Starting phenix.real_space_refine on Sun Sep 13 21:09:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25xo_80450/09_2026/25xo_80450.cif Found real_map, /net/cci-nas-00/data/ceres_data/25xo_80450/09_2026/25xo_80450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25xo_80450/09_2026/25xo_80450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25xo_80450/09_2026/25xo_80450.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25xo_80450/09_2026/25xo_80450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25xo_80450/09_2026/25xo_80450.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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 Mn 3 7.51 5 Zn 3 6.06 5 P 40 5.49 5 S 132 5.16 5 C 15527 2.51 5 N 4339 2.21 5 O 4497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24541 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 23679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3284, 23679 Classifications: {'peptide': 3284} Incomplete info: {'truncation_to_alanine': 751} Link IDs: {'PTRANS': 98, 'TRANS': 3185} Chain breaks: 27 Unresolved non-hydrogen bonds: 2624 Unresolved non-hydrogen angles: 3211 Unresolved non-hydrogen dihedrals: 2098 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 24, 'ASN:plan1': 45, 'ARG:plan': 42, 'ASP:plan': 109, 'GLU:plan': 174, 'TYR:plan': 6, 'PHE:plan': 9, 'HIS:plan': 9, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 1614 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 186 Classifications: {'DNA': 1, 'RNA': 9} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 7} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 254 Classifications: {'DNA': 1, 'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Classifications: {'DNA': 1, 'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 2} Link IDs: {'rna2p': 1, 'rna3p': 2} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G%5*END:plan': 1, ' G%5*END:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 130 Inner-chain residues flagged as termini: ['pdbres=" C F 16 "'] Classifications: {'DNA': 1, 'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 5} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MN': 3, ' ZN': 3} Classifications: {'undetermined': 6, 'water': 2} Link IDs: {None: 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19740 SG CYS A3280 41.355 37.619 65.315 1.00154.02 S ATOM 5195 SG CYS A1028 102.516 65.017 125.356 1.00150.55 S ATOM 5210 SG CYS A1031 104.075 61.645 124.491 1.00157.53 S ATOM 5442 SG CYS A1062 102.935 62.349 128.100 1.00158.51 S ATOM 5459 SG CYS A1065 100.429 61.829 125.476 1.00157.75 S ATOM 6892 SG CYS A1294 54.942 41.086 122.787 1.00124.90 S Time building chain proxies: 5.06, per 1000 atoms: 0.21 Number of scatterers: 24541 At special positions: 0 Unit cell: (120.65, 143.45, 167.2, 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 3 29.99 Mn 3 24.99 S 132 16.00 P 40 15.00 O 4497 8.00 N 4339 7.00 C 15527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1766 " - pdb=" SG CYS A2558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 875.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4001 " pdb="ZN ZN A4001 " - pdb=" SG CYS A3280 " pdb="ZN ZN A4001 " - pdb=" NE2 HIS A3551 " pdb="ZN ZN A4001 " - pdb=" NE2 HIS A3556 " pdb=" ZN A4003 " pdb="ZN ZN A4003 " - pdb=" SG CYS A1065 " pdb="ZN ZN A4003 " - pdb=" SG CYS A1062 " pdb="ZN ZN A4003 " - pdb=" SG CYS A1031 " pdb="ZN ZN A4003 " - pdb=" SG CYS A1028 " pdb=" ZN A4005 " pdb="ZN ZN A4005 " - pdb=" NE2 HIS A1090 " pdb="ZN ZN A4005 " - pdb=" SG CYS A1294 " pdb="ZN ZN A4005 " - pdb=" ND1 HIS A1365 " Number of angles added : 6 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6300 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 20 sheets defined 63.7% alpha, 7.4% beta 11 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.975A pdb=" N GLY A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.520A pdb=" N THR A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 374 Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 380 through 390 removed outlier: 4.304A pdb=" N ASN A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 399 through 424 removed outlier: 5.628A pdb=" N LYS A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 446 through 460 Processing helix chain 'A' and resid 466 through 485 Processing helix chain 'A' and resid 489 through 495 removed outlier: 3.965A pdb=" N GLN A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 522 Processing helix chain 'A' and resid 540 through 554 removed outlier: 3.899A pdb=" N VAL A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 Processing helix chain 'A' and resid 586 through 594 Processing helix chain 'A' and resid 594 through 605 Processing helix chain 'A' and resid 606 through 622 removed outlier: 4.091A pdb=" N GLU A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 650 removed outlier: 3.514A pdb=" N ARG A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.844A pdb=" N LYS A 659 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 673 through 681 removed outlier: 3.678A pdb=" N ASP A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 690 removed outlier: 3.681A pdb=" N ARG A 688 " --> pdb=" O PRO A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.553A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 818 removed outlier: 3.590A pdb=" N GLN A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 817 " --> pdb=" O GLU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 843 removed outlier: 3.552A pdb=" N TRP A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 854 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 876 through 898 removed outlier: 3.781A pdb=" N SER A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE A 889 " --> pdb=" O ASN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 912 Processing helix chain 'A' and resid 913 through 914 No H-bonds generated for 'chain 'A' and resid 913 through 914' Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 930 through 947 removed outlier: 5.264A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 Processing helix chain 'A' and resid 973 through 987 removed outlier: 3.611A pdb=" N CYS A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 998 removed outlier: 3.556A pdb=" N THR A 998 " --> pdb=" O GLU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1024 removed outlier: 3.633A pdb=" N THR A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A1024 " --> pdb=" O SER A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1042 Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.751A pdb=" N GLN A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 4.127A pdb=" N HIS A1066 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1111 Processing helix chain 'A' and resid 1118 through 1140 Processing helix chain 'A' and resid 1176 through 1187 Processing helix chain 'A' and resid 1196 through 1209 Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1237 through 1254 removed outlier: 3.851A pdb=" N VAL A1241 " --> pdb=" O ARG A1237 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1242 " --> pdb=" O ASP A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1281 removed outlier: 4.497A pdb=" N PHE A1279 " --> pdb=" O ASP A1275 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A1280 " --> pdb=" O VAL A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1309 removed outlier: 4.112A pdb=" N ARG A1307 " --> pdb=" O GLU A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1328 