Starting phenix.real_space_refine on Thu Aug 6 18:44:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r6y_18969/08_2026/8r6y_18969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r6y_18969/08_2026/8r6y_18969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r6y_18969/08_2026/8r6y_18969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r6y_18969/08_2026/8r6y_18969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r6y_18969/08_2026/8r6y_18969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r6y_18969/08_2026/8r6y_18969.map" } resolution = 3.4 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= 0.000 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: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 10394 2.51 5 N 2912 2.21 5 O 3222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16665 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1991, 15811 Classifications: {'peptide': 1991} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1918} Chain breaks: 7 Chain: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNA': 16} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain: "T" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 324 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 12} Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {'M7G': 1} Classifications: {'RNA': 3, 'undetermined': 1} Modifications used: {'rna2p_pur': 3} Link IDs: {'rna2p': 2, None: 1} Not linked: pdbres="M7G C 1 " pdbres=" A C 2 " Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, '2KH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.73, per 1000 atoms: 0.16 Number of scatterers: 16665 At special positions: 0 Unit cell: (106.53, 132.66, 121.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 41 15.00 Mg 1 11.99 O 3222 8.00 N 2912 7.00 C 10394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 550.1 milliseconds 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3722 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 19 sheets defined 52.0% alpha, 9.1% beta 9 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 72 through 76 removed outlier: 4.359A pdb=" N TYR A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.563A pdb=" N ASP A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.314A pdb=" N VAL A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 158 removed outlier: 3.567A pdb=" N LEU A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 184 through 206 Processing helix chain 'A' and resid 219 through 234 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 249 through 259 removed outlier: 4.117A pdb=" N LEU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 removed outlier: 3.505A pdb=" N HIS A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 318 removed outlier: 3.868A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.899A pdb=" N MET A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.594A pdb=" N ASP A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 372 " --> pdb=" O CYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.751A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 447 removed outlier: 3.756A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.534A pdb=" N LEU A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.523A pdb=" N HIS A 500 " --> pdb=" O THR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 605 through 611 removed outlier: 4.334A pdb=" N LEU A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 627 Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 656 through 671 removed outlier: 3.864A pdb=" N GLU A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 682 through 685 removed outlier: 4.038A pdb=" N LYS A 685 " --> pdb=" O LYS A 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 682 through 685' Processing helix chain 'A' and resid 686 through 691 removed outlier: 3.649A pdb=" N LEU A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 686 through 691' Processing helix chain 'A' and resid 696 through 716 removed outlier: 3.676A pdb=" N GLN A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 751 through 755 Processing helix chain 'A' and resid 767 through 780 removed outlier: 4.012A pdb=" N TYR A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 4.332A pdb=" N PHE A 787 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.551A pdb=" N LEU A 806 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 839 removed outlier: 3.614A pdb=" N THR A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.920A pdb=" N LEU A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 874 through 885 removed outlier: 3.502A pdb=" N THR A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 904 removed outlier: 3.958A pdb=" N ALA A 892 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 893 " --> pdb=" O TYR A 889 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 945 removed outlier: 4.251A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 960 removed outlier: 3.588A pdb=" N ASN A 959 " --> pdb=" O ARG A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 994 through 1005 removed outlier: 4.000A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1020 Processing helix chain 'A' and resid 1029 through 1039 removed outlier: 3.926A pdb=" N SER A1038 " --> pdb=" O ALA A1034 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A1039 " --> pdb=" O HIS A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1057 removed outlier: 3.869A pdb=" N GLU A1050 " --> pdb=" O ASP A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1108 removed outlier: 3.824A pdb=" N GLU A1108 " --> pdb=" O SER A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1155 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1210 through 1228 removed outlier: 3.603A pdb=" N ARG A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 Processing helix chain 'A' and resid 1257 through 1266 Processing helix chain 'A' and resid 1288 through 1300 removed outlier: 3.621A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1315 removed outlier: 3.826A pdb=" N LYS A1305 " --> pdb=" O ASP