoff:3.500A) Processing helix chain 'B' and resid 1327 through 1330 removed outlier: 4.036A 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 Processing helix chain 'B' and resid 1339 through 1349 removed outlier: 4.415A pdb=" N ILE B1343 " --> pdb=" O ASN B1339 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1397 Processing helix chain 'B' and resid 1403 through 1409 removed outlier: 4.334A pdb=" N ILE B1407 " --> pdb=" O SER B1403 " (cutoff:3.500A) Processing helix chain 'B' and resid 1413 through 1429 removed outlier: 3.826A pdb=" N THR B1429 " --> pdb=" O GLN B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1431 through 1452 removed outlier: 3.698A pdb=" N ASP B1452 " --> pdb=" O LEU B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1460 through 1478 Processing helix chain 'B' and resid 1484 through 1509 Processing helix chain 'B' and resid 1512 through 1515 removed outlier: 4.340A pdb=" N ASN B1515 " --> pdb=" O ALA B1512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1512 through 1515' Processing helix chain 'B' and resid 1516 through 1528 Proline residue: B1526 - end of helix Processing helix chain 'B' and resid 1531 through 1547 removed outlier: 3.646A pdb=" N GLN B1537 " --> pdb=" O GLU B1533 " (cutoff:3.500A) Processing helix chain 'B' and resid 1555 through 1562 removed outlier: 3.566A pdb=" N LYS B1560 " --> pdb=" O TYR B1556 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B1561 " --> pdb=" O ILE B1557 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B1562 " --> pdb=" O THR B1558 " (cutoff:3.500A) Processing helix chain 'B' and resid 1571 through 1583 Processing helix chain 'B' and resid 1589 through 1602 removed outlier: 3.528A pdb=" N VAL B1600 " --> pdb=" O HIS B1596 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B1601 " --> pdb=" O PHE B1597 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B1602 " --> pdb=" O LEU B1598 " (cutoff:3.500A) Processing helix chain 'B' and resid 1606 through 1609 Processing helix chain 'B' and resid 1610 through 1624 Processing helix chain 'B' and resid 1624 through 1634 removed outlier: 3.828A pdb=" N MET B1628 " --> pdb=" O HIS B1624 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B1629 " --> pdb=" O LYS B1625 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B1630 " --> pdb=" O ASP B1626 " (cutoff:3.500A) Processing helix chain 'B' and resid 1638 through 1641 removed outlier: 3.759A pdb=" N ASP B1641 " --> pdb=" O ASN B1638 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1638 through 1641' Processing helix chain 'B' and resid 1642 through 1659 Processing helix chain 'B' and resid 1663 through 1678 removed outlier: 4.201A pdb=" N VAL B1667 " --> pdb=" O GLY B1663 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B1678 " --> pdb=" O CYS B1674 " (cutoff:3.500A) Processing helix chain 'B' and resid 1693 through 1703 removed outlier: 3.530A pdb=" N LEU B1702 " --> pdb=" O LYS B1698 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE B1703 " --> pdb=" O ALA B1699 " (cutoff:3.500A) Processing helix chain 'B' and resid 1705 through 1721 Processing helix chain 'B' and resid 1726 through 1742 removed outlier: 3.649A pdb=" N ARG B1730 " --> pdb=" O CYS B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1743 through 1754 removed outlier: 3.555A pdb=" N GLU B1751 " --> pdb=" O HIS B1747 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B1752 " --> pdb=" O SER B1748 " (cutoff:3.500A) Processing helix chain 'B' and resid 1758 through 1764 removed outlier: 4.107A pdb=" N ALA B1762 " --> pdb=" O ASP B1758 " (cutoff:3.500A) Processing helix chain 'B' and resid 1791 through 1796 Processing helix chain 'B' and resid 1801 through 1816 Processing helix chain 'B' and resid 1821 through 1826 removed outlier: 4.067A pdb=" N GLN B1825 " --> pdb=" O CYS B1821 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B1826 " --> pdb=" O GLU B1822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1821 through 1826' Processing helix chain 'B' and resid 1827 through 1832 Processing helix chain 'B' and resid 1834 through 1852 removed outlier: 3.662A pdb=" N CYS B1838 " --> pdb=" O LYS B1834 " (cutoff:3.500A) Proline residue: B1843 - end of helix removed outlier: 4.024A pdb=" N GLN B1852 " --> pdb=" O ASP B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1856 through 1875 Processing helix chain 'B' and resid 1902 through 1918 removed outlier: 3.546A pdb=" N GLN B1906 " --> pdb=" O ASP B1902 " (cutoff:3.500A) removed outlier: 3.696A 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: 3.556A 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 1998 Processing helix chain 'B' and resid 2000 through 2013 removed outlier: 3.500A pdb=" N LEU B2006 " --> pdb=" O GLN B2002 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B2007 " --> pdb=" O ASP B2003 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B2008 " --> pdb=" O LEU B2004 " (cutoff:3.500A) Processing helix chain 'B' and resid 2015 through 2020 removed outlier: 3.578A pdb=" N LEU B2018 " --> pdb=" O PRO B2015 " (cutoff:3.500A) Processing helix chain 'B' and resid 2028 through 2039 Processing helix chain 'B' and resid 2041 through 2052 Processing helix chain 'B' and resid 2056 through 2071 removed outlier: 3.727A pdb=" N ALA B2062 " --> pdb=" O SER B2058 " (cutoff:3.500A) Processing helix chain 'B' and resid 2073 through 2088 Processing helix chain 'B' and resid 2092 through 2106 removed outlier: 3.550A pdb=" N GLU B2096 " --> pdb=" O CYS B2092 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B2098 " --> pdb=" O GLU B2094 " (cutoff:3.500A) Processing helix chain 'B' and resid 2123 through 2137 Processing helix chain 'B' and resid 2139 through 2160 removed outlier: 3.505A pdb=" N VAL B2155 " --> pdb=" O ARG B2151 " (cutoff:3.500A) Processing helix chain 'B' and resid 2165 through 2167 No H-bonds generated for 'chain 'B' and resid 2165 through 2167' Processing helix chain 'B' and resid 2168 through 2191 removed outlier: 4.434A pdb=" N THR B2172 " --> pdb=" O SER B2168 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU B2187 " --> pdb=" O GLU B2183 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B2188 " --> pdb=" O SER B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2211 removed outlier: 3.738A pdb=" N LEU B2211 " --> pdb=" O LYS B2207 " (cutoff:3.500A) Processing helix chain 'B' and resid 2216 through 2237 Proline residue: B2222 - end of helix Processing helix chain 'B' and resid 2244 through 2265 Processing helix chain 'B' and resid 2268 through 2282 removed outlier: 3.710A pdb=" N TYR B2281 " --> pdb=" O GLN B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2289 through 2302 removed outlier: 3.795A pdb=" N LEU B2293 " --> pdb=" O SER B2289 " (cutoff:3.500A) Processing helix chain 'B' and resid 2304 through 2323 Processing helix chain 'B' and resid 2327 through 2349 removed outlier: 4.023A pdb=" N LEU B2332 " --> pdb=" O PRO B2328 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR B2333 " --> pdb=" O SER B2329 " (cutoff:3.500A) Processing helix chain 'B' and resid 2352 through 2360 Processing helix chain 'B' and resid 2360 through 2371 removed outlier: 3.706A pdb=" N TYR B2371 " --> pdb=" O VAL B2367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2376 through 2407 removed outlier: 3.913A