Processing helix chain 'A' and resid 1330 through 1350 Processing helix chain 'A' and resid 1401 through 1409 removed outlier: 3.909A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1426 removed outlier: 3.656A pdb=" N GLN A1421 " --> pdb=" O THR A1417 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN A1424 " --> pdb=" O ILE A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1432 removed outlier: 3.552A pdb=" N VAL A1431 " --> pdb=" O CYS A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1464 Processing helix chain 'A' and resid 1465 through 1481 removed outlier: 3.668A pdb=" N SER A1469 " --> pdb=" O ARG A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1505 Processing helix chain 'A' and resid 1507 through 1514 removed outlier: 3.942A pdb=" N ASN A1514 " --> pdb=" O ASN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1524 Processing helix chain 'A' and resid 1524 through 1531 Processing helix chain 'A' and resid 1532 through 1534 No H-bonds generated for 'chain 'A' and resid 1532 through 1534' Processing helix chain 'A' and resid 1538 through 1547 removed outlier: 4.194A pdb=" N LYS A1544 " --> pdb=" O ASN A1540 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A1546 " --> pdb=" O LEU A1542 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1572 removed outlier: 4.460A pdb=" N ASP A1572 " --> pdb=" O CYS A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1582 removed outlier: 3.506A pdb=" N LYS A1581 " --> pdb=" O VAL A1577 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A1582 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1612 Processing helix chain 'A' and resid 1613 through 1616 removed outlier: 3.556A pdb=" N ILE A1616 " --> pdb=" O ASN A1613 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1613 through 1616' Processing helix chain 'A' and resid 1623 through 1650 removed outlier: 3.952A pdb=" N GLU A1634 " --> pdb=" O SER A1630 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A1635 " --> pdb=" O VAL A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1666 Processing helix chain 'A' and resid 1758 through 1773 Processing helix chain 'A' and resid 1780 through 1791 Processing helix chain 'A' and resid 1792 through 1795 Processing helix chain 'A' and resid 1796 through 1805 Processing helix chain 'A' and resid 1806 through 1811 removed outlier: 3.551A pdb=" N TRP A1810 " --> pdb=" O PRO A1807 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A1811 " --> pdb=" O LYS A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1816 Processing helix chain 'A' and resid 1831 through 1852 Processing helix chain 'A' and resid 1872 through 1877 Processing helix chain 'A' and resid 1883 through 1895 Processing helix chain 'A' and resid 1904 through 1909 Processing helix chain 'A' and resid 1912 through 1917 removed outlier: 3.785A pdb=" N VAL A1916 " --> pdb=" O ASN A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1941 Processing helix chain 'A' and resid 1944 through 1948 Processing helix chain 'A' and resid 1962 through 1975 Processing helix chain 'A' and resid 1988 through 2001 Processing helix chain 'A' and resid 2004 through 2013 Processing helix chain 'A' and resid 2015 through 2040 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2059 through 2061 No H-bonds generated for 'chain 'A' and resid 2059 through 2061' Processing helix chain 'A' and resid 2063 through 2080 Processing helix chain 'A' and resid 2081 through 2087 removed outlier: 4.535A pdb=" N LEU A2085 " --> pdb=" O PRO A2082 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A2086 " --> pdb=" O TRP A2083 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2094 Processing helix chain 'A' and resid 2117 through 2126 Processing helix chain 'A' and resid 2138 through 2155 Processing helix chain 'A' and resid 2157 through 2163 Processing helix chain 'A' and resid 2199 through 2210 Processing helix chain 'A' and resid 2211 through 2220 Processing helix chain 'A' and resid 2235 through 2247 Processing helix chain 'A' and resid 2250 through 2260 removed outlier: 3.587A pdb=" N LEU A2260 " --> pdb=" O PHE A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2305 Processing helix chain 'A' and resid 2316 through 2336 Processing helix chain 'A' and resid 2367 through 2379 removed outlier: 3.606A pdb=" N PHE A2371 " --> pdb=" O CYS A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2382 through 2398 removed outlier: 3.754A pdb=" N CYS A2398 " --> pdb=" O ILE A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2404 through 2420 removed outlier: 3.562A pdb=" N LEU A2415 " --> pdb=" O ILE A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2440 Processing helix chain 'A' and resid 2441 through 2445 Processing helix chain 'A' and resid 2447 through 2457 Processing helix chain 'A' and resid 2458 through 2461 Processing helix chain 'A' and resid 2476 through 2503 removed outlier: 3.523A pdb=" N VAL A2482 " --> pdb=" O ALA A2478 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A2483 " --> pdb=" O THR A2479 " (cutoff:3.500A) Processing helix chain 'A' and resid 2531 through 2540 removed outlier: 3.714A pdb=" N THR A2540 " --> pdb=" O GLN A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2540 through 2558 Processing helix chain 'A' and resid 2589 through 2594 removed outlier: 3.541A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2605 through 2623 Processing helix chain 'A' and resid 2626 through 2645 removed outlier: 4.339A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 3.609A pdb=" N ARG A2651 " --> pdb=" O ASP A2647 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU A2655 " --> pdb=" O ARG A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2659 No H-bonds generated for 'chain 'A' and resid 2658 through 2659' Processing helix chain 'A' and resid 2660 through 2664 Processing helix chain 'A' and resid 2670 through 2675 Processing helix chain 'A' and resid 2678 through 2697 removed outlier: 3.756A pdb=" N ASP A2683 " --> pdb=" O VAL A2679 " (cutoff:3.500A) Processing helix chain 'A' and resid 2753 through 2765 Processing helix chain 'A' and resid 2771 through 2783 Processing helix chain 'A' and resid 2801 through 2805 Processing helix chain 'A' and resid 2806 through 2814 Processing helix chain 'A' and resid 2816 through 2837 removed outlier: 3.678A pdb=" N SER A2826 " --> pdb=" O ASN A2822 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A2827 " --> pdb=" O ARG A2823 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A2837 " --> pdb=" O ALA A2833 " (cutoff:3.500A) Processing helix chain 'A' and resid 2869 through 2890 removed outlier: 4.591A pdb=" N GLU A2875 " --> pdb=" O LYS A2871 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A2877 " --> pdb=" O ARG A2873 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG A2878 " --> pdb=" O ARG A2874 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A2881 " --> pdb=" O GLU A2877 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2910 removed outlier: 3.503A pdb=" N SER A2909 " --> pdb=" O LYS A2905 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2930 Processing helix chain 'A' and resid 2932 through 2938 removed outlier: 3.946A pdb=" N GLY A2936 " --> pdb=" O ASN A2932 " (cutoff:3.500A) Processing helix chain 'A' and resid 2944 through 2954 Processing helix chain 'A' and resid 2994 through 3003 Processing helix chain 'A' and resid 3043 through 3061 removed outlier: 3.543A