A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1356 Processing helix chain 'A' and resid 1360 through 1368 Processing helix chain 'A' and resid 1369 through 1374 removed outlier: 3.566A pdb=" N LEU A1372 " --> pdb=" O PRO A1369 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A1373 " --> pdb=" O GLY A1370 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A1374 " --> pdb=" O VAL A1371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1369 through 1374' Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1403 through 1412 removed outlier: 3.532A pdb=" N ARG A1407 " --> pdb=" O HIS A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1447 Processing helix chain 'A' and resid 1448 through 1452 Processing helix chain 'A' and resid 1457 through 1465 Processing helix chain 'A' and resid 1467 through 1479 Processing helix chain 'A' and resid 1512 through 1523 Processing helix chain 'A' and resid 1530 through 1545 Processing helix chain 'A' and resid 1551 through 1559 removed outlier: 3.653A pdb=" N THR A1555 " --> pdb=" O ASP A1551 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A1556 " --> pdb=" O PRO A1552 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A1557 " --> pdb=" O SER A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1574 removed outlier: 3.759A pdb=" N VAL A1574 " --> pdb=" O PHE A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1604 Processing helix chain 'A' and resid 1616 through 1624 removed outlier: 4.298A pdb=" N GLN A1620 " --> pdb=" O SER A1616 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A1621 " --> pdb=" O LEU A1617 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A1622 " --> pdb=" O ASP A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1638 removed outlier: 4.145A pdb=" N ILE A1628 " --> pdb=" O GLU A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1657 Processing helix chain 'A' and resid 1669 through 1683 removed outlier: 3.571A pdb=" N THR A1673 " --> pdb=" O SER A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1696 Processing helix chain 'A' and resid 1758 through 1773 Processing helix chain 'A' and resid 1820 through 1824 removed outlier: 3.628A pdb=" N VAL A1824 " --> pdb=" O PRO A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1858 through 1868 Processing helix chain 'A' and resid 1872 through 1876 removed outlier: 3.903A pdb=" N GLY A1875 " --> pdb=" O PHE A1872 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A1876 " --> pdb=" O SER A1873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1872 through 1876' Processing helix chain 'A' and resid 1890 through 1903 removed outlier: 4.060A pdb=" N ASN A1903 " --> pdb=" O VAL A1899 " (cutoff:3.500A) Processing helix chain 'A' and resid 1914 through 1931 removed outlier: 3.695A pdb=" N GLN A1930 " --> pdb=" O SER A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1957 removed outlier: 4.233A pdb=" N ILE A1956 " --> pdb=" O GLU A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2005 removed outlier: 3.568A pdb=" N VAL A2003 " --> pdb=" O GLY A1999 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A2005 " --> pdb=" O VAL A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2015 through 2027 removed outlier: 3.923A pdb=" N ALA A2024 " --> pdb=" O ILE A2020 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A2025 " --> pdb=" O THR A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2038 removed outlier: 3.953A pdb=" N ARG A2032 " --> pdb=" O LYS A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2055 removed outlier: 4.648A pdb=" N GLN A2047 " --> pdb=" O ALA A2043 " (cutoff:3.500A) Proline residue: A2050 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 removed outlier: 6.438A pdb=" N ILE A 122 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 168 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 124 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 170 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU A 126 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL A 172 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 125 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 113 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.582A pdb=" N THR A 39 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.647A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 543 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.647A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 543 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 721 removed outlier: 3.586A pdb=" N GLU A 728 " --> pdb=" O ILE A 721 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 851 Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 925 removed outlier: 3.921A pdb=" N ARG A 920 " --> pdb=" O LYS A 913 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 913 " --> pdb=" O ARG A 920 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE A 908 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 3.726A pdb=" N SER A1128 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER A 983 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL A1173 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id=AB2, first strand: chain 'A' and resid 1328 through 1329 removed outlier: 3.543A pdb=" N THR A1333 " --> pdb=" O THR A1329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1337 through 1339 Processing sheet with id=AB4, first strand: chain 'A' and resid 1496 through 1497 Processing sheet with id=AB5, first strand: chain 'A' and resid 1500 through 1502 removed outlier: 3.654A pdb=" N LEU A1502 " --> pdb=" O ARG A1579 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A1579 " --> pdb=" O LEU A1502 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1699 through 1705 removed outlier: 6.836A pdb=" N VAL A1724 " --> pdb=" O SER A1704 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A1721 " --> pdb=" O GLY A1740 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A1727 " --> pdb=" O VAL A1734 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N HIS A1733 " --> pdb=" O LEU A1752 