pdb=" N ARG B2380 " --> pdb=" O SER B2376 " (cutoff:3.500A) Processing helix chain 'B' and resid 2407 through 2422 removed outlier: 3.528A pdb=" N GLU B2411 " --> pdb=" O SER B2407 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B2422 " --> pdb=" O LYS B2418 " (cutoff:3.500A) Processing helix chain 'B' and resid 2437 through 2476 removed outlier: 4.140A pdb=" N GLU B2449 " --> pdb=" O LEU B2445 " (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 2494 Processing helix chain 'B' and resid 2497 through 2507 removed outlier: 3.640A pdb=" N ASN B2501 " --> pdb=" O VAL B2497 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B2502 " --> pdb=" O SER B2498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2508 through 2511 Processing helix chain 'B' and resid 2512 through 2517 removed outlier: 3.556A pdb=" N LEU B2517 " --> pdb=" O TYR B2514 " (cutoff:3.500A) Processing helix chain 'B' and resid 2519 through 2526 removed outlier: 3.933A pdb=" N LEU B2523 " --> pdb=" O LEU B2519 " (cutoff:3.500A) Processing helix chain 'B' and resid 2536 through 2552 removed outlier: 3.531A pdb=" N VAL B2540 " --> pdb=" O GLY B2536 " (cutoff:3.500A) Processing helix chain 'B' and resid 2552 through 2565 removed outlier: 3.509A pdb=" N THR B2556 " --> pdb=" O HIS B2552 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N PHE B2558 " --> pdb=" O HIS B2554 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE B2559 " --> pdb=" O HIS B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2567 through 2573 removed outlier: 3.760A pdb=" N PHE B2571 " --> pdb=" O ASN B2567 " (cutoff:3.500A) Processing helix chain 'B' and resid 2592 through 2613 removed outlier: 3.886A pdb=" N GLU B2596 " --> pdb=" O SER B2592 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG B2612 " --> pdb=" O THR B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2613 through 2633 removed outlier: 3.664A pdb=" N VAL B2617 " --> pdb=" O ARG B2613 " (cutoff:3.500A) Processing helix chain 'B' and resid 2636 through 2641 removed outlier: 3.681A pdb=" N LYS B2639 " --> pdb=" O THR B2636 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR B2640 " --> pdb=" O GLN B2637 " (cutoff:3.500A) Processing helix chain 'B' and resid 2722 through 2742 removed outlier: 3.664A pdb=" N ASN B2742 " --> pdb=" O LEU B2738 " (cutoff:3.500A) Processing helix chain 'B' and resid 2742 through 2748 removed outlier: 3.928A 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 2808 Processing helix chain 'B' and resid 2812 through 2826 Processing helix chain 'B' and resid 2832 through 2839 removed outlier: 4.063A pdb=" N MET B2836 " --> pdb=" O ARG B2832 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B2838 " --> pdb=" O PHE B2834 " (cutoff:3.500A) Processing helix chain 'B' and resid 2841 through 2866 Processing helix chain 'B' and resid 2872 through 2874 No H-bonds generated for 'chain 'B' and resid 2872 through 2874' Processing helix chain 'B' and resid 2895 through 2900 Processing helix chain 'B' and resid 2911 through 2917 Processing helix chain 'B' and resid 2925 through 2941 Processing helix chain 'B' and resid 2941 through 2954 Processing helix chain 'B' and resid 2963 through 2971 Processing helix chain 'B' and resid 3002 through 3018 Processing helix chain 'B' and resid 3027 through 3041 Processing helix chain 'B' and resid 3041 through 3048 removed outlier: 3.640A pdb=" N ARG B3047 " --> pdb=" O LYS B3043 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B3048 " --> pdb=" O ASN B3044 " (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: 7.367A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP A2703 " --> pdb=" O PHE A2686 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE A2686 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A2705 " --> pdb=" O GLN A2684 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A2662 " --> pdb=" O ILE A2683 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N SER A2685 " --> pdb=" O GLU A2660 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N GLU A2660 " --> pdb=" O SER A2685 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 7.367A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (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: 7.360A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASP B2703 " --> pdb=" O GLU B2689 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASP B2703 " --> pdb=" O PHE B2686 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE B2686 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B2705 " --> pdb=" O GLN B2684 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL B2662 " --> pdb=" O ILE B2683 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N SER B2685 " --> pdb=" O GLU B2660 " (cutoff:3.500A) removed outlier: 10.649A pdb=" N GLU B2660 " --> pdb=" O SER B2685 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2645 through 2646 removed outlier: 7.360A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 4.813A 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 2810 hydrogen bonds defined for protein. 8283 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: 23.18 Time building geometry restraints manager: 12.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14340 1.34 - 1.46: 8342 1.46 - 1.58: 22146 1.58 - 1.70: 10 1.70 - 1.82: 450 Bond restraints: 45288 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 5.06e+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 5.03e+01 bond pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.65e+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 2.59e+01 bond pdb=" O5' ANP B3101 " pdb=" PA ANP B3101 " ideal model delta sigma weight residual 1.655 1.581 0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 45283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 61007 3.44 - 6.89: 176 6.89 - 10.33: 13 10.33 - 13.77: 2 13.77 - 17.21: 2 Bond angle restraints: 61200 Sorted by residual: angle pdb=" PB ANP B3101 " pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 126.95 109.74 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" PB ANP A3101 " pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 126.95 109.77 17.18 3.00e+00 1.11e-01 3.28e+01 angle pdb=" O1B ANP A3101 " pdb=" PB ANP A3101 " pdb=" O2B ANP A3101 " ideal model delta sigma weight residual 120.08 109.64 10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" O1B ANP B3101 " pdb=" PB ANP B3101 " pdb=" O2B ANP B3101 " ideal model delta sigma weight residual 120.08 109.66 10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N PRO B1378 " pdb=" CA PRO B1378 " pdb=" C PRO B1378 " ideal model delta sigma weight residual 110.70 114.78 -4.08 1.22e+00 6.72e-01 1.12e+01 ... (remaining 61195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 25141 17.73 - 35.46: 2156 35.46 - 53.18: 245 53.18 - 70.91: 62 70.91 - 88.64: 50 Dihedral angle restraints: 27654 sinusoidal: 11302 harmonic: 16352 Sorted by residual: dihedral pdb=" CA ASN B1377 " pdb=" C ASN B1377 " pdb=" N PRO B1378 " pdb=" CA PRO B1378 " ideal model delta harmonic sigma weight residual 180.00 -153.03 -26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA MET A2026 " pdb=" C MET A2026 " pdb=" N LEU A2027 " pdb=" CA LEU A2027 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PRO B 962 " pdb=" C PRO B 962 " pdb=" N MET B 