pdb=" N LYS A3047 " --> pdb=" O GLN A3043 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A3048 " --> pdb=" O SER A3044 " (cutoff:3.500A) Processing helix chain 'A' and resid 3062 through 3072 Processing helix chain 'A' and resid 3104 through 3114 Processing helix chain 'A' and resid 3115 through 3122 removed outlier: 4.440A pdb=" N SER A3119 " --> pdb=" O GLU A3115 " (cutoff:3.500A) Processing helix chain 'A' and resid 3130 through 3142 removed outlier: 3.531A pdb=" N MET A3139 " --> pdb=" O ARG A3135 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A3142 " --> pdb=" O ILE A3138 " (cutoff:3.500A) Processing helix chain 'A' and resid 3142 through 3163 Processing helix chain 'A' and resid 3167 through 3188 Processing helix chain 'A' and resid 3209 through 3217 removed outlier: 3.518A pdb=" N VAL A3213 " --> pdb=" O VAL A3209 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A3217 " --> pdb=" O VAL A3213 " (cutoff:3.500A) Processing helix chain 'A' and resid 3237 through 3252 Processing helix chain 'A' and resid 3255 through 3268 Processing helix chain 'A' and resid 3272 through 3276 Processing helix chain 'A' and resid 3283 through 3294 removed outlier: 3.787A pdb=" N SER A3288 " --> pdb=" O SER A3284 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A3292 " --> pdb=" O SER A3288 " (cutoff:3.500A) Processing helix chain 'A' and resid 3297 through 3305 Processing helix chain 'A' and resid 3306 through 3309 Processing helix chain 'A' and resid 3311 through 3327 removed outlier: 3.576A pdb=" N LEU A3321 " --> pdb=" O GLY A3317 " (cutoff:3.500A) Processing helix chain 'A' and resid 3328 through 3334 Processing helix chain 'A' and resid 3382 through 3399 removed outlier: 3.501A pdb=" N LEU A3386 " --> pdb=" O SER A3382 " (cutoff:3.500A) Processing helix chain 'A' and resid 3406 through 3417 removed outlier: 3.653A pdb=" N LEU A3417 " --> pdb=" O PHE A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3419 through 3423 removed outlier: 3.564A pdb=" N CYS A3423 " --> pdb=" O SER A3420 " (cutoff:3.500A) Processing helix chain 'A' and resid 3504 through 3514 Processing helix chain 'A' and resid 3543 through 3556 removed outlier: 4.379A pdb=" N LEU A3549 " --> pdb=" O ASN A3545 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A3550 " --> pdb=" O SER A3546 " (cutoff:3.500A) Processing helix chain 'A' and resid 3556 through 3569 removed outlier: 3.601A pdb=" N ASP A3560 " --> pdb=" O HIS A3556 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A3563 " --> pdb=" O SER A3559 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A3567 " --> pdb=" O MET A3563 " (cutoff:3.500A) Processing helix chain 'A' and resid 3569 through 3579 removed outlier: 3.527A pdb=" N HIS A3573 " --> pdb=" O SER A3569 " (cutoff:3.500A) Processing helix chain 'A' and resid 3585 through 3596 removed outlier: 4.158A pdb=" N LEU A3589 " --> pdb=" O ASN A3585 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS A3596 " --> pdb=" O GLU A3592 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3624 Processing helix chain 'A' and resid 3627 through 3629 No H-bonds generated for 'chain 'A' and resid 3627 through 3629' Processing helix chain 'A' and resid 3630 through 3641 Processing helix chain 'A' and resid 3678 through 3686 Processing helix chain 'A' and resid 3691 through 3699 removed outlier: 4.938A pdb=" N ALA A3696 " --> pdb=" O PHE A3693 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A3699 " --> pdb=" O ALA A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3700 through 3722 removed outlier: 3.964A pdb=" N ASN A3706 " --> pdb=" O GLU A3702 " (cutoff:3.500A) Processing helix chain 'A' and resid 3724 through 3739 removed outlier: 3.772A pdb=" N PHE A3737 " --> pdb=" O THR A3733 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3758 Processing helix chain 'A' and resid 3802 through 3817 removed outlier: 3.563A pdb=" N ARG A3809 " --> pdb=" O VAL A3805 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A3817 " --> pdb=" O HIS A3813 " (cutoff:3.500A) Processing helix chain 'A' and resid 3824 through 3832 Processing helix chain 'A' and resid 3859 through 3868 Processing helix chain 'A' and resid 3869 through 3888 removed outlier: 3.684A pdb=" N ARG A3874 " --> pdb=" O MET A3870 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU A3875 " --> pdb=" O GLU A3871 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ALA A3876 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A3888 " --> pdb=" O ILE A3884 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 260 removed outlier: 6.146A pdb=" N THR A 265 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 694 through 697 Processing sheet with id=AA3, first strand: chain 'A' and resid 970 through 972 removed outlier: 4.630A pdb=" N PHE A1752 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL A 725 " --> pdb=" O ARG A1671 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA5, first strand: chain 'A' and resid 1151 through 1152 removed outlier: 3.927A pdb=" N CYS A1143 " --> pdb=" O VAL A1220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1357 through 1362 removed outlier: 4.394A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1821 through 1825 removed outlier: 6.847A pdb=" N VAL A2231 " --> pdb=" O ALA A1824 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2278 through 2285 removed outlier: 3.886A pdb=" N GLN A2275 " --> pdb=" O GLY A2278 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A2270 " --> pdb=" O GLU A2402 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A2399 " --> pdb=" O SER A2467 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2507 through 2515 removed outlier: 3.814A pdb=" N ASP A2518 " --> pdb=" O SER A2515 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2574 through 2576 Processing sheet with id=AB2, first strand: chain 'A' and resid 2956 through 2960 removed outlier: 4.380A pdb=" N ILE A2990 " --> pdb=" O ASP A2960 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3005 through 3009 removed outlier: 6.149A pdb=" N SER A3005 " --> pdb=" O LEU A3039 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL A3041 " --> pdb=" O SER A3005 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3078 through 3080 removed outlier: 3.804A pdb=" N SER A3078 " --> pdb=" O ARG A3224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3086 through 3094 Processing sheet with id=AB6, first strand: chain 'A' and resid 3343 through 3346 removed outlier: 7.161A pdb=" N VAL A3456 " --> pdb=" O LEU A3374 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE A3376 " --> pdb=" O VAL A3456 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A3455 " --> pdb=" O VAL A3435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3466 through 3469 Processing sheet with id=AB8, first strand: chain 'A' and resid 3479 through 3480 removed outlier: 6.409A pdb=" N LEU A3487 " --> pdb=" O ARG A3535 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG A3535 " --> pdb=" O LEU A3487 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A3489 " --> pdb=" O LEU A3533 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 3598 through 3599 Processing sheet with id=AC1, first strand: chain 'A' and resid 3646 through 3651 Processing sheet with id=AC2, first strand: chain 'A' and resid 3777 through 3778 1497 hydrogen bonds defined for protein. 