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU A1752 " --> pdb=" O HIS A1733 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN A1735 " --> pdb=" O ILE A1750 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE A1750 " --> pdb=" O GLN A1735 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A1737 " --> pdb=" O GLU A1748 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1709 through 1712 removed outlier: 4.962A pdb=" N ARG A1712 " --> pdb=" O GLY A1716 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY A1716 " --> pdb=" O ARG A1712 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1794 through 1796 Processing sheet with id=AB9, first strand: chain 'A' and resid 1827 through 1829 Processing sheet with id=AC1, first strand: chain 'A' and resid 2039 through 2040 removed outlier: 3.982A pdb=" N CYS A2040 " --> pdb=" O SER A2063 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 737 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2654 1.30 - 1.43: 4627 1.43 - 1.56: 9568 1.56 - 1.68: 77 1.68 - 1.81: 156 Bond restraints: 17082 Sorted by residual: bond pdb=" C3' 2KH A2101 " pdb=" C4' 2KH A2101 " ideal model delta sigma weight residual 1.550 1.305 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" N3A 2KH A2101 " pdb=" PA 2KH A2101 " ideal model delta sigma weight residual 1.933 1.700 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" N7 A C 2 " pdb=" C5 A C 2 " ideal model delta sigma weight residual 1.388 1.330 0.058 6.00e-03 2.78e+04 9.27e+01 bond pdb=" N3A 2KH A2101 " pdb=" PB 2KH A2101 " ideal model delta sigma weight residual 1.890 1.701 0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" O2G 2KH A2101 " pdb=" PG 2KH A2101 " ideal model delta sigma weight residual 1.682 1.504 0.178 2.00e-02 2.50e+03 7.93e+01 ... (remaining 17077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.34: 23226 12.34 - 24.69: 14 24.69 - 37.03: 0 37.03 - 49.37: 0 49.37 - 61.71: 2 Bond angle restraints: 23242 Sorted by residual: angle pdb=" N1 A C 2 " pdb=" C2 A C 2 " pdb=" N3 A C 2 " ideal model delta sigma weight residual 129.30 118.46 10.84 5.00e-01 4.00e+00 4.70e+02 angle pdb=" N3A 2KH A2101 " pdb=" PA 2KH A2101 " pdb=" O2A 2KH A2101 " ideal model delta sigma weight residual 48.17 109.88 -61.71 3.00e+00 1.11e-01 4.23e+02 angle pdb=" C2 A C 2 " pdb=" N3 A C 2 " pdb=" C4 A C 2 " ideal model delta sigma weight residual 110.60 119.72 -9.12 5.00e-01 4.00e+00 3.33e+02 angle pdb=" O2G 2KH A2101 " pdb=" PG 2KH A2101 " pdb=" O3G 2KH A2101 " ideal model delta sigma weight residual 53.94 108.06 -54.12 3.00e+00 1.11e-01 3.25e+02 angle pdb=" N9 A C 2 " pdb=" C8 A C 2 " pdb=" N7 A C 2 " ideal model delta sigma weight residual 113.80 107.61 6.19 5.00e-01 4.00e+00 1.53e+02 ... (remaining 23237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 9993 35.35 - 70.71: 338 70.71 - 106.06: 38 106.06 - 141.42: 1 141.42 - 176.77: 7 Dihedral angle restraints: 10377 sinusoidal: 4617 harmonic: 5760 Sorted by residual: dihedral pdb=" C5' A C 3 " pdb=" C4' A C 3 " pdb=" C3' A C 3 " pdb=" O3' A C 3 " ideal model delta sinusoidal sigma weight residual 147.00 82.02 64.98 1 8.00e+00 1.56e-02 8.66e+01 dihedral pdb=" O4' U T 18 " pdb=" C1' U T 18 " pdb=" N1 U T 18 " pdb=" C2 U T 18 " ideal model delta sinusoidal sigma weight residual 200.00 33.10 166.90 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" C4' A C 3 " pdb=" C3' A C 3 " pdb=" C2' A C 3 " pdb=" C1' A C 3 " ideal model delta sinusoidal sigma weight residual -35.00 25.99 -60.99 1 8.00e+00 1.56e-02 7.72e+01 ... (remaining 10374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 2592 0.196 - 0.392: 9 0.392 - 0.588: 0 0.588 - 0.784: 0 0.784 - 0.980: 1 Chirality restraints: 2602 Sorted by residual: chirality pdb=" C1' A C 3 " pdb=" O4' A C 3 " pdb=" C2' A C 3 " pdb=" N9 A C 3 " both_signs ideal model delta sigma weight residual False 2.44 1.46 0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" P A C 3 " pdb=" OP1 A C 3 " pdb=" OP2 A C 3 " pdb=" O5' A C 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.80 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" C4' A C 2 " pdb=" C5' A C 2 " pdb=" O4' A C 2 " pdb=" C3' A C 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 2599 not shown) Planarity restraints: 2819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1160 " 0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO A1161 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A1161 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1161 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U T 22 " -0.027 2.00e-02 2.50e+03 1.48e-02 4.90e+00 pdb=" N1 U T 22 " 0.033 2.00e-02 2.50e+03 pdb=" C2 U T 22 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U T 22 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U T 22 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U T 22 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U T 22 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U T 22 " 0.006 2.00e-02 2.50e+03 pdb=" C6 U T 22 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C T 10 " 0.026 2.00e-02 2.50e+03 1.45e-02 4.73e+00 pdb=" N1 C T 10 " -0.033 2.00e-02 2.50e+03 pdb=" C2 C T 10 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C T 10 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C T 10 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C T 10 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C T 10 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C T 10 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C T 10 " -0.004 2.00e-02 2.50e+03 ... (remaining 2816 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 174 2.60 - 3.18: 13763 3.18 - 3.75: 26468 3.75 - 4.33: 34226 4.33 - 4.90: 56974 Nonbonded interactions: 131605 Sorted by model distance: nonbonded pdb=" O3B 2KH A2101 " pdb="MG MG A2102 " model vdw 2.029 2.170 nonbonded pdb=" O1A 2KH A2101 " pdb="MG MG A2102 " model vdw 2.186 2.170 nonbonded pdb=" O2 C P 14 " pdb=" N2 G T 12 " model vdw 2.232 2.496 nonbonded pdb=" OG1 THR A 558 " pdb=" O HIS A 563 " model vdw 2.246 3.040 nonbonded