963 " pdb=" CA MET B 963 " ideal model delta harmonic sigma weight residual -180.00 -163.25 -16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 27651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6177 0.055 - 0.110: 800 0.110 - 0.165: 41 0.165 - 0.220: 0 0.220 - 0.274: 2 Chirality restraints: 7020 Sorted by residual: 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 1.88e+00 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 1.88e+00 chirality pdb=" CA ILE A2055 " pdb=" N ILE A2055 " pdb=" C ILE A2055 " pdb=" CB ILE A2055 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 7017 not shown) Planarity restraints: 7702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A2055 " 0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A2056 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A2056 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2056 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B2055 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B2056 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B2056 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B2056 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 595 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 596 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 596 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 596 " 0.025 5.00e-02 4.00e+02 ... (remaining 7699 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 453 2.67 - 3.23: 43228 3.23 - 3.78: 69708 3.78 - 4.34: 94026 4.34 - 4.90: 152319 Nonbonded interactions: 359734 Sorted by model distance: nonbonded pdb=" OD1 ASN A2875 " pdb="MG MG A3102 " model vdw 2.109 2.170 nonbonded pdb=" OD1 ASN B2875 " pdb="MG MG B3102 " model vdw 2.113 2.170 nonbonded pdb=" O SER B 941 " pdb=" ND1 HIS B 945 " model vdw 2.221 3.120 nonbonded pdb=" O HIS B 399 " pdb=" OG SER B 403 " model vdw 2.222 3.040 nonbonded pdb=" O HIS A 399 " pdb=" OG SER A 403 " model vdw 2.222 3.040 ... (remaining 359729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 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: 0.040 Extract box with map and model: 1.860 Check model and map are aligned: 0.300 Set scattering table: 0.400 Process input model: 106.550 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.190 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:12.320 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 45288 Z= 0.140 Angle : 0.498 17.215 61200 Z= 0.242 Chirality : 0.035 0.274 7020 Planarity : 0.003 0.046 7702 Dihedral : 13.270 88.641 16990 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 1.84 (0.11), residues: 5468 helix: 1.70 (0.08), residues: 3838 sheet: 1.59 (0.63), residues: 66 loop : 0.13 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B2091 HIS 0.006 0.001 HIS A1083 PHE 0.019 0.001 PHE B 652 TYR 0.013 0.001 TYR B1442 ARG 0.009 0.000 ARG A2443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 5.306 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 577 MET cc_start: 0.8329 (tmm) cc_final: 0.7214 (ptm) REVERT: A 578 LYS cc_start: 0.9456 (mmpt) cc_final: 0.9100 (mmtt) REVERT: A 624 MET cc_start: 0.7710 (mmt) cc_final: 0.7405 (mmt) REVERT: A 652 PHE cc_start: 0.8027 (m-80) cc_final: 0.7722 (m-10) REVERT: A 929 MET cc_start: 0.8652 (mpp) cc_final: 0.8363 (ppp) REVERT: A 996 HIS cc_start: 0.8485 (m-70) cc_final: 0.8276 (m-70) REVERT: A 1064 MET cc_start: 0.5098 (pmm) cc_final: 0.4494 (pmm) REVERT: A 1204 ARG cc_start: 0.8223 (mpp-170) cc_final: 0.7909 (mtm-85) REVERT: A 1210 MET cc_start: 0.9249 (mmp) cc_final: 0.8953 (mmm) REVERT: A 1308 MET cc_start: 0.7351 (tmm) cc_final: 0.7063 (tmm) REVERT: A 1342 GLU cc_start: 0.9263 (mp0) cc_final: 0.9047 (pm20) REVERT: A 1343 ILE cc_start: 0.9070 (pt) cc_final: 0.8852 (pp) REVERT: A 1349 MET cc_start: 0.8349 (tmm) cc_final: 0.7990 (tmm) REVERT: A 1425 GLN cc_start: 0.9275 (mm-40) cc_final: 0.9037 (mm-40) REVERT: A 1434 LYS cc_start: 0.9382 (tptt) cc_final: 0.8853 (tppt) REVERT: A 1693 ASP cc_start: 0.8352 (t0) cc_final: 0.8097 (t70) REVERT: A 1836 ASP cc_start: 0.8885 (t70) cc_final: 0.8580 (t0) REVERT: A 2157 GLU cc_start: 0.8132 (mp0) cc_final: 0.7874 (mp0) REVERT: A 2314 GLN cc_start: 0.8771 (tp-100) cc_final: 0.7836 (tp-100) REVERT: A 2479 GLU cc_start: 0.8439 (tp30) cc_final: 0.8153 (tp30) REVERT: A 2728 MET cc_start: 0.9067 (mmm) cc_final: 0.8836 (mmm) REVERT: B 624 MET cc_start: 0.7849 (mmt) cc_final: 0.7626 (mmt) REVERT: B 652 PHE cc_start: 0.8045 (m-80) cc_final: 0.7768 (m-10) REVERT: B 996 HIS cc_start: 0.8506 (m-70) cc_final: 0.8296 (m-70) REVERT: B 1204 ARG cc_start: 0.8154 (mpp-170) cc_final: 0.7874 (mtm-85) REVERT: B 1210 MET cc_start: 0.9278 (mmp) cc_final: 0.8970 (mmm) REVERT: B 1308 MET cc_start: 0.7369 (tmm) cc_final: 0.7085 (tmm) REVERT: B 1343 ILE cc_start: 0.9091 (pt) cc_final: 0.8799 (pp) REVERT: B 1425 GLN cc_start: 0.8755 (mp10) cc_final: 0.8499 (mp10) REVERT: B 1434 LYS cc_start: 0.9418 (tptt) cc_final: 0.8992 (tppt) REVERT: B 1760 MET cc_start: 0.8438 (ttp) cc_final: 0.8082 (ttp) REVERT: B 1773 LYS cc_start: 0.9328 (tptp) cc_final: 0.9101 (tptt) REVERT: B 2314 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8182 (tp-100) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 1.7198 time to fit residues: 849.5142 Evaluate side-chains 291 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 4.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 467 optimal weight: 1.9990 chunk 419 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 434 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 264 optimal weight: 0.5980 chunk 323 optimal weight: 50.0000 chunk 503 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 ASN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 HIS A1719 ASN ** A1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2327 ASN A3014 GLN B 975 ASN ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1334 HIS ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2305 GLN B2327 ASN B2730 GLN B3014 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 45288 Z= 0.191 Angle : 0.555 9.538 61200 Z= 0.277 Chirality : 0.038 0.158 7020 Planarity : 0.004 0.047 7702 Dihedral : 4.220 87.820 6014 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.97 % Allowed : 5.98 % Favored : 93.05 % 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: 2.50 (0.12), residues: 5468 helix: 2.22 (0.08), residues: 3850 sheet: 1.25 (0.65), residues: 66 loop : 0.34 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B2091 HIS 0.008 0.001 HIS A1518 PHE 0.025 0.001 PHE B 652 TYR 0.018 0.001 TYR A2437 ARG 0.006 0.001 ARG A2196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 337 time to evaluate : 5.