4293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 8.20 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6278 1.33 - 1.45: 4762 1.45 - 1.58: 13733 1.58 - 1.70: 77 1.70 - 1.82: 189 Bond restraints: 25039 Sorted by residual: bond pdb=" C TRP A2083 " pdb=" N CYS A2084 " ideal model delta sigma weight residual 1.334 1.266 0.068 1.79e-02 3.12e+03 1.44e+01 bond pdb=" N GLY A1095 " pdb=" CA GLY A1095 " ideal model delta sigma weight residual 1.447 1.477 -0.030 1.01e-02 9.80e+03 8.95e+00 bond pdb=" N VAL A 746 " pdb=" CA VAL A 746 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.19e-02 7.06e+03 8.50e+00 bond pdb=" O3' U B4004 " pdb=" P G B4005 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.20e-02 6.94e+03 8.21e+00 bond pdb=" C PRO A 729 " pdb=" O PRO A 729 " ideal model delta sigma weight residual 1.235 1.213 0.022 7.90e-03 1.60e+04 7.82e+00 ... (remaining 25034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 33872 2.25 - 4.51: 362 4.51 - 6.76: 25 6.76 - 9.02: 8 9.02 - 11.27: 2 Bond angle restraints: 34269 Sorted by residual: angle pdb=" O5' A D 7 " pdb=" C5' A D 7 " pdb=" C4' A D 7 " ideal model delta sigma weight residual 109.40 112.60 -3.20 8.00e-01 1.56e+00 1.60e+01 angle pdb=" CA LYS A2057 " pdb=" CB LYS A2057 " pdb=" CG LYS A2057 " ideal model delta sigma weight residual 114.10 121.80 -7.70 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CB MET A 808 " pdb=" CG MET A 808 " pdb=" SD MET A 808 " ideal model delta sigma weight residual 112.70 123.97 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" O5' U B4008 " pdb=" C5' U B4008 " pdb=" C4' U B4008 " ideal model delta sigma weight residual 109.40 112.40 -3.00 8.00e-01 1.56e+00 1.41e+01 angle pdb=" N LYS A3150 " pdb=" CA LYS A3150 " pdb=" C LYS A3150 " ideal model delta sigma weight residual 111.07 107.07 4.00 1.07e+00 8.73e-01 1.40e+01 ... (remaining 34264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 13898 23.81 - 47.63: 916 47.63 - 71.44: 153 71.44 - 95.26: 30 95.26 - 119.07: 1 Dihedral angle restraints: 14998 sinusoidal: 5362 harmonic: 9636 Sorted by residual: dihedral pdb=" CB CYS A1766 " pdb=" SG CYS A1766 " pdb=" SG CYS A2558 " pdb=" CB CYS A2558 " ideal model delta sinusoidal sigma weight residual 93.00 128.20 -35.20 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CA SER A2515 " pdb=" C SER A2515 " pdb=" N SER A2516 " pdb=" CA SER A2516 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" O4' U B4002 " pdb=" C2' U B4002 " pdb=" C1' U B4002 " pdb=" C3' U B4002 " ideal model delta sinusoidal sigma weight residual 25.59 37.94 -12.35 3 3.80e+00 6.93e-02 1.49e+01 ... (remaining 14995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3253 0.039 - 0.078: 711 0.078 - 0.118: 211 0.118 - 0.157: 51 0.157 - 0.196: 10 Chirality restraints: 4236 Sorted by residual: chirality pdb=" C3' G B4005 " pdb=" C4' G B4005 " pdb=" O3' G B4005 " pdb=" C2' G B4005 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA VAL A 746 " pdb=" N VAL A 746 " pdb=" C VAL A 746 " pdb=" CB VAL A 746 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CA LEU A2090 " pdb=" N LEU A2090 " pdb=" C LEU A2090 " pdb=" CB LEU A2090 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 4233 not shown) Planarity restraints: 4158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A2083 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C TRP A2083 " 0.042 2.00e-02 2.50e+03 pdb=" O TRP A2083 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS A2084 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A1146 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A1147 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1147 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1147 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A2363 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A2364 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A2364 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A2364 " 0.026 5.00e-02 4.00e+02 ... (remaining 4155 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 69 2.53 - 3.12: 19058 3.12 - 3.71: 39746 3.71 - 4.31: 52967 4.31 - 4.90: 88826 Nonbonded interactions: 200666 Sorted by model distance: nonbonded pdb=" OE2 GLU A3286 " pdb="ZN ZN A4001 " model vdw 1.936 2.230 nonbonded pdb=" OE2 GLU A2788 " pdb="ZN ZN A4005 " model vdw 2.015 2.230 nonbonded pdb=" OP2 G E 1 " pdb="MN MN A4002 " model vdw 2.049 2.320 nonbonded pdb=" O VAL A 826 " pdb="MN MN A4002 " model vdw 2.085 2.320 nonbonded pdb=" OD2 ASP A 693 " pdb="MN MN A4002 " model vdw 2.111 2.320 ... (remaining 200661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 30.590 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.003 0.068 25050 Z= 0.177 Angle : 0.519 11.272 34277 Z= 0.308 Chirality : 0.039 0.196 4236 Planarity : 0.003 0.065 4158 Dihedral : 16.001 119.070 8695 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 22.33 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3228 helix: 1.29 (0.12), residues: 1856 sheet: -0.45 (0.34), residues: 257 loop : -0.50 (0.20), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 733 TYR 0.009 0.001 TYR A2468 PHE 0.015 0.001 PHE A1946 TRP 0.016 0.001 TRP A1928 HIS 0.008 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.18 (25039) covalent geometry : angle 0.51784 / 0.31 (34269) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 0.12185 / 0.07 ( 2) hydrogen bonds : bond 0.21526 / 15.13 ( 1523) hydrogen bonds : angle 6.68589 / 4.82 ( 4345) metal coordination : bond 0.00454 / 0.27 ( 10) metal coordination : angle 2.53737 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 555 LYS cc_start: 0.8319 (ptpp) cc_final: 0.7726 (ptpp) REVERT: A 573 LYS cc_start: 0.9098 (mttm) cc_final: 0.8858 (mttm) REVERT: A 983 MET cc_start: 0.8985 (tmm) cc_final: 0.8596 (tmm) REVERT: A 1517 GLN cc_start: 0.8483 (mt0) cc_final: 0.8202 (mt0) REVERT: A 1574 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8594 (mt-10) REVERT: A 1764 LYS cc_start: 0.9053 (mtmt) cc_final: 0.8840 (mtmt) REVERT: A 1792 MET cc_start: 0.8875 (mmm) cc_final: 0.8356 (tpp) REVERT: A 1928 TRP cc_start: 0.8680 (t60) cc_final: 0.8350 (t60) REVERT: A 2023 LEU cc_start: 0.7929 (mt) cc_final: 0.7685 (tp) REVERT: A 2075 PHE cc_start: 0.9312 (m-10) cc_final: 0.8890 (m-80) REVERT: A 2332 MET cc_start: 0.9065 (ttt) cc_final: 0.8726 (ttm) REVERT: A 2836 TYR cc_start: 0.8361 (m-80) cc_final: 0.7679 (m-80) REVERT: A 3104 ASN cc_start: 0.9217 (t0) cc_final: 0.8999 (t0) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1438 time to fit residues: 69.2542 Evaluate side-chains 176 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS A 473 ASN A 567 GLN A 622 ASN A2911 ASN A3170 GLN A3285 HIS ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.081050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.063876 restraints weight = 67882.755| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.73 r_work: 0.2844 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25050 Z= 0.139 Angle : 0.529 11.712 34277 Z= 0.281 Chirality : 0.039 0.237 4236 Planarity : 0.004 0.048 4158 Dihedral : 8.753 115.638 4028 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.99 % Allowed : 22.55 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.15), residues: 3228 helix: 1.84 (0.12), residues: 1885 sheet: -0.47 (0.33), residues: 258 loop : -0.48 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 478 TYR 0.013 0.001 TYR A1413 PHE 0.019 0.001 PHE A2159 TRP 0.035 0.001 TRP A 494 HIS 0.005 0.001 HIS A2477 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (25039) covalent