Starting phenix.real_space_refine on Fri Jul 3 18:49:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8asb_15610/07_2026/8asb_15610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asb_15610/07_2026/8asb_15610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8asb_15610/07_2026/8asb_15610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asb_15610/07_2026/8asb_15610.map" model { file = "/net/cci-nas-00/data/ceres_data/8asb_15610/07_2026/8asb_15610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asb_15610/07_2026/8asb_15610.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8asb_15610/07_2026/8asb_15610.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8asb_15610/07_2026/8asb_15610.cif" } resolution = 3.6 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 873 atoms to isotropic. 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 40 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 9019 2.51 5 N 2529 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14487 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1715, 13628 Classifications: {'peptide': 1715} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1651} Chain breaks: 10 Conformer: "B" Number of residues, atoms: 1715, 13628 Classifications: {'peptide': 1715} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1651} Chain breaks: 10 bond proxies already assigned to first conformer: 13879 Chain: "P" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 363 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "T" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 381 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 3, 'rna3p': 14} 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: "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: 5.35, per 1000 atoms: 0.37 Number of scatterers: 14487 At special positions: 0 Unit cell: (115.6, 110.5, 126.65, 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 82 16.00 P 40 15.00 Mg 1 11.99 O 2816 8.00 N 2529 7.00 C 9019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 17 sheets defined 53.8% alpha, 10.9% beta 6 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.610A pdb=" N ARG A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.768A pdb=" N VAL A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 158 removed outlier: 4.596A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix removed outlier: 4.447A pdb=" N ASP A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 206 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.731A pdb=" N LEU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 262 through 285 Processing helix chain 'A' and resid 292 through 318 removed outlier: 3.706A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.971A pdb=" N GLY A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 3.729A pdb=" N ILE A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.705A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 447 removed outlier: 3.734A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.692A pdb=" N GLY A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 492 through 495 removed outlier: 3.662A pdb=" N ASP A 495 " --> pdb=" O ALA A 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 492 through 495' Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.699A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 4.176A pdb=" N THR A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 656 through 665 removed outlier: 3.808A pdb=" N ILE A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 671 Processing helix chain 'A' and resid 672 through 675 removed outlier: 3.521A pdb=" N VAL A 675 " --> pdb=" O GLU A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 672 through 675' Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.871A pdb=" N LYS A 685 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 687 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 682 through 688' Processing helix chain 'A' and resid 696 through 716 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 751 through 756 removed outlier: 3.701A pdb=" N TYR A 754 " --> pdb=" O TYR A 751 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 756 " --> pdb=" O GLY A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 767 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 771 through 777 removed outlier: 3.559A pdb=" N VAL A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 4.041A pdb=" N PHE A 787 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 Processing helix chain 'A' and resid 824 through 840 removed outlier: 3.977A pdb=" N ASN A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 840 " --> pdb=" O GLU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 874 through 884 Processing helix chain 'A' and resid 889 through 904 removed outlier: 3.586A pdb=" N VAL A 893 " --> pdb=" O TYR A 889 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLN A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 947 removed outlier: 3.669A pdb=" N ARG A 930 " --> pdb=" O ASP A 926 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 946 " --> pdb=" O CYS A 942 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 947 " --> pdb=" O VAL A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 959 removed outlier: 3.777A pdb=" N ASN A 959 " --> pdb=" O ARG A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 974 removed outlier: 4.038A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 removed outlier: 4.123A pdb=" N HIS A 993 " --> pdb=" O TRP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1006 removed outlier: 3.878A pdb=" N PHE A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1010 through 1020 removed outlier: 4.278A pdb=" N ALA A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1038 removed outlier: 3.971A pdb=" N SER A1038 " --> pdb=" O ALA