pdb=" O MET A1729 " pdb=" OG1 THR A1732 " model vdw 2.262 3.040 ... (remaining 131600 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.690 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.006 0.245 17083 Z= 0.334 Angle : 0.984 61.713 23242 Z= 0.563 Chirality : 0.049 0.980 2602 Planarity : 0.004 0.066 2819 Dihedral : 17.341 176.771 6655 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.38 % Allowed : 9.81 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.60 (0.18), residues: 1975 helix: 0.85 (0.17), residues: 916 sheet: -0.46 (0.38), residues: 191 loop : -1.79 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 667 TYR 0.010 0.001 TYR A1101 PHE 0.009 0.001 PHE A1148 TRP 0.024 0.001 TRP A1894 HIS 0.003 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.33 (17082) covalent geometry : angle 0.98368 / 0.56 (23242) hydrogen bonds : bond 0.17401 / 11.91 ( 748) hydrogen bonds : angle 6.01843 / 4.38 ( 2145) Misc. bond : bond 0.07129 / 3.75 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 174 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8308 (ptm) cc_final: 0.8020 (tpp) REVERT: A 274 GLU cc_start: 0.8717 (tp30) cc_final: 0.8477 (tp30) REVERT: A 356 MET cc_start: 0.9045 (mpp) cc_final: 0.8825 (mpp) REVERT: A 406 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.8023 (mt) REVERT: A 436 MET cc_start: 0.8505 (mpp) cc_final: 0.8183 (mpp) REVERT: A 777 MET cc_start: 0.7819 (tpp) cc_final: 0.7394 (tpp) REVERT: A 1270 ASP cc_start: 0.8275 (t70) cc_final: 0.7971 (t0) REVERT: A 1515 ASP cc_start: 0.8843 (m-30) cc_final: 0.8431 (m-30) REVERT: A 1524 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8880 (pp) REVERT: A 1672 MET cc_start: 0.8828 (tmm) cc_final: 0.8594 (tmm) REVERT: A 1694 ARG cc_start: 0.8601 (tmm160) cc_final: 0.8025 (tmm160) REVERT: A 1752 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 1832 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7762 (mm) REVERT: A 1845 MET cc_start: 0.8487 (tpt) cc_final: 0.8276 (tpt) REVERT: A 1868 ASN cc_start: 0.8506 (m-40) cc_final: 0.8221 (p0) REVERT: A 1896 HIS cc_start: 0.9385 (t70) cc_final: 0.9155 (t-170) REVERT: A 1913 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7308 (ttp80) REVERT: A 1924 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 2022 MET cc_start: 0.8922 (tmm) cc_final: 0.8720 (tmm) REVERT: A 2026 MET cc_start: 0.8980 (tpt) cc_final: 0.8521 (tpp) outliers start: 59 outliers final: 19 residues processed: 226 average time/residue: 0.1090 time to fit residues: 37.8591 Evaluate side-chains 168 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain A residue 991 GLN Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1519 GLU Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1832 ILE Chi-restraints excluded: chain A residue 1908 GLN Chi-restraints excluded: chain A residue 1913 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS A 421 GLN A 466 ASN A 644 GLN A 757 ASN ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1483 HIS A1494 ASN A1745 ASN ** A1775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.101556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074652 restraints weight = 42572.667| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.50 r_work: 0.3044 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 17083 Z= 0.258 Angle : 0.668 11.788 23242 Z= 0.347 Chirality : 0.043 0.453 2602 Planarity : 0.005 0.061 2819 Dihedral : 15.893 165.920 2824 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.98 % Allowed : 13.60 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.37 (0.18), residues: 1975 helix: 1.16 (0.17), residues: 923 sheet: -0.55 (0.37), residues: 191 loop : -1.78 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1843 TYR 0.016 0.002 TYR A 923 PHE 0.013 0.002 PHE A1465 TRP 0.017 0.002 TRP A1894 HIS 0.018 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.26 (17082) covalent geometry : angle 0.66760 / 0.35 (23242) hydrogen bonds : bond 0.06079 / 3.98 ( 748) hydrogen bonds : angle 4.85838 / 3.50 ( 2145) Misc. bond : bond 0.00699 / 0.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8913 (tp30) cc_final: 0.8686 (tp30) REVERT: A 356 MET cc_start: 0.9132 (mpp) cc_final: 0.8922 (mpp) REVERT: A 436 MET cc_start: 0.8658 (mpp) cc_final: 0.8037 (mpp) REVERT: A 777 MET cc_start: 0.8179 (tpp) cc_final: 0.7732 (tpp) REVERT: A 1029 ASP cc_start: 0.8918 (t0) cc_final: 0.8601 (t0) REVERT: A 1222 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8989 (tt) REVERT: A 1270 ASP cc_start: 0.8365 (t70) cc_final: 0.8041 (t0) REVERT: A 1528 LYS cc_start: 0.8593 (mttm) cc_final: 0.8045 (mttp) REVERT: A 1672 MET cc_start: 0.8934 (tmm) cc_final: 0.8514 (tmm) REVERT: A 1694 ARG cc_start: 0.8714 (tmm160) cc_final: 0.8160 (tmm160) REVERT: A 1752 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8723 (tt) REVERT: A 1845 MET cc_start: 0.8323 (tpt) cc_final: 0.8111 (tpt) REVERT: A 1913 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7409 (ttp80) REVERT: A 1924 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7267 (tm-30) REVERT: A 1989 TRP cc_start: 0.8758 (p-90) cc_final: 0.8351 (p-90) REVERT: A 2022 MET cc_start: 0.8822 (tmm) cc_final: 0.8590 (tmm) REVERT: A 2026 MET cc_start: 0.8536 (tpt) cc_final: 0.8035 (tpp) outliers start: 52 outliers final: 33 residues processed: 186 average time/residue: 0.1075 time to fit residues: 31.3290 Evaluate side-chains 174 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1519 GLU Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1627 SER Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1908 GLN Chi-restraints excluded: chain A residue 1913 ARG Chi-restraints excluded: chain A residue 2054 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 79 optimal weight: 10.0000 chunk 194 optimal weight: 30.0000 chunk 158 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 33 optimal weight: 0.0980 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN A 928 ASN ** A1775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN A1896 