geometry : angle 0.52813 / 0.28 (34269) SS BOND : bond 0.00049 / 0.03 ( 1) SS BOND : angle 0.47272 / 0.26 ( 2) hydrogen bonds : bond 0.05161 / 3.66 ( 1523) hydrogen bonds : angle 4.63630 / 3.37 ( 4345) metal coordination : bond 0.00344 / 0.20 ( 10) metal coordination : angle 1.86056 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 LYS cc_start: 0.8271 (ptpp) cc_final: 0.7754 (ptpp) REVERT: A 573 LYS cc_start: 0.9108 (mttm) cc_final: 0.8839 (mttm) REVERT: A 808 MET cc_start: 0.8271 (tmm) cc_final: 0.7703 (tmm) REVERT: A 1517 GLN cc_start: 0.8456 (mt0) cc_final: 0.8231 (mt0) REVERT: A 1524 MET cc_start: 0.8831 (mmm) cc_final: 0.8599 (mmm) REVERT: A 1610 ASP cc_start: 0.8590 (m-30) cc_final: 0.8307 (m-30) REVERT: A 1764 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8835 (mtmt) REVERT: A 1792 MET cc_start: 0.8856 (mmm) cc_final: 0.8351 (tpp) REVERT: A 1831 MET cc_start: 0.8893 (mmp) cc_final: 0.8629 (mmp) REVERT: A 1928 TRP cc_start: 0.8694 (t60) cc_final: 0.8335 (t60) REVERT: A 2023 LEU cc_start: 0.8040 (mt) cc_final: 0.7617 (tp) REVERT: A 2075 PHE cc_start: 0.9345 (m-10) cc_final: 0.8730 (m-80) REVERT: A 2332 MET cc_start: 0.9047 (ttt) cc_final: 0.8711 (ttm) REVERT: A 3109 MET cc_start: 0.8736 (mtt) cc_final: 0.8485 (mtm) REVERT: A 3397 MET cc_start: 0.9114 (mtm) cc_final: 0.8906 (mtm) REVERT: A 3697 PHE cc_start: 0.9196 (m-80) cc_final: 0.8897 (m-80) outliers start: 45 outliers final: 19 residues processed: 224 average time/residue: 0.1341 time to fit residues: 52.7227 Evaluate side-chains 187 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 1917 LEU Chi-restraints excluded: chain A residue 2036 LEU Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2586 VAL Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 3271 VAL Chi-restraints excluded: chain A residue 3284 SER Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3723 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 246 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 307 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN A 597 ASN A 667 GLN A1002 HIS A1563 GLN A2476 HIS ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.061615 restraints weight = 68599.767| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.71 r_work: 0.2792 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 25050 Z= 0.181 Angle : 0.511 12.098 34277 Z= 0.269 Chirality : 0.039 0.258 4236 Planarity : 0.003 0.043 4158 Dihedral : 8.782 115.917 4028 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.52 % Allowed : 21.88 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3228 helix: 1.93 (0.12), residues: 1890 sheet: -0.49 (0.32), residues: 259 loop : -0.42 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2232 TYR 0.012 0.001 TYR A3684 PHE 0.023 0.001 PHE A 325 TRP 0.016 0.001 TRP A2083 HIS 0.006 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (25039) covalent geometry : angle 0.50965 / 0.27 (34269) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 0.91460 / 0.50 ( 2) hydrogen bonds : bond 0.04314 / 3.04 ( 1523) hydrogen bonds : angle 4.28236 / 3.12 ( 4345) metal coordination : bond 0.02423 / 1.25 ( 10) metal coordination : angle 2.82637 / 1.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 LYS cc_start: 0.8377 (ptpp) cc_final: 0.7726 (ptpp) REVERT: A 573 LYS cc_start: 0.9215 (mttm) cc_final: 0.8901 (mttm) REVERT: A 652 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 808 MET cc_start: 0.8453 (tmm) cc_final: 0.7600 (tmm) REVERT: A 1517 GLN cc_start: 0.8450 (mt0) cc_final: 0.8240 (mt0) REVERT: A 1764 LYS cc_start: 0.9188 (mtmt) cc_final: 0.8951 (mtmt) REVERT: A 1831 MET cc_start: 0.8980 (mmp) cc_final: 0.8717 (mmp) REVERT: A 1928 TRP cc_start: 0.8659 (t60) cc_final: 0.8402 (t60) REVERT: A 2042 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8354 (p) REVERT: A 2075 PHE cc_start: 0.9338 (m-10) cc_final: 0.8878 (m-80) REVERT: A 2150 THR cc_start: 0.9045 (m) cc_final: 0.8827 (p) REVERT: A 2332 MET cc_start: 0.9087 (ttt) cc_final: 0.8769 (ttm) REVERT: A 2581 MET cc_start: 0.8750 (tmm) cc_final: 0.8006 (tmm) REVERT: A 2953 MET cc_start: 0.9205 (mmm) cc_final: 0.8970 (mmm) outliers start: 57 outliers final: 37 residues processed: 222 average time/residue: 0.1318 time to fit residues: 51.0610 Evaluate side-chains 194 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2024 TYR Chi-restraints excluded: chain A residue 2042 SER Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2496 ILE Chi-restraints excluded: chain A residue 2586 VAL Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2802 MET Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3171 VAL Chi-restraints excluded: chain A residue 3271 VAL Chi-restraints excluded: chain A residue 3284 SER Chi-restraints excluded: chain A residue 3302 LEU Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3540 THR Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3868 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 284 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 262 optimal weight: 0.0770 chunk 157 optimal weight: 8.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3419 GLN A3421 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.079486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.061877 restraints weight = 67801.485| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.71 r_work: 0.2799 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25050 Z= 0.127 Angle : 0.469 9.913 34277 Z= 0.245 Chirality : 0.037 0.173 4236 Planarity : 0.003 0.043 4158 Dihedral : 8.777 115.055 4028 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.48 % Allowed : 22.68 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 3228 helix: 2.04 (0.12), residues: 1896 sheet: -0.50 (0.32), residues: 259 loop : -0.43 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2232 TYR 0.011 0.001 TYR A 641 PHE 0.016 0.001 PHE A 325 TRP 0.011 0.001 TRP A2542 HIS 0.013 0.001 HIS A1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (25039) covalent geometry : angle 0.46808 / 0.25 (34269) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 0.74894 / 0.40 ( 2) hydrogen bonds : bond 0.03754 / 2.66 ( 1523) hydrogen bonds : angle 4.07068 / 2.98 ( 4345) metal coordination : bond 0.00944 / 0.51 ( 10) metal coordination : angle 2.35498 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 SER cc_start: 0.7928 (OUTLIER) cc_final: 0.7592 (t) REVERT: A 555 LYS cc_start: 0.8401 (ptpp) cc_final: 0.7728 (ptpp) REVERT: A 573 LYS cc_start: 0.9211 (mttm) cc_final: 0.8884 (mttm) REVERT: A 652 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7821 (tm-30) REVERT: A 808 MET cc_start: 0.8455 (tmm) cc_final: 0.7526 (tmm) REVERT: A 1065 CYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7449 (m) REVERT: A 1764 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8918 (mtmt) REVERT: A 1831 MET cc_start: 0.8970 (mmp) cc_final: 0.8702 (mmp) REVERT: A 1904 HIS cc_start: 0.7956 (t70) cc_final: 0.7697 (t70) REVERT: A 1928 TRP cc_start: 0.8636 (t60) cc_final: 0.8323 (t60) REVERT: A 2075 PHE cc_start: 0.9351 (m-10) cc_final: 0.8872 (m-80) REVERT: A 2150 THR cc_start: 0.9139 (m) cc_final: 0.8781 (t) REVERT: A 2248 MET cc_start: 0.9004 (mtm) cc_final: 0.8636 (mtm) REVERT: A 2332 MET cc_start: 0.9062 (ttt) cc_final: 0.8701 (ttm) REVERT: A 2890 MET cc_start: 0.8760 (mmm) cc_final: 0.8382 (tpt) outliers start: 56 outliers final: 34 residues processed: 218 average time/residue: 0.1345 time to