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.8165 (tmm) cc_final: 0.7851 (tmm) REVERT: A 617 MET cc_start: 0.6467 (ppp) cc_final: 0.5854 (ppp) REVERT: A 624 MET cc_start: 0.7385 (mmt) cc_final: 0.7035 (mmt) REVERT: A 1064 MET cc_start: 0.4707 (pmm) cc_final: 0.4401 (pmm) REVERT: A 1087 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8116 (mtt) REVERT: A 1095 ARG cc_start: 0.8240 (mpt180) cc_final: 0.7933 (mtt90) REVERT: A 1134 MET cc_start: 0.7051 (mtm) cc_final: 0.6475 (mmt) REVERT: A 1204 ARG cc_start: 0.8216 (mpp-170) cc_final: 0.7863 (mtm-85) REVERT: A 1210 MET cc_start: 0.9259 (mmp) cc_final: 0.9010 (mmm) REVERT: A 1308 MET cc_start: 0.7345 (tmm) cc_final: 0.7080 (tmm) REVERT: A 1321 MET cc_start: 0.7082 (pp-130) cc_final: 0.6672 (pp-130) REVERT: A 1349 MET cc_start: 0.8741 (tmm) cc_final: 0.8501 (tmm) REVERT: A 1425 GLN cc_start: 0.9414 (mm-40) cc_final: 0.9185 (mm-40) REVERT: A 1693 ASP cc_start: 0.8325 (t0) cc_final: 0.7977 (t0) REVERT: A 1836 ASP cc_start: 0.8943 (t70) cc_final: 0.8686 (t0) REVERT: A 2314 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8097 (tp-100) REVERT: A 2479 GLU cc_start: 0.8453 (tp30) cc_final: 0.8171 (tp30) REVERT: A 2728 MET cc_start: 0.9286 (mmm) cc_final: 0.9043 (mmm) REVERT: B 624 MET cc_start: 0.7526 (mmt) cc_final: 0.7273 (mmt) REVERT: B 652 PHE cc_start: 0.8004 (m-80) cc_final: 0.7739 (m-10) REVERT: B 1064 MET cc_start: 0.4622 (pmm) cc_final: 0.4317 (pmm) REVERT: B 1134 MET cc_start: 0.6991 (mtm) cc_final: 0.6414 (mmt) REVERT: B 1204 ARG cc_start: 0.8169 (mpp-170) cc_final: 0.7830 (mtm-85) REVERT: B 1210 MET cc_start: 0.9296 (mmp) cc_final: 0.9036 (mmm) REVERT: B 1308 MET cc_start: 0.7363 (tmm) cc_final: 0.7102 (tmm) REVERT: B 1321 MET cc_start: 0.7077 (pp-130) cc_final: 0.6712 (pp-130) REVERT: B 1425 GLN cc_start: 0.8997 (mp10) cc_final: 0.8669 (mm-40) REVERT: B 1434 LYS cc_start: 0.9446 (tptt) cc_final: 0.9014 (tppt) REVERT: B 1773 LYS cc_start: 0.9308 (tptp) cc_final: 0.9078 (tptt) REVERT: B 1836 ASP cc_start: 0.8999 (t70) cc_final: 0.8773 (t0) REVERT: B 2025 LYS cc_start: 0.8720 (mmpt) cc_final: 0.8485 (mmtm) REVERT: B 2039 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: B 2157 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8074 (mm-30) REVERT: B 2314 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8202 (tp-100) outliers start: 48 outliers final: 15 residues processed: 363 average time/residue: 1.6504 time to fit residues: 746.2514 Evaluate side-chains 294 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 277 time to evaluate : 5.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1452 ASP Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1989 LEU Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 1027 HIS Chi-restraints excluded: chain B residue 1452 ASP Chi-restraints excluded: chain B residue 1662 THR Chi-restraints excluded: chain B residue 2039 GLU Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 279 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 418 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 503 optimal weight: 4.9990 chunk 544 optimal weight: 0.6980 chunk 448 optimal weight: 5.9990 chunk 499 optimal weight: 3.9990 chunk 171 optimal weight: 0.1980 chunk 404 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1431 ASN A1876 HIS B 42 HIS B 704 ASN B 945 HIS ** B 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1188 HIS ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1443 HIS B1876 HIS B2210 GLN ** B2942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 45288 Z= 0.225 Angle : 0.542 9.790 61200 Z= 0.270 Chirality : 0.038 0.155 7020 Planarity : 0.004 0.076 7702 Dihedral : 4.243 88.772 6014 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.32 % Allowed : 7.66 % Favored : 91.02 % 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: 2.58 (0.12), residues: 5468 helix: 2.31 (0.08), residues: 3866 sheet: 1.02 (0.63), residues: 66 loop : 0.25 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1279 HIS 0.009 0.001 HIS A 993 PHE 0.015 0.001 PHE B 652 TYR 0.020 0.001 TYR B1319 ARG 0.010 0.000 ARG A1249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 294 time to evaluate : 5.378 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 617 MET cc_start: 0.6538 (ppp) cc_final: 0.6306 (ppp) REVERT: A 624 MET cc_start: 0.7403 (mmt) cc_final: 0.7108 (mmt) REVERT: A 1064 MET cc_start: 0.4710 (pmm) cc_final: 0.4342 (pmm) REVERT: A 1087 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8160 (mtp) REVERT: A 1134 MET cc_start: 0.7192 (mtm) cc_final: 0.6561 (mmt) REVERT: A 1204 ARG cc_start: 0.8179 (mpp-170) cc_final: 0.7877 (mtm-85) REVERT: A 1210 MET cc_start: 0.9244 (mmp) cc_final: 0.8986 (mmm) REVERT: A 1279 TRP cc_start: 0.4639 (p-90) cc_final: 0.4341 (p-90) REVERT: A 1308 MET cc_start: 0.7357 (tmm) cc_final: 0.7145 (tmm) REVERT: A 1321 MET cc_start: 0.7056 (pp-130) cc_final: 0.6729 (pp-130) REVERT: A 1349 MET cc_start: 0.8889 (tmm) cc_final: 0.8671 (tmm) REVERT: A 1425 GLN cc_start: 0.9470 (mm-40) cc_final: 0.9201 (mm-40) REVERT: A 1693 ASP cc_start: 0.8304 (t0) cc_final: 0.7933 (t0) REVERT: A 1836 ASP cc_start: 0.9001 (t70) cc_final: 0.8626 (t0) REVERT: A 2479 GLU cc_start: 0.8507 (tp30) cc_final: 0.8197 (tp30) REVERT: B 624 MET cc_start: 0.7480 (mmt) cc_final: 0.7198 (mmt) REVERT: B 652 PHE cc_start: 0.8027 (m-80) cc_final: 0.7756 (m-10) REVERT: B 1134 MET cc_start: 0.7259 (mtm) cc_final: 0.6653 (mmt) REVERT: B 1204 ARG cc_start: 0.8150 (mpp-170) cc_final: 0.7855 (mtm-85) REVERT: B 1210 MET cc_start: 0.9262 (mmp) cc_final: 0.9001 (mmm) REVERT: B 1308 MET cc_start: 0.7374 (tmm) cc_final: 0.7164 (tmm) REVERT: B 1321 MET cc_start: 0.7087 (pp-130) cc_final: 0.6755 (pp-130) REVERT: B 1434 LYS cc_start: 0.9485 (tptt) cc_final: 0.9038 (tppt) REVERT: B 1693 ASP cc_start: 0.8063 (t0) cc_final: 0.7849 (t0) REVERT: B 1773 LYS cc_start: 0.9320 (tptp) cc_final: 0.9104 (tptt) REVERT: B 1836 ASP cc_start: 0.9023 (t70) cc_final: 0.8660 (t0) REVERT: B 1851 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9067 (mm) REVERT: B 2003 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8718 (m-30) REVERT: B 2086 TYR cc_start: 0.8551 (t80) cc_final: 0.8281 (t80) REVERT: B 2157 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8223 (mm-30) REVERT: B 2239 MET cc_start: 0.6154 (mpp) cc_final: 0.5699 (mpp) REVERT: B 2307 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8915 (mt) REVERT: B 2561 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9264 (mm) REVERT: B 2612 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8270 (ptm160) REVERT: B 2744 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8749 (mm-30) outliers start: 65 outliers final: 20 residues processed: 331 average time/residue: 1.6546 time to fit residues: 685.5951 Evaluate side-chains 291 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 5.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1452 ASP Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2405 MET Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 1452 ASP Chi-restraints excluded: chain B residue 1570 VAL Chi-restraints excluded: chain B residue 1662 THR Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1851 LEU Chi-restraints excluded: chain B residue 2003 ASP Chi-restraints excluded: chain B residue 2307 LEU Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2744 GLU Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 497 optimal weight: 3.9990 chunk 378 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 240 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 505 optimal weight: 3.9990 chunk 535 optimal weight: 0.9980 chunk 264 optimal weight: 0.6980 chunk 479 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1689 GLN A2305 GLN ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1689 GLN B2241 ASN ** B2942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 45288 Z= 0.222 Angle : 0.530 10.366 61200 Z= 0.261 Chirality : 0.037 0.155 7020 Planarity : 0.003 0.049 7702 Dihedral : 4.233 87.775 6014 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.34 % Allowed : 8.94 % Favored : 89.72 % 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: 2.69 (0.12), residues: 5468 helix: 2.41 (0.08), residues: 3868 sheet: 0.91 (0.64), residues: 66 loop : 0.22 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B2104 HIS 0.006 0.001 HIS B1876 PHE 0.022 0.001 PHE A1336 TYR 0.012 0.001 TYR A2437 ARG 0.005 0.000 ARG B2161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 276 time to evaluate : 5.