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.103202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.076815 restraints weight = 42886.892| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.48 r_work: 0.3099 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17083 Z= 0.127 Angle : 0.535 9.565 23242 Z= 0.282 Chirality : 0.039 0.198 2602 Planarity : 0.003 0.059 2819 Dihedral : 15.429 164.825 2806 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.98 % Allowed : 14.74 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.10 (0.19), residues: 1975 helix: 1.45 (0.17), residues: 925 sheet: -0.43 (0.38), residues: 189 loop : -1.74 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 823 TYR 0.010 0.001 TYR A1348 PHE 0.008 0.001 PHE A1163 TRP 0.020 0.001 TRP A 520 HIS 0.008 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (17082) covalent geometry : angle 0.53549 / 0.28 (23242) hydrogen bonds : bond 0.05088 / 3.34 ( 748) hydrogen bonds : angle 4.46758 / 3.20 ( 2145) Misc. bond : bond 0.00278 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8146 (pm20) cc_final: 0.7924 (pm20) REVERT: A 274 GLU cc_start: 0.8876 (tp30) cc_final: 0.8646 (tp30) REVERT: A 436 MET cc_start: 0.8668 (mpp) cc_final: 0.8150 (mpp) REVERT: A 777 MET cc_start: 0.8158 (tpp) cc_final: 0.7713 (tpp) REVERT: A 1029 ASP cc_start: 0.8910 (t0) cc_final: 0.8609 (t0) REVERT: A 1270 ASP cc_start: 0.8355 (t70) cc_final: 0.8031 (t0) REVERT: A 1396 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8825 (t) REVERT: A 1528 LYS cc_start: 0.8577 (mttm) cc_final: 0.8023 (mttp) REVERT: A 1672 MET cc_start: 0.8889 (tmm) cc_final: 0.8629 (tmm) REVERT: A 1694 ARG cc_start: 0.8687 (tmm160) cc_final: 0.8127 (tmm160) REVERT: A 1752 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8697 (tt) REVERT: A 1924 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 1989 TRP cc_start: 0.8735 (p-90) cc_final: 0.8296 (p-90) REVERT: A 2022 MET cc_start: 0.8848 (tmm) cc_final: 0.8619 (tmm) REVERT: A 2026 MET cc_start: 0.8585 (tpt) cc_final: 0.8031 (tpp) outliers start: 52 outliers final: 32 residues processed: 188 average time/residue: 0.1122 time to fit residues: 33.1650 Evaluate side-chains 172 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1519 GLU Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1908 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 178 optimal weight: 20.0000 chunk 200 optimal weight: 50.0000 chunk 154 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.103233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076275 restraints weight = 42515.231| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.44 r_work: 0.3095 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17083 Z= 0.111 Angle : 0.505 7.318 23242 Z= 0.264 Chirality : 0.038 0.193 2602 Planarity : 0.003 0.057 2819 Dihedral : 15.124 163.920 2801 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.56 % Allowed : 15.20 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.06 (0.19), residues: 1975 helix: 1.58 (0.17), residues: 931 sheet: -0.35 (0.38), residues: 189 loop : -1.68 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1493 TYR 0.016 0.001 TYR A1864 PHE 0.009 0.001 PHE A 911 TRP 0.020 0.001 TRP A 520 HIS 0.003 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (17082) covalent geometry : angle 0.50528 / 0.26 (23242) hydrogen bonds : bond 0.04611 / 3.04 ( 748) hydrogen bonds : angle 4.26851 / 3.06 ( 2145) Misc. bond : bond 0.00083 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 145 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8605 (tpp) cc_final: 0.8367 (tpt) REVERT: A 274 GLU cc_start: 0.8842 (tp30) cc_final: 0.8597 (tp30) REVERT: A 436 MET cc_start: 0.8638 (mpp) cc_final: 0.8236 (mpp) REVERT: A 777 MET cc_start: 0.8184 (tpp) cc_final: 0.7768 (tpp) REVERT: A 800 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: A 1029 ASP cc_start: 0.8886 (t0) cc_final: 0.8594 (t0) REVERT: A 1270 ASP cc_start: 0.8399 (t70) cc_final: 0.8067 (t0) REVERT: A 1396 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8792 (t) REVERT: A 1528 LYS cc_start: 0.8581 (mttm) cc_final: 0.8034 (mttp) REVERT: A 1672 MET cc_start: 0.8855 (tmm) cc_final: 0.8593 (tmm) REVERT: A 1694 ARG cc_start: 0.8676 (tmm160) cc_final: 0.8104 (tmm160) REVERT: A 1752 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8710 (tt) REVERT: A 1913 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7427 (ttp80) REVERT: A 1924 GLU cc_start: 0.7647 (tm-30) cc_final: 0.6954 (tm-30) REVERT: A 1989 TRP cc_start: 0.8736 (p-90) cc_final: 0.8278 (p-90) REVERT: A 2022 MET cc_start: 0.8842 (tmm) cc_final: 0.8616 (tmm) REVERT: A 2026 MET cc_start: 0.8487 (tpt) cc_final: 0.7886 (tpp) outliers start: 62 outliers final: 38 residues processed: 195 average time/residue: 0.1278 time to fit residues: 38.7633 Evaluate side-chains 177 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1519 GLU Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1619 ASN Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1913 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 124 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 HIS A 757 ASN A1091 HIS ** A1775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN A1896 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.102483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074893 restraints weight = 42920.663| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.67 r_work: 0.3068 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17083 Z= 0.164 Angle : 0.548 9.853 23242 Z= 0.282 Chirality : 0.039 0.192 2602 Planarity : 0.003 0.059 2819 Dihedral : 14.957 164.391 2797 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.96 % Allowed : 15.55 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.05 (0.19), residues: 1975 helix: 1.59 (0.17), residues: 933 sheet: -0.34 (0.38), residues: 189 loop : -1.71 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 823 TYR 0.010 0.001 TYR A 923 PHE 0.011 0.001 PHE A 195 TRP 0.018 0.001 TRP A 520 HIS 0.009 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (17082) covalent