fit residues: 51.0112 Evaluate side-chains 192 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1065 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2024 TYR Chi-restraints excluded: chain A residue 2496 ILE Chi-restraints excluded: chain A residue 2586 VAL Chi-restraints excluded: chain A residue 2802 MET Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3271 VAL Chi-restraints excluded: chain A residue 3284 SER Chi-restraints excluded: chain A residue 3302 LEU Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3540 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3868 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 304 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 280 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 HIS ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1446 HIS A1556 ASN ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.079261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061814 restraints weight = 67976.112| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.68 r_work: 0.2793 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25050 Z= 0.135 Angle : 0.470 13.546 34277 Z= 0.245 Chirality : 0.037 0.225 4236 Planarity : 0.003 0.042 4158 Dihedral : 8.759 112.974 4028 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.74 % Allowed : 22.37 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.15), residues: 3228 helix: 2.06 (0.12), residues: 1905 sheet: -0.46 (0.33), residues: 258 loop : -0.41 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1662 TYR 0.012 0.001 TYR A1612 PHE 0.013 0.001 PHE A3739 TRP 0.011 0.001 TRP A2542 HIS 0.007 0.001 HIS A1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (25039) covalent geometry : angle 0.46951 / 0.25 (34269) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 0.74595 / 0.40 ( 2) hydrogen bonds : bond 0.03581 / 2.53 ( 1523) hydrogen bonds : angle 3.96031 / 2.91 ( 4345) metal coordination : bond 0.00521 / 0.33 ( 10) metal coordination : angle 1.93709 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 151 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 SER cc_start: 0.8006 (OUTLIER) cc_final: 0.7668 (t) REVERT: A 808 MET cc_start: 0.8525 (tmm) cc_final: 0.7567 (tmm) REVERT: A 1065 CYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7409 (m) REVERT: A 1549 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8851 (p) REVERT: A 1764 LYS cc_start: 0.9186 (mtmt) cc_final: 0.8934 (mtmt) REVERT: A 1928 TRP cc_start: 0.8581 (t60) cc_final: 0.8217 (t60) REVERT: A 2042 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 2075 PHE cc_start: 0.9349 (m-10) cc_final: 0.8727 (m-10) REVERT: A 2150 THR cc_start: 0.9200 (m) cc_final: 0.8846 (t) REVERT: A 2248 MET cc_start: 0.9030 (mtm) cc_final: 0.8680 (mtm) REVERT: A 2890 MET cc_start: 0.8708 (mmm) cc_final: 0.8334 (tpt) REVERT: A 2953 MET cc_start: 0.9182 (mmm) cc_final: 0.8968 (mmm) outliers start: 62 outliers final: 43 residues processed: 204 average time/residue: 0.1288 time to fit residues: 44.6804 Evaluate side-chains 189 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1065 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2024 TYR Chi-restraints excluded: chain A residue 2042 SER Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2586 VAL Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2750 ARG Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3096 THR Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3193 THR Chi-restraints excluded: chain A residue 3271 VAL Chi-restraints excluded: chain A residue 3284 SER Chi-restraints excluded: chain A residue 3302 LEU Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3540 THR Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3723 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 165 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 chunk 268 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 207 optimal weight: 0.3980 chunk 288 optimal weight: 0.3980 chunk 296 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 276 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1556 ASN A1579 HIS ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.079926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062369 restraints weight = 67651.977| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.73 r_work: 0.2813 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25050 Z= 0.098 Angle : 0.444 10.574 34277 Z= 0.232 Chirality : 0.036 0.166 4236 Planarity : 0.003 0.041 4158 Dihedral : 8.740 110.784 4028 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.61 % Allowed : 22.59 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.15), residues: 3228 helix: 2.13 (0.12), residues: 1911 sheet: -0.36 (0.33), residues: 257 loop : -0.39 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3774 TYR 0.012 0.001 TYR A3738 PHE 0.012 0.001 PHE A2200 TRP 0.011 0.001 TRP A2542 HIS 0.004 0.001 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (25039) covalent geometry : angle 0.44316 / 0.23 (34269) SS BOND : bond 0.00025 / 0.01 ( 1) SS BOND : angle 0.63464 / 0.34 ( 2) hydrogen bonds : bond 0.03258 / 2.32 ( 1523) hydrogen bonds : angle 3.82744 / 2.82 ( 4345) metal coordination : bond 0.00305 / 0.19 ( 10) metal coordination : angle 1.36319 / 0.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7661 (t) REVERT: A 652 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 760 MET cc_start: 0.8684 (mtp) cc_final: 0.8397 (mtp) REVERT: A 808 MET cc_start: 0.8514 (tmm) cc_final: 0.7521 (tmm) REVERT: A 1065 CYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7295 (m) REVERT: A 1764 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8903 (mtmt) REVERT: A 1928 TRP cc_start: 0.8553 (t60) cc_final: 0.8132 (t60) REVERT: A 2042 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8356 (p) REVERT: A 2075 PHE cc_start: 0.9352 (m-10) cc_final: 0.8775 (m-10) REVERT: A 2150 THR cc_start: 0.9232 (m) cc_final: 0.8897 (t) REVERT: A 2248 MET cc_start: 0.9011 (mtm) cc_final: 0.8669 (mtm) REVERT: A 2292 MET cc_start: 0.8936 (mmm) cc_final: 0.8733 (mtt) REVERT: A 2830 ILE cc_start: 0.8766 (tp) cc_final: 0.8532 (tp) REVERT: A 2836 TYR cc_start: 0.8800 (m-80) cc_final: 0.8523 (m-80) REVERT: A 2890 MET cc_start: 0.8652 (mmm) cc_final: 0.8286 (tpt) REVERT: A 2902 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9093 (mt) outliers start: 59 outliers final: 44 residues processed: 214 average time/residue: 0.1365 time to fit residues: 49.6128 Evaluate side-chains 196 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1065 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 1917 LEU Chi-restraints excluded: chain A residue 2024 TYR Chi-restraints excluded: chain A residue 2042 SER Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2496 ILE Chi-restraints excluded: chain A residue 2586 VAL Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2750 ARG Chi-restraints excluded: chain A residue 2802 MET Chi-restraints excluded: chain A residue 2902 LEU Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3271 VAL Chi-restraints excluded: chain A residue 3284 SER Chi-restraints excluded: chain A residue 3302 LEU Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3540 THR Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3723 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 315 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 161 optimal weight: 0.2980 chunk 305 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1556 