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.7966 (tmm) cc_final: 0.7030 (ptm) REVERT: A 578 LYS cc_start: 0.9484 (tppt) cc_final: 0.9232 (mmpt) REVERT: A 617 MET cc_start: 0.6719 (ppp) cc_final: 0.6497 (ppp) REVERT: A 624 MET cc_start: 0.7407 (mmt) cc_final: 0.7105 (mmt) REVERT: A 1064 MET cc_start: 0.4786 (pmm) cc_final: 0.4383 (pmm) REVERT: A 1087 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8087 (mtp) REVERT: A 1134 MET cc_start: 0.7212 (mtm) cc_final: 0.6608 (mmt) REVERT: A 1204 ARG cc_start: 0.8187 (mpp-170) cc_final: 0.7882 (mtm-85) REVERT: A 1210 MET cc_start: 0.9272 (mmp) cc_final: 0.9013 (mmm) REVERT: A 1321 MET cc_start: 0.7105 (pp-130) cc_final: 0.6792 (pp-130) REVERT: A 1349 MET cc_start: 0.8975 (tmm) cc_final: 0.8727 (tmm) REVERT: A 1425 GLN cc_start: 0.9498 (mm-40) cc_final: 0.9219 (mm-40) REVERT: A 1693 ASP cc_start: 0.8328 (t0) cc_final: 0.7951 (t0) REVERT: A 1836 ASP cc_start: 0.9006 (t70) cc_final: 0.8575 (t0) REVERT: A 2239 MET cc_start: 0.6455 (mpp) cc_final: 0.5437 (mpp) REVERT: A 2479 GLU cc_start: 0.8546 (tp30) cc_final: 0.8212 (tp30) REVERT: B 624 MET cc_start: 0.7487 (mmt) cc_final: 0.7092 (mmt) REVERT: B 652 PHE cc_start: 0.7937 (m-80) cc_final: 0.7653 (m-10) REVERT: B 1134 MET cc_start: 0.7252 (mtm) cc_final: 0.6670 (mmt) REVERT: B 1204 ARG cc_start: 0.8165 (mpp-170) cc_final: 0.7860 (mtm-85) REVERT: B 1210 MET cc_start: 0.9291 (mmp) cc_final: 0.9017 (mmm) REVERT: B 1321 MET cc_start: 0.7129 (pp-130) cc_final: 0.6822 (pp-130) REVERT: B 1434 LYS cc_start: 0.9514 (tptt) cc_final: 0.9142 (tppt) REVERT: B 1693 ASP cc_start: 0.8042 (t0) cc_final: 0.7761 (t0) REVERT: B 1773 LYS cc_start: 0.9282 (tptp) cc_final: 0.9077 (tptt) REVERT: B 1836 ASP cc_start: 0.9020 (t70) cc_final: 0.8592 (t0) REVERT: B 2025 LYS cc_start: 0.8763 (mmpt) cc_final: 0.8415 (mmtm) REVERT: B 2086 TYR cc_start: 0.8630 (t80) cc_final: 0.8337 (t80) REVERT: B 2096 GLU cc_start: 0.8860 (tp30) cc_final: 0.8563 (mm-30) REVERT: B 2157 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8393 (mm-30) REVERT: B 2479 GLU cc_start: 0.8326 (tp30) cc_final: 0.8119 (tp30) REVERT: B 2561 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9334 (mm) REVERT: B 2612 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8300 (ptm160) outliers start: 66 outliers final: 20 residues processed: 323 average time/residue: 1.6242 time to fit residues: 656.2740 Evaluate side-chains 279 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 256 time to evaluate : 5.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1659 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 1545 LEU Chi-restraints excluded: chain B residue 1570 VAL Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2198 LEU Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2935 MET Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 445 optimal weight: 3.9990 chunk 303 optimal weight: 50.0000 chunk 7 optimal weight: 7.9990 chunk 398 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 456 optimal weight: 0.9980 chunk 370 optimal weight: 8.9990 chunk 0 optimal weight: 80.0000 chunk 273 optimal weight: 0.8980 chunk 480 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 GLN A 945 HIS ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2241 ASN A2292 GLN B 754 GLN ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2197 GLN B2292 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 45288 Z= 0.242 Angle : 0.559 11.373 61200 Z= 0.276 Chirality : 0.038 0.167 7020 Planarity : 0.003 0.050 7702 Dihedral : 4.272 85.262 6014 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.44 % Allowed : 9.57 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.12), residues: 5468 helix: 2.42 (0.08), residues: 3868 sheet: 0.65 (0.64), residues: 66 loop : 0.22 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1279 HIS 0.018 0.001 HIS B 943 PHE 0.019 0.001 PHE A 626 TYR 0.017 0.001 TYR B1508 ARG 0.007 0.000 ARG B2161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 285 time to evaluate : 5.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.7993 (tmm) cc_final: 0.6961 (ptm) REVERT: A 578 LYS cc_start: 0.9515 (tppt) cc_final: 0.9284 (mmpt) REVERT: A 617 MET cc_start: 0.6764 (ppp) cc_final: 0.6517 (ppp) REVERT: A 624 MET cc_start: 0.7410 (mmt) cc_final: 0.7043 (mmt) REVERT: A 1064 MET cc_start: 0.4852 (pmm) cc_final: 0.4432 (pmm) REVERT: A 1087 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8058 (mtp) REVERT: A 1134 MET cc_start: 0.7291 (mtm) cc_final: 0.6672 (mmt) REVERT: A 1204 ARG cc_start: 0.8208 (mpp-170) cc_final: 0.7892 (mtm-85) REVERT: A 1210 MET cc_start: 0.9294 (mmp) cc_final: 0.9032 (mmm) REVERT: A 1308 MET cc_start: 0.7367 (tmm) cc_final: 0.6991 (pp-130) REVERT: A 1321 MET cc_start: 0.7127 (pp-130) cc_final: 0.6834 (pp-130) REVERT: A 1397 HIS cc_start: 0.7952 (t70) cc_final: 0.7737 (t70) REVERT: A 1657 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8440 (mtt) REVERT: A 1693 ASP cc_start: 0.8317 (t0) cc_final: 0.7915 (t0) REVERT: A 1836 ASP cc_start: 0.9013 (t70) cc_final: 0.8500 (t0) REVERT: A 2479 GLU cc_start: 0.8581 (tp30) cc_final: 0.8251 (tp30) REVERT: B 617 MET cc_start: 0.6120 (ppp) cc_final: 0.5739 (ppp) REVERT: B 624 MET cc_start: 0.7356 (mmt) cc_final: 0.7110 (mmt) REVERT: B 652 PHE cc_start: 0.7943 (m-80) cc_final: 0.7664 (m-10) REVERT: B 946 MET cc_start: 0.7991 (ptt) cc_final: 0.7550 (ptt) REVERT: B 1134 MET cc_start: 0.7304 (mtm) cc_final: 0.6740 (mmt) REVERT: B 1204 ARG cc_start: 0.8196 (mpp-170) cc_final: 0.7882 (mtm-85) REVERT: B 1210 MET cc_start: 0.9314 (mmp) cc_final: 0.9035 (mmm) REVERT: B 1308 MET cc_start: 0.7385 (tmm) cc_final: 0.7019 (pp-130) REVERT: B 1321 MET cc_start: 0.7229 (pp-130) cc_final: 0.6930 (pp-130) REVERT: B 1397 HIS cc_start: 0.7936 (t70) cc_final: 0.7681 (t70) REVERT: B 1693 ASP cc_start: 0.8064 (t0) cc_final: 0.7715 (t0) REVERT: B 1755 MET cc_start: 0.9163 (mpm) cc_final: 0.8950 (mpm) REVERT: B 1773 LYS cc_start: 0.9275 (tptp) cc_final: 0.9073 (tptt) REVERT: B 1836 ASP cc_start: 0.9038 (t70) cc_final: 0.8559 (t0) REVERT: B 2086 TYR cc_start: 0.8714 (t80) cc_final: 0.8375 (t80) REVERT: B 2091 TRP cc_start: 0.7549 (t-100) cc_final: 0.6989 (t-100) REVERT: B 2096 GLU cc_start: 0.8861 (tp30) cc_final: 0.8599 (mm-30) REVERT: B 2157 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8497 (mm-30) REVERT: B 2479 GLU cc_start: 0.8436 (tp30) cc_final: 0.8085 (tp30) REVERT: B 2561 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9357 (mm) REVERT: B 2612 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8491 (ptm160) outliers start: 71 outliers final: 24 residues processed: 326 average time/residue: 1.6702 time to fit residues: 677.2083 Evaluate side-chains 289 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 5.