geometry : angle 0.54831 / 0.28 (23242) hydrogen bonds : bond 0.04733 / 3.13 ( 748) hydrogen bonds : angle 4.26327 / 3.06 ( 2145) Misc. bond : bond 0.00073 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 139 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8885 (tp30) cc_final: 0.8639 (tp30) REVERT: A 406 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7973 (mt) REVERT: A 436 MET cc_start: 0.8663 (mpp) cc_final: 0.8434 (mpp) REVERT: A 777 MET cc_start: 0.8226 (tpp) cc_final: 0.7797 (tpp) REVERT: A 800 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8486 (mm-30) REVERT: A 1029 ASP cc_start: 0.8934 (t0) cc_final: 0.8639 (t0) REVERT: A 1270 ASP cc_start: 0.8383 (t70) cc_final: 0.8047 (t0) REVERT: A 1339 MET cc_start: 0.8656 (ptp) cc_final: 0.8442 (pmm) REVERT: A 1396 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8807 (t) REVERT: A 1528 LYS cc_start: 0.8595 (mttm) cc_final: 0.8051 (mttp) REVERT: A 1672 MET cc_start: 0.8904 (tmm) cc_final: 0.8644 (tmm) REVERT: A 1694 ARG cc_start: 0.8683 (tmm160) cc_final: 0.8106 (tmm160) REVERT: A 1752 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8717 (tt) REVERT: A 1913 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7428 (ttp80) REVERT: A 1933 MET cc_start: 0.7950 (tmm) cc_final: 0.7726 (tmm) REVERT: A 2022 MET cc_start: 0.8827 (tmm) cc_final: 0.8590 (tmm) REVERT: A 2026 MET cc_start: 0.8433 (tpt) cc_final: 0.7819 (tpp) outliers start: 69 outliers final: 48 residues processed: 195 average time/residue: 0.1207 time to fit residues: 37.2323 Evaluate side-chains 187 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1519 GLU Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1619 ASN Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1913 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 0.0570 chunk 120 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN ** A1775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN ** A1896 HIS ** 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 = 0.3780 r_free = 0.3780 target = 0.102097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074076 restraints weight = 42456.812| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.45 r_work: 0.3073 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17083 Z= 0.168 Angle : 0.551 8.605 23242 Z= 0.284 Chirality : 0.039 0.192 2602 Planarity : 0.003 0.059 2819 Dihedral : 14.920 164.792 2797 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.02 % Allowed : 16.41 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.04 (0.19), residues: 1975 helix: 1.56 (0.17), residues: 939 sheet: -0.31 (0.39), residues: 190 loop : -1.73 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1493 TYR 0.012 0.001 TYR A1864 PHE 0.010 0.001 PHE A 911 TRP 0.018 0.001 TRP A 520 HIS 0.010 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (17082) covalent geometry : angle 0.55118 / 0.28 (23242) hydrogen bonds : bond 0.04737 / 3.14 ( 748) hydrogen bonds : angle 4.24889 / 3.05 ( 2145) Misc. bond : bond 0.00089 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 134 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8127 (ptt180) REVERT: A 181 MET cc_start: 0.8635 (tpp) cc_final: 0.8381 (tpt) REVERT: A 274 GLU cc_start: 0.8863 (tp30) cc_final: 0.8613 (tp30) REVERT: A 406 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7944 (mt) REVERT: A 777 MET cc_start: 0.8225 (tpp) cc_final: 0.7817 (tpp) REVERT: A 800 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8472 (mm-30) REVERT: A 1029 ASP cc_start: 0.8931 (t0) cc_final: 0.8627 (t0) REVERT: A 1270 ASP cc_start: 0.8406 (t70) cc_final: 0.8083 (t0) REVERT: A 1339 MET cc_start: 0.8657 (ptp) cc_final: 0.8369 (pmm) REVERT: A 1396 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8774 (t) REVERT: A 1528 LYS cc_start: 0.8595 (mttm) cc_final: 0.8049 (mttp) REVERT: A 1672 MET cc_start: 0.8907 (tmm) cc_final: 0.8641 (tmm) REVERT: A 1694 ARG cc_start: 0.8687 (tmm160) cc_final: 0.8104 (tmm160) REVERT: A 1752 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8746 (tt) REVERT: A 1913 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7388 (ttp80) REVERT: A 1933 MET cc_start: 0.8001 (tmm) cc_final: 0.7746 (tmm) REVERT: A 2022 MET cc_start: 0.8834 (tmm) cc_final: 0.8595 (tmm) REVERT: A 2026 MET cc_start: 0.8444 (tpt) cc_final: 0.7860 (tpp) outliers start: 70 outliers final: 49 residues processed: 192 average time/residue: 0.1304 time to fit residues: 39.3087 Evaluate side-chains 187 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 132 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1619 ASN Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1913 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 149 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 74 optimal weight: 0.0970 chunk 137 optimal weight: 0.0980 chunk 87 optimal weight: 0.0870 chunk 151 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.4560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN A 757 ASN ** A1775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN A1896 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.104268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077003 restraints weight = 42102.685| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.61 r_work: 0.3113 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17083 Z= 0.097 Angle : 0.523 8.812 23242 Z= 0.266 Chirality : 0.038 0.193 2602 Planarity : 0.003 0.057 2819 Dihedral : 14.816 164.133 2794 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.44 % Allowed : 17.33 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.15 (0.19), residues: 1975 helix: 1.65 (0.18), residues: 939 sheet: -0.19 (0.39), residues: 190 loop : -1.69 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1869 TYR 0.010 0.001 TYR A1348 PHE 0.010 0.001 PHE A 911 TRP 0.030 0.001 TRP A1892 HIS 0.009 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (17082) covalent geometry : angle 0.52289 / 0.27 (23242) hydrogen bonds : bond 0.04180 / 2.79 ( 748) hydrogen bonds : angle 4.05859 / 2.91 ( 