ASN ** A3409 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 = 0.3295 r_free = 0.3295 target = 0.078230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.060406 restraints weight = 67896.826| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.70 r_work: 0.2779 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25050 Z= 0.147 Angle : 0.463 9.898 34277 Z= 0.243 Chirality : 0.037 0.164 4236 Planarity : 0.003 0.040 4158 Dihedral : 8.757 109.782 4028 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.87 % Allowed : 22.55 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.15), residues: 3228 helix: 2.19 (0.12), residues: 1905 sheet: -0.40 (0.32), residues: 257 loop : -0.42 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3774 TYR 0.012 0.001 TYR A3684 PHE 0.027 0.001 PHE A2212 TRP 0.010 0.001 TRP A2362 HIS 0.004 0.001 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (25039) covalent geometry : angle 0.46231 / 0.24 (34269) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 0.67247 / 0.36 ( 2) hydrogen bonds : bond 0.03442 / 2.44 ( 1523) hydrogen bonds : angle 3.85336 / 2.83 ( 4345) metal coordination : bond 0.00537 / 0.34 ( 10) metal coordination : angle 1.61610 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 142 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 652 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 760 MET cc_start: 0.8720 (mtp) cc_final: 0.8417 (mtp) REVERT: A 808 MET cc_start: 0.8564 (tmm) cc_final: 0.7581 (tmm) REVERT: A 1065 CYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7286 (m) REVERT: A 1764 LYS cc_start: 0.9223 (mtmt) cc_final: 0.8972 (mtmt) REVERT: A 1928 TRP cc_start: 0.8565 (t60) cc_final: 0.8099 (t60) REVERT: A 2042 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8460 (p) REVERT: A 2075 PHE cc_start: 0.9359 (m-10) cc_final: 0.8721 (m-10) REVERT: A 2150 THR cc_start: 0.9234 (m) cc_final: 0.8899 (t) REVERT: A 2248 MET cc_start: 0.9050 (mtm) cc_final: 0.8705 (mtm) REVERT: A 2830 ILE cc_start: 0.8763 (tp) cc_final: 0.8536 (tp) REVERT: A 2890 MET cc_start: 0.8627 (mmm) cc_final: 0.8231 (tpt) REVERT: A 2902 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9076 (mt) REVERT: A 3697 PHE cc_start: 0.9245 (m-80) cc_final: 0.8991 (m-80) outliers start: 65 outliers final: 44 residues processed: 201 average time/residue: 0.1363 time to fit residues: 47.2546 Evaluate side-chains 185 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1065 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 1917 LEU Chi-restraints excluded: chain A residue 2042 SER Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2496 ILE Chi-restraints excluded: chain A residue 2586 VAL Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2640 ILE Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2750 ARG Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2802 MET Chi-restraints excluded: chain A residue 2902 LEU Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3284 SER Chi-restraints excluded: chain A residue 3302 LEU Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3540 THR Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3717 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 115 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 chunk 239 optimal weight: 0.7980 chunk 225 optimal weight: 0.0470 chunk 15 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2614 GLN ** A3409 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 = 0.3318 r_free = 0.3318 target = 0.079691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.062182 restraints weight = 67923.671| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.72 r_work: 0.2807 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 25050 Z= 0.096 Angle : 0.442 11.038 34277 Z= 0.230 Chirality : 0.036 0.167 4236 Planarity : 0.003 0.039 4158 Dihedral : 8.752 108.324 4028 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.30 % Allowed : 23.17 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.15), residues: 3228 helix: 2.24 (0.12), residues: 1905 sheet: -0.31 (0.33), residues: 257 loop : -0.39 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3774 TYR 0.010 0.001 TYR A 641 PHE 0.018 0.001 PHE A2212 TRP 0.011 0.001 TRP A2542 HIS 0.004 0.001 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (25039) covalent geometry : angle 0.44180 / 0.23 (34269) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 0.59679 / 0.32 ( 2) hydrogen bonds : bond 0.03163 / 2.25 ( 1523) hydrogen bonds : angle 3.75571 / 2.77 ( 4345) metal coordination : bond 0.00285 / 0.18 ( 10) metal coordination : angle 1.25881 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7700 (t) REVERT: A 652 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 760 MET cc_start: 0.8697 (mtp) cc_final: 0.8393 (mtp) REVERT: A 808 MET cc_start: 0.8554 (tmm) cc_final: 0.7573 (tmm) REVERT: A 1065 CYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7212 (m) REVERT: A 1764 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8922 (mtmt) REVERT: A 1928 TRP cc_start: 0.8556 (t60) cc_final: 0.8100 (t60) REVERT: A 2042 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8467 (p) REVERT: A 2075 PHE cc_start: 0.9350 (m-10) cc_final: 0.8703 (m-10) REVERT: A 2150 THR cc_start: 0.9226 (m) cc_final: 0.8903 (t) REVERT: A 2248 MET cc_start: 0.9024 (mtm) cc_final: 0.8698 (mtm) REVERT: A 2581 MET cc_start: 0.8643 (tmm) cc_final: 0.7919 (tmm) REVERT: A 2830 ILE cc_start: 0.8822 (tp) cc_final: 0.8605 (tp) REVERT: A 2836 TYR cc_start: 0.8795 (m-80) cc_final: 0.8545 (m-80) REVERT: A 2890 MET cc_start: 0.8655 (mmm) cc_final: 0.8285 (tpt) REVERT: A 3591 ARG cc_start: 0.8491 (mtm110) cc_final: 0.8123 (mtp180) REVERT: A 3697 PHE cc_start: 0.9213 (m-80) cc_final: 0.8961 (m-80) outliers start: 52 outliers final: 45 residues processed: 200 average time/residue: 0.1378 time to fit residues: 46.9443 Evaluate side-chains 195 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1065 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 1917 LEU Chi-restraints excluded: chain A residue 2024 TYR Chi-restraints excluded: chain A residue 2042 SER Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2586 VAL Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2614 GLN Chi-restraints excluded: chain A residue 2633 PHE Chi-restraints excluded: chain A residue 2640 ILE Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2750 ARG Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2802 MET Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3284 SER Chi-restraints excluded: chain A residue 3302 LEU Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3540 THR Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3717 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 106 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 202 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 299 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.079585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.062055 restraints weight = 68098.355| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.73 r_work: 0.2807 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25050 Z= 0.101 Angle : 0.449 11.732 34277 Z= 0.231 Chirality : 0.036 0.167 4236 Planarity : 0.003 0.038 4158 Dihedral : 8.736 107.068 4028 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.25 % Allowed : 23.21 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.16), residues: 3228 helix: 2.27 (0.12), residues: 1904 sheet: -0.31 (0.32), residues: 257 loop : -0.38 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1910 TYR 0.011 0.001 TYR A3684 PHE 0.024 0.001 PHE A2143 TRP 0.010 0.001 TRP A2542 HIS 0.004 0.001 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (25039) covalent geometry : angle 0.44851 / 0.23 (34269) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.62564 / 0.33 ( 2) hydrogen bonds : bond 0.03136 / 2.22 ( 1523) hydrogen bonds : angle 3.73665 / 2.76 ( 4345) metal coordination : bond 0.00312 / 0.20 ( 10) metal coordination : angle 1.17689 / 0.