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1478 GLN Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain B residue 1570 VAL Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2003 ASP Chi-restraints excluded: chain B residue 2006 LEU Chi-restraints excluded: chain B residue 2198 LEU Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2935 MET Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 180 optimal weight: 0.6980 chunk 482 optimal weight: 0.0970 chunk 105 optimal weight: 7.9990 chunk 314 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 536 optimal weight: 0.6980 chunk 444 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 281 optimal weight: 20.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1443 HIS ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2730 GLN B2942 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 45288 Z= 0.143 Angle : 0.537 14.528 61200 Z= 0.259 Chirality : 0.036 0.215 7020 Planarity : 0.003 0.049 7702 Dihedral : 4.185 83.326 6014 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.07 % Allowed : 10.74 % Favored : 88.18 % 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: 2.79 (0.12), residues: 5468 helix: 2.49 (0.08), residues: 3864 sheet: 0.78 (0.65), residues: 66 loop : 0.27 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2104 HIS 0.006 0.001 HIS B1876 PHE 0.024 0.001 PHE B1336 TYR 0.017 0.001 TYR B1508 ARG 0.004 0.000 ARG B2244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 5.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.7987 (tmm) cc_final: 0.7134 (ptm) REVERT: A 617 MET cc_start: 0.6779 (ppp) cc_final: 0.6525 (ppp) REVERT: A 624 MET cc_start: 0.7298 (mmt) cc_final: 0.7037 (mmt) REVERT: A 1064 MET cc_start: 0.4880 (pmm) cc_final: 0.4629 (pmm) REVERT: A 1087 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: A 1134 MET cc_start: 0.7252 (mtm) cc_final: 0.6629 (mmt) REVERT: A 1204 ARG cc_start: 0.8216 (mpp-170) cc_final: 0.7893 (mtm-85) REVERT: A 1210 MET cc_start: 0.9298 (mmp) cc_final: 0.9041 (mmm) REVERT: A 1308 MET cc_start: 0.7354 (tmm) cc_final: 0.7080 (pp-130) REVERT: A 1321 MET cc_start: 0.7114 (pp-130) cc_final: 0.6733 (pp-130) REVERT: A 1693 ASP cc_start: 0.8300 (t0) cc_final: 0.7921 (t0) REVERT: A 1836 ASP cc_start: 0.8963 (t70) cc_final: 0.8453 (t0) REVERT: A 2479 GLU cc_start: 0.8565 (tp30) cc_final: 0.8255 (tp30) REVERT: A 2532 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7509 (mmm) REVERT: B 437 MET cc_start: 0.7933 (mpt) cc_final: 0.7431 (pp-130) REVERT: B 617 MET cc_start: 0.5963 (ppp) cc_final: 0.5603 (ppp) REVERT: B 624 MET cc_start: 0.7381 (mmt) cc_final: 0.7052 (mmt) REVERT: B 652 PHE cc_start: 0.7943 (m-80) cc_final: 0.7688 (m-10) REVERT: B 946 MET cc_start: 0.7907 (ptt) cc_final: 0.7684 (ppp) REVERT: B 1134 MET cc_start: 0.7237 (mtm) cc_final: 0.6663 (mmt) REVERT: B 1204 ARG cc_start: 0.8190 (mpp-170) cc_final: 0.7866 (mtm-85) REVERT: B 1210 MET cc_start: 0.9317 (mmp) cc_final: 0.9041 (mmm) REVERT: B 1308 MET cc_start: 0.7375 (tmm) cc_final: 0.7106 (pp-130) REVERT: B 1321 MET cc_start: 0.7168 (pp-130) cc_final: 0.6873 (pp-130) REVERT: B 1556 TYR cc_start: 0.8928 (t80) cc_final: 0.8725 (t80) REVERT: B 1693 ASP cc_start: 0.8111 (t0) cc_final: 0.7761 (t0) REVERT: B 1773 LYS cc_start: 0.9278 (tptp) cc_final: 0.9074 (tptt) REVERT: B 1836 ASP cc_start: 0.8960 (t70) cc_final: 0.8479 (t0) REVERT: B 2025 LYS cc_start: 0.8795 (mmpt) cc_final: 0.8240 (mmtp) REVERT: B 2086 TYR cc_start: 0.8720 (t80) cc_final: 0.8370 (t80) REVERT: B 2091 TRP cc_start: 0.7431 (t-100) cc_final: 0.7192 (t-100) REVERT: B 2157 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8462 (mm-30) REVERT: B 2479 GLU cc_start: 0.8436 (tp30) cc_final: 0.8094 (tp30) REVERT: B 2561 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9350 (mm) outliers start: 53 outliers final: 18 residues processed: 306 average time/residue: 1.6080 time to fit residues: 617.9331 Evaluate side-chains 276 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 4.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1659 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 1570 VAL Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2006 LEU Chi-restraints excluded: chain B residue 2198 LEU Chi-restraints excluded: chain B residue 2235 MET Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 516 optimal weight: 0.6980 chunk 60 optimal weight: 20.0000 chunk 305 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 303 optimal weight: 50.0000 chunk 451 optimal weight: 0.9980 chunk 299 optimal weight: 8.9990 chunk 533 optimal weight: 7.9990 chunk 334 optimal weight: 7.9990 chunk 325 optimal weight: 50.0000 chunk 246 optimal weight: 1.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 HIS ** A2111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2069 GLN B2942 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 45288 Z= 0.383 Angle : 0.628 12.831 61200 Z= 0.309 Chirality : 0.041 0.190 7020 Planarity : 0.004 0.051 7702 Dihedral : 4.396 86.090 6014 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.24 % Allowed : 10.94 % Favored : 87.82 % 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: 2.64 (0.12), residues: 5468 helix: 2.39 (0.08), residues: 3866 sheet: 0.51 (0.63), residues: 66 loop : 0.17 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1279 HIS 0.007 0.001 HIS B1876 PHE 0.020 0.001 PHE B2143 TYR 0.015 0.001 TYR B1844 ARG 0.004 0.000 ARG B2613 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 266 time to evaluate : 5.466 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 577 MET cc_start: 0.8085 (tmm) cc_final: 0.6565 (ptm) REVERT: A 578 LYS cc_start: 0.9074 (mmpt) cc_final: 0.8643 (tmmt) REVERT: A 617 MET cc_start: 0.6989 (ppp) cc_final: 0.6540 (ppp) REVERT: A 624 MET cc_start: 0.7296 (mmt) cc_final: 0.6985 (mmt) REVERT: A 946 MET cc_start: 0.8183 (ptp) cc_final: 0.7736 (mpp) REVERT: A 1064 MET cc_start: 0.4897 (pmm) cc_final: 0.4633 (pmm) REVERT: A 1087 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8021 (mtp) REVERT: A 1134 MET cc_start: 0.7349 (mtm) cc_final: 0.6720 (mmt) REVERT: A 1204 ARG cc_start: 0.8221 (mpp-170) cc_final: 0.7919 (mtm-85) REVERT: A 1210 MET cc_start: 0.9300 (mmp) cc_final: 0.9037 (mmm) REVERT: A 1308 MET cc_start: 0.7447 (tmm) cc_final: 0.7200 (pp-130) REVERT: A 1321 MET cc_start: 0.7309 (pp-130) cc_final: 0.7030 (pp-130) REVERT: A 1349 MET cc_start: 0.9312 (tpp) cc_final: 0.9043 (mmm) REVERT: A 1693 ASP cc_start: 0.8349 (t0) cc_final: 0.7967 (t0) REVERT: A 1836 ASP cc_start: 0.9051 (t70) cc_final: 0.8543 (t0) REVERT: A 2479 GLU cc_start: 0.8667 (tp30) cc_final: 0.8233 (tp30) REVERT: A 2532 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7557 (mmm) REVERT: B 437 MET cc_start: 0.8032 (mpt) cc_final: 0.7559 (pp-130) REVERT: B 617 MET cc_start: 0.6102 (ppp) cc_final: 0.5831 (ppp) REVERT: B 624 MET cc_start: 0.7410 (mmt) cc_final: 0.7108 (mmt) REVERT: B 652 PHE cc_start: 0.7882 (m-80) cc_final: 0.7640 (m-10) REVERT: B 1134 MET cc_start: 0.7313 (mtm) cc_final: 0.6705 (mmt) REVERT: B 1204 ARG cc_start: 0.8226 (mpp-170) cc_final: 0.7916 (mtm-85) REVERT: B 1210 MET cc_start: 0.9322 (mmp) cc_final: 0.9055 (mmm) REVERT: B 1308 MET cc_start: 0.7470 (tmm) cc_final: 0.7251 (pp-130) REVERT: B 1321 MET cc_start: 0.7231 (pp-130) cc_final: 0.6908 (pp-130) REVERT: B 1556 TYR cc_start: 0.8997 (t80) cc_final: 0.8725 (t80) REVERT: B 1693 ASP cc_start: 0.8219 (t0) cc_final: 0.7845 (t0) REVERT: B 1773 LYS cc_start: 0.9215 (tptp) cc_final: 0.8973 (tptt) REVERT: B 1836 ASP cc_start: 0.9074 (t70) cc_final: 0.8574 (t0) REVERT: B 2479 GLU cc_start: 0.8533 (tp30) cc_final: 0.8171 (tp30) REVERT: B 2561 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9446 (mm) outliers start: 61 outliers final: 22 residues processed: 304 average time/residue: 1.6187 time to fit residues: 620.0826 Evaluate side-chains 273 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 5.