2145) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8616 (tpp) cc_final: 0.8369 (tpt) REVERT: A 274 GLU cc_start: 0.8866 (tp30) cc_final: 0.8606 (tp30) REVERT: A 406 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7982 (mt) REVERT: A 436 MET cc_start: 0.8639 (mpp) cc_final: 0.8316 (mpp) REVERT: A 686 MET cc_start: 0.9158 (mmm) cc_final: 0.8786 (mmp) REVERT: A 710 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8199 (ttp) REVERT: A 777 MET cc_start: 0.8218 (tpp) cc_final: 0.7777 (tpp) REVERT: A 800 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8429 (mm-30) REVERT: A 1029 ASP cc_start: 0.8921 (t0) cc_final: 0.8610 (t0) REVERT: A 1270 ASP cc_start: 0.8420 (t70) cc_final: 0.8054 (t0) REVERT: A 1339 MET cc_start: 0.8663 (ptp) cc_final: 0.8402 (pmm) REVERT: A 1396 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8771 (t) REVERT: A 1528 LYS cc_start: 0.8575 (mttm) cc_final: 0.8042 (mttp) REVERT: A 1672 MET cc_start: 0.8883 (tmm) cc_final: 0.8610 (tmm) REVERT: A 1694 ARG cc_start: 0.8682 (tmm160) cc_final: 0.8094 (tmm160) REVERT: A 1752 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8710 (tt) REVERT: A 1868 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8191 (p0) REVERT: A 1913 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7407 (ttp80) REVERT: A 1933 MET cc_start: 0.8064 (tmm) cc_final: 0.7855 (tmm) REVERT: A 2022 MET cc_start: 0.8839 (tmm) cc_final: 0.8604 (tmm) REVERT: A 2026 MET cc_start: 0.8482 (tpt) cc_final: 0.7876 (tpp) outliers start: 60 outliers final: 39 residues processed: 182 average time/residue: 0.1338 time to fit residues: 38.3223 Evaluate side-chains 181 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1619 ASN Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1913 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 182 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 149 optimal weight: 0.0030 chunk 2 optimal weight: 9.9990 chunk 192 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 173 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN A 439 ASN ** A1775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN A1896 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.102845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.074810 restraints weight = 42525.933| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.46 r_work: 0.3092 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17083 Z= 0.148 Angle : 0.536 9.141 23242 Z= 0.274 Chirality : 0.039 0.192 2602 Planarity : 0.003 0.057 2819 Dihedral : 14.746 164.672 2789 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.61 % Allowed : 17.33 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.16 (0.19), residues: 1975 helix: 1.66 (0.18), residues: 940 sheet: -0.21 (0.39), residues: 190 loop : -1.69 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1493 TYR 0.018 0.001 TYR A1306 PHE 0.010 0.001 PHE A 911 TRP 0.034 0.001 TRP A1892 HIS 0.017 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (17082) covalent geometry : angle 0.53639 / 0.27 (23242) hydrogen bonds : bond 0.04426 / 2.96 ( 748) hydrogen bonds : angle 4.09759 / 2.94 ( 2145) Misc. bond : bond 0.00079 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 132 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8867 (tp30) cc_final: 0.8604 (tp30) REVERT: A 406 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8049 (mt) REVERT: A 436 MET cc_start: 0.8615 (mpp) cc_final: 0.8290 (mpp) REVERT: A 710 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.8260 (ttp) REVERT: A 777 MET cc_start: 0.8251 (tpp) cc_final: 0.7809 (tpp) REVERT: A 800 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8470 (mm-30) REVERT: A 1029 ASP cc_start: 0.8941 (t0) cc_final: 0.8637 (t0) REVERT: A 1270 ASP cc_start: 0.8440 (t70) cc_final: 0.8099 (t0) REVERT: A 1339 MET cc_start: 0.8643 (ptp) cc_final: 0.8375 (pmm) REVERT: A 1396 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8754 (t) REVERT: A 1528 LYS cc_start: 0.8594 (mttm) cc_final: 0.8050 (mttp) REVERT: A 1672 MET cc_start: 0.8894 (tmm) cc_final: 0.8628 (tmm) REVERT: A 1694 ARG cc_start: 0.8704 (tmm160) cc_final: 0.8102 (tmm160) REVERT: A 1752 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8750 (tt) REVERT: A 1913 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7392 (ttp80) REVERT: A 1933 MET cc_start: 0.8103 (tmm) cc_final: 0.7871 (tmm) REVERT: A 2022 MET cc_start: 0.8834 (tmm) cc_final: 0.8589 (tmm) REVERT: A 2026 MET cc_start: 0.8425 (tpt) cc_final: 0.7823 (tpp) outliers start: 63 outliers final: 48 residues processed: 182 average time/residue: 0.1364 time to fit residues: 38.8672 Evaluate side-chains 187 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 133 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1442 LEU Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1619 ASN Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1913 ARG Chi-restraints excluded: chain A residue 2011 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 172 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN A 757 ASN A1691 GLN ** A1775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN A1896 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.103350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.075709 restraints weight = 42597.526| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.73 r_work: 0.3084 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17083 Z= 0.120 Angle : 0.534 9.656 23242 Z= 0.271 Chirality : 0.039 0.197 2602 Planarity : 0.003 0.057 2819 Dihedral : 14.731 167.716 2789 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.44 % Allowed : 17.50 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.17 (0.19), residues: 1975 helix: 1.67 (0.18), residues: 939 sheet: -0.15 (0.39), residues: 190 loop : -1.70 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1493 TYR 0.021 0.001 TYR A1306 PHE 0.010 0.001 PHE A 911 TRP 0.037 0.001 TRP A1892 HIS 0.016 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (17082) covalent geometry : angle 0.53388 / 0.27 (23242) hydrogen bonds : bond 0.04278 / 