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7717 (t) REVERT: A 652 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 760 MET cc_start: 0.8721 (mtp) cc_final: 0.8385 (mtp) REVERT: A 808 MET cc_start: 0.8568 (tmm) cc_final: 0.7594 (tmm) REVERT: A 1065 CYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7207 (m) REVERT: A 1764 LYS cc_start: 0.9229 (mtmt) cc_final: 0.8986 (mtmt) REVERT: A 1928 TRP cc_start: 0.8520 (t60) cc_final: 0.8118 (t60) REVERT: A 2075 PHE cc_start: 0.9349 (m-10) cc_final: 0.8700 (m-10) REVERT: A 2150 THR cc_start: 0.9230 (m) cc_final: 0.8905 (t) REVERT: A 2248 MET cc_start: 0.9023 (mtm) cc_final: 0.8701 (mtm) REVERT: A 2581 MET cc_start: 0.8629 (tmm) cc_final: 0.7942 (tmm) REVERT: A 2830 ILE cc_start: 0.8804 (tp) cc_final: 0.8589 (tp) REVERT: A 2836 TYR cc_start: 0.8797 (m-80) cc_final: 0.8552 (m-80) REVERT: A 2890 MET cc_start: 0.8647 (mmm) cc_final: 0.8267 (tpt) REVERT: A 3591 ARG cc_start: 0.8498 (mtm110) cc_final: 0.8134 (mtp180) REVERT: A 3697 PHE cc_start: 0.9217 (m-80) cc_final: 0.8968 (m-80) outliers start: 51 outliers final: 46 residues processed: 196 average time/residue: 0.1475 time to fit residues: 50.1155 Evaluate side-chains 194 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1065 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 1917 LEU Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2586 VAL Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2633 PHE Chi-restraints excluded: chain A residue 2640 ILE Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2750 ARG Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2802 MET Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3284 SER Chi-restraints excluded: chain A residue 3302 LEU Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3540 THR Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3717 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 121 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 327 optimal weight: 0.3980 chunk 115 optimal weight: 3.9990 chunk 229 optimal weight: 0.4980 chunk 247 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2285 GLN A2614 GLN ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.062478 restraints weight = 67892.830| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.74 r_work: 0.2817 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25050 Z= 0.096 Angle : 0.443 12.534 34277 Z= 0.228 Chirality : 0.036 0.168 4236 Planarity : 0.003 0.038 4158 Dihedral : 8.701 104.332 4028 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.21 % Allowed : 23.17 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.16), residues: 3228 helix: 2.37 (0.12), residues: 1898 sheet: -0.30 (0.32), residues: 257 loop : -0.32 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1910 TYR 0.011 0.001 TYR A3684 PHE 0.023 0.001 PHE A2143 TRP 0.016 0.001 TRP A1905 HIS 0.004 0.001 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (25039) covalent geometry : angle 0.44293 / 0.23 (34269) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 0.58274 / 0.31 ( 2) hydrogen bonds : bond 0.03025 / 2.15 ( 1523) hydrogen bonds : angle 3.67750 / 2.72 ( 4345) metal coordination : bond 0.00276 / 0.18 ( 10) metal coordination : angle 1.07368 / 0.58 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 455 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7732 (t) REVERT: A 652 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 760 MET cc_start: 0.8722 (mtp) cc_final: 0.8400 (mtp) REVERT: A 808 MET cc_start: 0.8583 (tmm) cc_final: 0.7623 (tmm) REVERT: A 1065 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7356 (m) REVERT: A 1420 ILE cc_start: 0.9286 (tt) cc_final: 0.9054 (tt) REVERT: A 1764 LYS cc_start: 0.9262 (mtmt) cc_final: 0.9006 (mtmt) REVERT: A 1928 TRP cc_start: 0.8530 (t60) cc_final: 0.8159 (t60) REVERT: A 2075 PHE cc_start: 0.9357 (m-10) cc_final: 0.8715 (m-10) REVERT: A 2150 THR cc_start: 0.9230 (m) cc_final: 0.8908 (t) REVERT: A 2248 MET cc_start: 0.9006 (mtm) cc_final: 0.8699 (mtm) REVERT: A 2561 MET cc_start: 0.8362 (mmm) cc_final: 0.8141 (mmm) REVERT: A 2581 MET cc_start: 0.8605 (tmm) cc_final: 0.7907 (tmm) REVERT: A 2830 ILE cc_start: 0.8815 (tp) cc_final: 0.8589 (tp) REVERT: A 2836 TYR cc_start: 0.8778 (m-80) cc_final: 0.8521 (m-80) REVERT: A 2890 MET cc_start: 0.8613 (mmm) cc_final: 0.8214 (tpt) REVERT: A 3591 ARG cc_start: 0.8454 (mtm110) cc_final: 0.8094 (mtp180) REVERT: A 3697 PHE cc_start: 0.9179 (m-80) cc_final: 0.8951 (m-80) outliers start: 50 outliers final: 45 residues processed: 205 average time/residue: 0.1512 time to fit residues: 53.6723 Evaluate side-chains 197 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1065 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 1917 LEU Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2586 VAL Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2614 GLN Chi-restraints excluded: chain A residue 2633 PHE Chi-restraints excluded: chain A residue 2640 ILE Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2750 ARG Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2802 MET Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3284 SER Chi-restraints excluded: chain A residue 3302 LEU Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3540 THR Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 28 optimal weight: 6.9990 chunk 271 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 50 optimal weight: 0.0980 chunk 306 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2614 GLN ** A3409 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 = 0.3322 r_free = 0.3322 target = 0.079836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062311 restraints weight = 68175.853| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.74 r_work: 0.2813 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.221 25050 Z= 0.172 Angle : 0.615 59.200 34277 Z= 0.360 Chirality : 0.038 0.660 4236 Planarity : 0.003 0.038 4158 Dihedral : 8.699 104.240 4028 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.08 % Allowed : 23.34 % Favored : 74.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.16), residues: 3228 helix: 2.33 (0.12), residues: 1905 sheet: -0.30 (0.32), residues: 257 loop : -0.35 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3774 TYR 0.011 0.001 TYR A3684 PHE 0.017 0.001 PHE A1505 TRP 0.014 0.001 TRP A3240 HIS 0.004 0.000 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (25039) covalent geometry : angle 0.61462 / 0.36 (34269) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 0.66423 / 0.36 ( 2) hydrogen bonds : bond 0.03067 / 2.17 ( 1523) hydrogen bonds : angle 3.68460 / 2.72 ( 4345) metal coordination : bond 0.00316 / 0.20 ( 10) metal coordination : angle 1.07571 / 0.58 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5138.16 seconds wall clock time: 89 minutes 13.91 seconds (5353.91 seconds total)