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1478 GLN Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1659 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 1986 ILE Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2503 MET Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1570 VAL Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2006 LEU Chi-restraints excluded: chain B residue 2069 GLN Chi-restraints excluded: chain B residue 2198 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 330 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 160 optimal weight: 0.0770 chunk 104 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 339 optimal weight: 0.6980 chunk 363 optimal weight: 7.9990 chunk 263 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 419 optimal weight: 0.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2197 GLN ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2069 GLN B2412 ASN B2942 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 45288 Z= 0.169 Angle : 0.569 12.085 61200 Z= 0.275 Chirality : 0.037 0.242 7020 Planarity : 0.003 0.050 7702 Dihedral : 4.267 82.477 6014 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.95 % Allowed : 11.69 % Favored : 87.35 % 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: 2.75 (0.12), residues: 5468 helix: 2.46 (0.08), residues: 3870 sheet: 0.56 (0.65), residues: 66 loop : 0.23 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2104 HIS 0.010 0.001 HIS B1876 PHE 0.026 0.001 PHE A 652 TYR 0.015 0.001 TYR B1248 ARG 0.009 0.000 ARG A3008 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 268 time to evaluate : 5.526 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 577 MET cc_start: 0.8011 (tmm) cc_final: 0.6518 (ptm) REVERT: A 578 LYS cc_start: 0.9110 (mmpt) cc_final: 0.8663 (tmmt) REVERT: A 617 MET cc_start: 0.6991 (ppp) cc_final: 0.6540 (ppp) REVERT: A 624 MET cc_start: 0.7318 (mmt) cc_final: 0.7031 (mmt) REVERT: A 900 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5842 (pmt) REVERT: A 1064 MET cc_start: 0.4970 (pmm) cc_final: 0.4709 (pmm) REVERT: A 1087 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8011 (mtp) REVERT: A 1134 MET cc_start: 0.7207 (mtm) cc_final: 0.6577 (mmt) REVERT: A 1204 ARG cc_start: 0.8234 (mpp-170) cc_final: 0.7912 (mtm-85) REVERT: A 1210 MET cc_start: 0.9307 (mmp) cc_final: 0.9054 (mmm) REVERT: A 1308 MET cc_start: 0.7429 (tmm) cc_final: 0.7197 (pp-130) REVERT: A 1321 MET cc_start: 0.7238 (pp-130) cc_final: 0.6907 (pp-130) REVERT: A 1349 MET cc_start: 0.9365 (tpp) cc_final: 0.9087 (mmm) REVERT: A 1448 LEU cc_start: 0.9659 (tm) cc_final: 0.9452 (pp) REVERT: A 1693 ASP cc_start: 0.8308 (t0) cc_final: 0.7918 (t0) REVERT: A 1836 ASP cc_start: 0.8968 (t70) cc_final: 0.8557 (t0) REVERT: A 2025 LYS cc_start: 0.8837 (mmpt) cc_final: 0.8343 (mmtp) REVERT: A 2479 GLU cc_start: 0.8634 (tp30) cc_final: 0.8225 (tp30) REVERT: A 2532 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7514 (mmm) REVERT: B 437 MET cc_start: 0.7996 (mpt) cc_final: 0.7563 (pp-130) REVERT: B 617 MET cc_start: 0.6136 (ppp) cc_final: 0.5878 (ppp) REVERT: B 624 MET cc_start: 0.7456 (mmt) cc_final: 0.7185 (mmt) REVERT: B 652 PHE cc_start: 0.7882 (m-80) cc_final: 0.7641 (m-10) REVERT: B 946 MET cc_start: 0.7725 (ptt) cc_final: 0.7079 (ptt) REVERT: B 1134 MET cc_start: 0.7254 (mtm) cc_final: 0.6662 (mmt) REVERT: B 1204 ARG cc_start: 0.8236 (mpp-170) cc_final: 0.7910 (mtm-85) REVERT: B 1210 MET cc_start: 0.9326 (mmp) cc_final: 0.9056 (mmm) REVERT: B 1308 MET cc_start: 0.7456 (tmm) cc_final: 0.7228 (pp-130) REVERT: B 1321 MET cc_start: 0.7232 (pp-130) cc_final: 0.6904 (pp-130) REVERT: B 1484 MET cc_start: 0.7786 (mmm) cc_final: 0.7521 (mpm) REVERT: B 1556 TYR cc_start: 0.8968 (t80) cc_final: 0.8668 (t80) REVERT: B 1693 ASP cc_start: 0.8244 (t0) cc_final: 0.7885 (t0) REVERT: B 1773 LYS cc_start: 0.9214 (tptp) cc_final: 0.8973 (tptt) REVERT: B 1836 ASP cc_start: 0.8989 (t70) cc_final: 0.8498 (t0) REVERT: B 2025 LYS cc_start: 0.8842 (mmpt) cc_final: 0.8438 (mmtm) REVERT: B 2479 GLU cc_start: 0.8513 (tp30) cc_final: 0.8157 (tp30) REVERT: B 2532 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7166 (mmm) REVERT: B 2561 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9414 (mm) outliers start: 47 outliers final: 17 residues processed: 300 average time/residue: 1.5650 time to fit residues: 595.2113 Evaluate side-chains 278 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 5.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1478 GLN Chi-restraints excluded: chain A residue 1659 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 2503 MET Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1659 ILE Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2006 LEU Chi-restraints excluded: chain B residue 2198 LEU Chi-restraints excluded: chain B residue 2503 MET Chi-restraints excluded: chain B residue 2532 MET Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2656 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 485 optimal weight: 0.8980 chunk 511 optimal weight: 2.9990 chunk 466 optimal weight: 7.9990 chunk 497 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 390 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 449 optimal weight: 2.9990 chunk 470 optimal weight: 0.7980 chunk 495 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 45288 Z= 0.210 Angle : 0.582 14.278 61200 Z= 0.280 Chirality : 0.038 0.259 7020 Planarity : 0.003 0.050 7702 Dihedral : 4.219 81.096 6014 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.73 % Allowed : 12.10 % Favored : 87.17 % 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: 2.76 (0.12), residues: 5468 helix: 2.48 (0.08), residues: 3868 sheet: 0.54 (0.65), residues: 66 loop : 0.23 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1279 HIS 0.008 0.001 HIS B1876 PHE 0.014 0.001 PHE B2143 TYR 0.016 0.001 TYR B1319 ARG 0.012 0.000 ARG A3008 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 5.161 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 577 MET cc_start: 0.8093 (tmm) cc_final: 0.7549 (tmm) REVERT: A 617 MET cc_start: 0.7000 (ppp) cc_final: 0.6565 (ppp) REVERT: A 624 MET cc_start: 0.7333 (mmt) cc_final: 0.7035 (mmt) REVERT: A 946 MET cc_start: 0.8061 (ptp) cc_final: 0.7761 (mpp) REVERT: A 1064 MET cc_start: 0.5081 (pmm) cc_final: 0.4799 (pmm) REVERT: A 1087 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8007 (mtp) REVERT: A 1204 ARG cc_start: 0.8250 (mpp-170) cc_final: 0.7918 (mtm-85) REVERT: A 1210 MET cc_start: 0.9317 (mmp) cc_final: 0.9067 (mmm) REVERT: A 1308 MET cc_start: 0.7485 (tmm) cc_final: 0.7267 (pp-130) REVERT: A 1321 MET cc_start: 0.7271 (pp-130) cc_final: 0.6949 (pp-130) REVERT: A 1349 MET cc_start: 0.9427 (tpp) cc_final: 0.9137 (mmm) REVERT: A 1693 ASP cc_start: 0.8311 (t0) cc_final: 0.7934 (t0) REVERT: A 1836 ASP cc_start: 0.8939 (t70) cc_final: 0.8456 (t0) REVERT: A 2479 GLU cc_start: 0.8647 (tp30) cc_final: 0.8239 (tp30) REVERT: A 2532 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7504 (mmm) REVERT: A 2805 MET cc_start: 0.9217 (mmm) cc_final: 0.9014 (mmt) REVERT: B 624 MET cc_start: 0.7519 (mmt) cc_final: 0.7239 (mmt) REVERT: B 652 PHE cc_start: 0.7865 (m-80) cc_final: 0.7624 (m-10) REVERT: B 946 MET cc_start: 0.7784 (ptt) cc_final: 0.7563 (ppp) REVERT: B 1134 MET cc_start: 0.7253 (mtm) cc_final: 0.6656 (mmt) REVERT: B 1204 ARG cc_start: 0.8231 (mpp-170) cc_final: 0.7901 (mtm-85) REVERT: B 1210 MET cc_start: 0.9334 (mmp) cc_final: 0.9066 (mmm) REVERT: B 1308 MET cc_start: 0.7497 (tmm) cc_final: 0.7285 (pp-130) REVERT: B 1321 MET cc_start: 0.7298 (pp-130) cc_final: 0.6986 (pp-130) REVERT: B 1484 MET cc_start: 0.7770 (mmm) cc_final: 0.7496 (mpm) REVERT: B 1556 TYR cc_start: 0.8959 (t80) cc_final: 0.8630 (t80) REVERT: B 1693 ASP cc_start: 0.8255 (t0) cc_final: 0.7899 (t0) REVERT: B 1773 LYS cc_start: 0.9212 (tptp) cc_final: 0.8979 (tptt) REVERT: B 1836 ASP cc_start: 0.8964 (t70) cc_final: 0.8518 (t0) REVERT: B 2479 GLU cc_start: 0.8518 (tp30) cc_final: 0.8152 (tp30) REVERT: B 2532 MET cc_start: 0.7728 (tpt) cc_final: 0.7176 (mmm) REVERT: B 2561 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9413 (mm) outliers start: 36 outliers final: 20 residues processed: 298 average time/residue: 1.6648 time to fit residues: 621.0859 Evaluate side-chains 281 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 5.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1478 GLN Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1659 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2503 MET Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2006 LEU Chi-restraints excluded: chain B residue 2198 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2656 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 326 optimal weight: 8.9990 chunk 526 optimal weight: 2.9990 chunk 321 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 365 optimal weight: 8.9990 chunk 551 optimal weight: 0.5980 chunk 507 optimal weight: 1.9990 chunk 439 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 339 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1518 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 45288 Z= 0.216 Angle : 0.604 14.752 61200 Z= 0.288 Chirality : 0.038 0.258 7020 Planarity : 0.003 0.050 7702 Dihedral : 4.220 81.461 6014 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.71 % Allowed : 12.46 % Favored : 86.83 % 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: 2.76 (0.12), residues: 5468 helix: 2.47 (0.08), residues: 3866 sheet: 0.51 (0.64), residues: 66 loop : 0.25 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1279 HIS 0.008 0.001 HIS B1876 PHE 0.037 0.001 PHE A 652 TYR 0.014 0.001 TYR A 731 ARG 0.007 0.000 ARG B2161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 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 617 MET cc_start: 0.7069 (ppp) cc_final: 0.6643 (ppp) REVERT: A 624 MET cc_start: 0.7397 (mmt) cc_final: 0.7100 (mmt) REVERT: A 946 MET cc_start: 0.8110 (ptp) cc_final: 0.7848 (mpp) REVERT: A 1064 MET cc_start: 0.5085 (pmm) cc_final: 0.4803 (pmm) REVERT: A 1087 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8003 (mtp) REVERT: A 1204 ARG cc_start: 0.8225 (mpp-170) cc_final: 0.7881 (mtm-85) REVERT: A 1210 MET cc_start: 0.9319 (mmp) cc_final: 0.9070 (mmm) REVERT: A 1308 MET cc_start: 0.7503 (tmm) cc_final: 0.7287 (pp-130) REVERT: A 1321 MET cc_start: 0.7311 (pp-130) cc_final: 0.7002 (pp-130) REVERT: A 1349 MET cc_start: 0.9427 (tpp) cc_final: 0.9130 (mmm) REVERT: A 1693 ASP cc_start: 0.8318 (t0) cc_final: 0.7936 (t0) REVERT: A 1836 ASP cc_start: 0.8937 (t70) cc_final: 0.8566 (t0) REVERT: A 2025 LYS cc_start: 0.8807 (mmpt) cc_final: 0.8343 (mmtp) REVERT: A 2479 GLU cc_start: 0.8647 (tp30) cc_final: 0.8245 (tp30) REVERT: A 2532 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7491 (mmm) REVERT: B 437 MET cc_start: 0.8020 (mpt) cc_final: 0.7590 (pp-130) REVERT: B 617 MET cc_start: 0.6089 (ppp) cc_final: 0.5678 (ppp) REVERT: B 624 MET cc_start: 0.7484 (mmt) cc_final: 0.7189 (mmt) REVERT: B 652 PHE cc_start: 0.7853 (m-80) cc_final: 0.7605 (m-10) REVERT: B 946 MET cc_start: 0.7750 (ptt) cc_final: 0.7544 (ppp) REVERT: B 1134 MET cc_start: 0.7275 (mtm) cc_final: 0.6658 (mmt) REVERT: B 1204 ARG cc_start: 0.8238 (mpp-170) cc_final: 0.7899 (mtm-85) REVERT: B 1210 MET cc_start: 0.9342 (mmp) cc_final: 0.9076 (mmm) REVERT: B 1308 MET cc_start: 0.7527 (tmm) cc_final: 0.7317 (pp-130) REVERT: B 1321 MET cc_start: 0.7361 (pp-130) cc_final: 0.7046 (pp-130) REVERT: B 1448 LEU cc_start: 0.9643 (tm) cc_final: 0.9413 (pp) REVERT: B 1484 MET cc_start: 0.7763 (mmm) cc_final: 0.7447 (mpm) REVERT: B 1556 TYR cc_start: 0.8942 (t80) cc_final: 0.8626 (t80) REVERT: B 1693 ASP cc_start: 0.8255 (t0) cc_final: 0.7893 (t0) REVERT: B 1836 ASP cc_start: 0.8926 (t70) cc_final: 0.8618 (t0) REVERT: B 2025 LYS cc_start: 0.8896 (mmpt) cc_final: 0.8545 (mmtm) REVERT: B 2479 GLU cc_start: 0.8535 (tp30) cc_final: 0.8167 (tp30) REVERT: B 2532 MET cc_start: 0.7720 (tpt) cc_final: 0.7164 (mmm) REVERT: B 2561 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9388 (mm) outliers start: 35 outliers final: 20 residues processed: 289 average time/residue: 1.6380 time to fit residues: 594.7178 Evaluate side-chains 278 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 5.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1478 GLN Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1659 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2503 MET Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1659 ILE Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2006 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2656 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 349 optimal weight: 6.9990 chunk 468 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 405 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 440 optimal weight: 0.9990 chunk 184 optimal weight: 0.3980 chunk 452 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 996 HIS ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.135731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.075741 restraints weight = 119155.822| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.23 r_work: 0.3041 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 45288 Z= 0.171 Angle : 0.595 14.523 61200 Z= 0.282 Chirality : 0.037 0.270 7020 Planarity : 0.003 0.050 7702 Dihedral : 4.186 80.000 6014 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.63 % Allowed : 12.81 % 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: 2.78 (0.12), residues: 5468 helix: 2.48 (0.08), residues: 3868 sheet: 0.55 (0.65), residues: 66 loop : 0.27 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1279 HIS 0.008 0.001 HIS B1876 PHE 0.019 0.001 PHE A2189 TYR 0.017 0.001 TYR A1319 ARG 0.007 0.000 ARG B2161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15133.63 seconds wall clock time: 273 minutes 15.81 seconds (16395.81 seconds total)