2.87 ( 748) hydrogen bonds : angle 4.04446 / 2.91 ( 2145) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8555 (tpp) cc_final: 0.8305 (tpt) REVERT: A 274 GLU cc_start: 0.8874 (tp30) cc_final: 0.8613 (tp30) REVERT: A 406 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8085 (mt) REVERT: A 436 MET cc_start: 0.8650 (mpp) cc_final: 0.8344 (mpp) REVERT: A 710 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.8191 (ttp) REVERT: A 800 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8491 (mm-30) REVERT: A 1029 ASP cc_start: 0.8948 (t0) cc_final: 0.8639 (t0) REVERT: A 1270 ASP cc_start: 0.8460 (t70) cc_final: 0.8100 (t0) REVERT: A 1339 MET cc_start: 0.8664 (ptp) cc_final: 0.8386 (pmm) REVERT: A 1396 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8741 (t) REVERT: A 1528 LYS cc_start: 0.8592 (mttm) cc_final: 0.8047 (mttp) REVERT: A 1672 MET cc_start: 0.8905 (tmm) cc_final: 0.8633 (tmm) REVERT: A 1694 ARG cc_start: 0.8699 (tmm160) cc_final: 0.8088 (tmm160) REVERT: A 1752 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8716 (tt) REVERT: A 1913 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7407 (ttp80) REVERT: A 1933 MET cc_start: 0.8120 (tmm) cc_final: 0.7857 (tmm) REVERT: A 2022 MET cc_start: 0.8809 (tmm) cc_final: 0.8566 (tmm) REVERT: A 2026 MET cc_start: 0.8358 (tpt) cc_final: 0.7764 (tpp) outliers start: 60 outliers final: 46 residues processed: 183 average time/residue: 0.1336 time to fit residues: 38.5433 Evaluate side-chains 185 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1442 LEU Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1619 ASN Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1913 ARG Chi-restraints excluded: chain A residue 2011 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 63 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN A1896 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.103311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075366 restraints weight = 42307.322| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.46 r_work: 0.3097 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17083 Z= 0.129 Angle : 0.539 10.030 23242 Z= 0.274 Chirality : 0.039 0.261 2602 Planarity : 0.003 0.057 2819 Dihedral : 14.716 171.158 2789 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.56 % Allowed : 17.50 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.18 (0.19), residues: 1975 helix: 1.68 (0.18), residues: 939 sheet: -0.14 (0.39), residues: 190 loop : -1.69 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1783 TYR 0.028 0.001 TYR A1306 PHE 0.019 0.001 PHE A 411 TRP 0.040 0.001 TRP A1892 HIS 0.013 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (17082) covalent geometry : angle 0.53939 / 0.27 (23242) hydrogen bonds : bond 0.04278 / 2.87 ( 748) hydrogen bonds : angle 4.03779 / 2.90 ( 2145) Misc. bond : bond 0.00077 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 132 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.8589 (tpp) cc_final: 0.8334 (tpt) REVERT: A 274 GLU cc_start: 0.8858 (tp30) cc_final: 0.8591 (tp30) REVERT: A 406 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8111 (mt) REVERT: A 436 MET cc_start: 0.8642 (mpp) cc_final: 0.8310 (mpp) REVERT: A 686 MET cc_start: 0.9135 (mmm) cc_final: 0.8767 (mmp) REVERT: A 710 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.8232 (ttp) REVERT: A 777 MET cc_start: 0.8419 (mmm) cc_final: 0.8102 (tpp) REVERT: A 800 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8441 (mm-30) REVERT: A 1029 ASP cc_start: 0.8934 (t0) cc_final: 0.8638 (t0) REVERT: A 1270 ASP cc_start: 0.8460 (t70) cc_final: 0.8093 (t0) REVERT: A 1339 MET cc_start: 0.8616 (ptp) cc_final: 0.8338 (pmm) REVERT: A 1396 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8741 (t) REVERT: A 1528 LYS cc_start: 0.8591 (mttm) cc_final: 0.8042 (mttp) REVERT: A 1672 MET cc_start: 0.8902 (tmm) cc_final: 0.8631 (tmm) REVERT: A 1694 ARG cc_start: 0.8702 (tmm160) cc_final: 0.8092 (tmm160) REVERT: A 1752 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8731 (tt) REVERT: A 1913 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7392 (ttp80) REVERT: A 1933 MET cc_start: 0.8154 (tmm) cc_final: 0.7936 (tmm) REVERT: A 2022 MET cc_start: 0.8829 (tmm) cc_final: 0.8585 (tmm) REVERT: A 2026 MET cc_start: 0.8441 (tpt) cc_final: 0.7837 (tpp) outliers start: 62 outliers final: 47 residues processed: 183 average time/residue: 0.1240 time to fit residues: 35.8286 Evaluate side-chains 183 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1442 LEU Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1619 ASN Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1913 ARG Chi-restraints excluded: chain A residue 2011 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 93 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 928 ASN ** A1775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN A1896 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.101207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.073114 restraints weight = 42827.038| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.46 r_work: 0.3049 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17083 Z= 0.234 Angle : 0.611 8.374 23242 Z= 0.311 Chirality : 0.041 0.252 2602 Planarity : 0.004 0.061 2819 Dihedral : 14.760 173.610 2789 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.21 % Allowed : 17.79 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.06 (0.19), residues: 1975 helix: 1.57 (0.18), residues: 938 sheet: -0.23 (0.39), residues: 190 loop : -1.73 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1783 TYR 0.033 0.002 TYR A1306 PHE 0.017 0.002 PHE A 411 TRP 0.040 0.002 TRP A1892 HIS 0.020 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (17082) covalent geometry : angle 0.61080 / 0.31 (23242) hydrogen bonds : bond 0.04953 / 3.31 ( 748) hydrogen bonds : angle 4.25985 / 3.06 ( 2145) Misc. bond : bond 0.00144 / 0.08 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3886.65 seconds wall clock time: 67 minutes 32.42 seconds (4052.42 seconds total)