A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1057 removed outlier: 4.036A pdb=" N GLU A1050 " --> pdb=" O ASP A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1109 Processing helix chain 'A' and resid 1138 through 1155 removed outlier: 3.861A pdb=" N VAL A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A1144 " --> pdb=" O MET A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1161 through 1164 Processing helix chain 'A' and resid 1194 through 1200 removed outlier: 4.376A pdb=" N TRP A1198 " --> pdb=" O PRO A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1228 removed outlier: 3.875A pdb=" N GLN A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 Processing helix chain 'A' and resid 1255 through 1257 No H-bonds generated for 'chain 'A' and resid 1255 through 1257' Processing helix chain 'A' and resid 1258 through 1268 removed outlier: 3.798A pdb=" N SER A1267 " --> pdb=" O GLY A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1274 Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 4.181A pdb=" N ALA A1284 " --> pdb=" O PRO A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1300 removed outlier: 3.541A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.549A pdb=" N LYS A1305 " --> pdb=" O ASP A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1344 No H-bonds generated for 'chain 'A' and resid 1342 through 1344' Processing helix chain 'A' and resid 1345 through 1356 removed outlier: 3.502A pdb=" N ALA A1350 " --> pdb=" O LYS A1346 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET A1355 " --> pdb=" O LEU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1368 removed outlier: 3.902A pdb=" N GLN A1364 " --> pdb=" O ASP A1360 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A1368 " --> pdb=" O GLN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1372 removed outlier: 3.700A pdb=" N LEU A1372 " --> pdb=" O PRO A1369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1369 through 1372' Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1392 through 1397 Processing helix chain 'A' and resid 1403 through 1410 Processing helix chain 'A' and resid 1437 through 1448 removed outlier: 3.564A pdb=" N SER A1448 " --> pdb=" O MET A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1465 Processing helix chain 'A' and resid 1467 through 1476 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 1558 Processing helix chain 'A' and resid 1563 through 1575 removed outlier: 3.820A pdb=" N PHE A1567 " --> pdb=" O SER A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1605 Processing helix chain 'A' and resid 1669 through 1683 Processing helix chain 'A' and resid 1687 through 1695 Processing helix chain 'A' and resid 1757 through 1773 removed outlier: 3.604A pdb=" N ASP A1771 " --> pdb=" O ARG A1767 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A1772 " --> pdb=" O LEU A1768 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 6.700A pdb=" N GLY A 168 " --> pdb=" O GLU A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.540A pdb=" N ARG A 577 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.672A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 543 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.672A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 543 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA8, first strand: chain 'A' and resid 850 through 851 Processing sheet with id=AA9, first strand: chain 'A' and resid 921 through 925 removed outlier: 6.197A pdb=" N MET A 906 " --> pdb=" O LYS A1025 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N MET A1027 " --> pdb=" O MET A 906 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE A 908 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 4.622A pdb=" N TYR A1166 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 6.875A pdb=" N SER A 983 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A1173 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id=AB4, first strand: chain 'A' and resid 1339 through 1340 Processing sheet with id=AB5, first strand: chain 'A' and resid 1486 through 1488 Processing sheet with id=AB6, first strand: chain 'A' and resid 1496 through 1500 Processing sheet with id=AB7, first strand: chain 'A' and resid 1700 through 1703 Processing sheet with id=AB8, first strand: chain 'A' and resid 1750 through 1752 removed outlier: 4.023A pdb=" N ILE A1750 " --> pdb=" O PRO A1805 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A1788 " --> pdb=" O VAL A1806 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A1789 " --> pdb=" O LYS A1796 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A1794 " --> pdb=" O SER A1791 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1887 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2301 1.31 - 1.43: 4162 1.43 - 1.56: 8185 1.56 - 1.69: 76 1.69 - 1.81: 136 Bond restraints: 14860 Sorted by residual: bond pdb=" C3' 2KH A2102 " pdb=" C4' 2KH A2102 " ideal model delta sigma weight residual 1.550 1.297 0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" N3A 2KH A2102 " pdb=" PA 2KH A2102 " ideal model delta sigma weight residual 1.933 1.704 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" N3A 2KH A2102 " pdb=" PB 2KH A2102 " ideal model delta sigma weight residual 1.890 1.704 0.186 2.00e-02 2.50e+03 8.69e+01 bond pdb=" O2G 2KH A2102 " pdb=" PG 2KH A2102 " ideal model delta sigma weight residual 1.682 1.509 0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" O3G 2KH A2102 " pdb=" PG 2KH A2102 " ideal model delta sigma weight residual 1.669 1.509 0.160 2.00e-02 2.50e+03 6.41e+01 ... (remaining 14855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.40: 20226 12.40 - 24.81: 6 24.81 - 37.21: 0 37.21 - 49.62: 0 49.62 - 62.02: 2 Bond angle restraints: 20234 Sorted by residual: angle pdb=" N3A 2KH A2102 " pdb=" PA 2KH A2102 " pdb=" O2A 2KH A2102 " ideal model delta sigma weight residual 48.17 110.19 -62.02 3.00e+00 1.11e-01 4.27e+02 angle pdb=" O2G 2KH A2102 " pdb=" PG 2KH A2102 " pdb=" O3G 2KH A2102 " ideal model delta sigma weight residual 53.94 109.54 -55.60 3.00e+00 1.11e-01 3.43e+02 angle pdb=" O1A 2KH A2102 " pdb=" PA 2KH A2102 " pdb=" O2A 2KH A2102 " ideal model delta sigma weight residual 130.82 109.12 21.70 3.00e+00 1.11e-01 5.23e+01 angle pdb=" O1B 2KH A2102 " pdb=" PB 2KH A2102 " pdb=" O2B 2KH A2102 " ideal model delta sigma weight residual 130.56 109.35 21.21 3.00e+00 1.11e-01 5.00e+01 angle pdb=" O1G 2KH A2102 " pdb=" PG 2KH A2102 " pdb=" O2G 2KH A2102 " ideal model delta sigma weight residual 130.21 109.24 20.97 3.00e+00 1.11e-01 4.89e+01 ... (remaining 20229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 8509 27.34 - 54.69: 370 54.69 - 82.03: 35 82.03 - 109.38: 7 109.38 - 136.72: 1 Dihedral angle restraints: 8922 sinusoidal: 3950 harmonic: 4972 Sorted by residual: dihedral pdb=" CA GLU A 126 " pdb=" C GLU A 126 " pdb=" N PHE A 127 " pdb=" CA PHE A 127 " ideal model delta harmonic sigma weight residual -180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA THR A 995 " pdb=" C THR A 995 " pdb=" N THR A 996 " pdb=" CA THR A 996 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR A 83 " pdb=" C THR A 83 " pdb=" N PHE A 84 " pdb=" CA PHE A 84 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 8919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1826 0.052 - 0.104: 353 0.104 - 0.157: 80 0.157 - 0.209: 5 0.209 - 0.261: 4 Chirality restraints: 2268 Sorted by residual: chirality pdb=" C2' 2KH A2102 " pdb=" C1' 2KH A2102 " pdb=" C3' 2KH A2102 " pdb=" O2' 2KH A2102 " both_signs ideal model delta sigma weight residual False -2.85 -2.59 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C3' 2KH A2102 " pdb=" C2' 2KH A2102 " pdb=" C4' 2KH A2102 " pdb=" O3' 2KH A2102 " both_signs ideal model delta sigma weight residual False -2.66 -2.41 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' G T 13 " pdb=" C4' G T 13 " pdb=" O3' G T 13 " pdb=" C2' G T 13 " both_signs ideal model delta sigma weight residual False -2.48 -2.23 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2265 not shown) Planarity restraints: 2438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 897 " -0.028 2.00e-02 2.50e+03 2.22e-02 1.24e+01 pdb=" CG TRP A 897 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 897 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 897 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 897 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 897 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 897 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 897 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 897 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 897 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 556 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.83e+00 pdb=" N PRO A 557 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1712 " 0.036 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A1713 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A1713 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1713 " 0.031 5.00e-02 4.00e+02 ... (remaining 2435 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 285 2.68 - 3.24: 13502 3.24 - 3.79: 23185 3.79 - 4.35: 30233 4.35 - 4.90: 49013 Nonbonded interactions: 116218 Sorted by model distance: nonbonded pdb="MG MG A2101 " pdb=" O2A 2KH A2102 " model vdw 2.130 2.170 nonbonded pdb=" OD1 ASP A 985 " pdb="MG MG A2101 " model vdw 2.134 2.170 nonbonded pdb=" OH TYR A 286 " pdb=" OE1 GLU A 303 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR A 951 " pdb=" OH TYR A1181 " model vdw 2.222 3.040 nonbonded pdb=" OD2 ASP A1126 " pdb="MG MG A2101 " model vdw 2.226 2.170 ... (remaining 116213 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=0.31 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.940 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 0.253 14860 Z= 0.278 Angle : 0.975 62.020 20234 Z= 0.426 Chirality : 0.045 0.261 2268 Planarity : 0.005 0.060 2438 Dihedral : 14.383 136.722 5710 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.94 (0.19), residues: 1697 helix: 0.43 (0.18), residues: 791 sheet: -0.38 (0.43), residues: 148 loop : -1.83 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1542 TYR 0.035 0.002 TYR A 202 PHE 0.037 0.002 PHE A 84 TRP 0.059 0.002 TRP A 897 HIS 0.010 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.28 (14860) covalent geometry : angle 0.97543 / 0.43 (20234) hydrogen bonds : bond 0.15393 / 10.53 ( 656) hydrogen bonds : angle 6.22677 / 4.48 ( 1919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.491 Fit side-chains REVERT: A 200 GLU cc_start: 0.7317 (tp30) cc_final: 0.6444 (tp30) REVERT: A 204 LYS cc_start: 0.7705 (mtmm) cc_final: 0.6986 (mtmm) REVERT: A 213 GLU cc_start: 0.6865 (mp0) cc_final: 0.6419 (mp0) REVERT: A 271 LYS cc_start: 0.7641 (ptpp) cc_final: 0.7095 (ptpp) REVERT: A 302 CYS cc_start: 0.7799 (t) cc_final: 0.7396 (t) REVERT: A 306 ASP cc_start: 0.7321 (m-30) cc_final: 0.6981 (m-30) REVERT: A 488 GLU cc_start: 0.7103 (tp30) cc_final: 0.6776 (tp30) REVERT: A 489 LYS cc_start: 0.7722 (ttmt) cc_final: 0.7440 (tttt) REVERT: A 495 ASP cc_start: 0.7373 (p0) cc_final: 0.7170 (p0) REVERT: A 618 ASN cc_start: 0.7334 (m-40) cc_final: 0.7017 (m-40) REVERT: A 661 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6585 (mm-30) REVERT: A 719 SER cc_start: 0.8394 (t) cc_final: 0.8109 (t) REVERT: A 759 GLU cc_start: 0.6815 (tp30) cc_final: 0.6492 (mm-30) REVERT: A 856 LYS cc_start: 0.7637 (tmtt) cc_final: 0.7405 (tmtt) REVERT: A 864 VAL cc_start: 0.8017 (m) cc_final: 0.7802 (p) REVERT: A 887 MET cc_start: 0.6732 (tmm) cc_final: 0.6177 (tmm) REVERT: A 964 ASN cc_start: 0.7780 (m-40) cc_final: 0.7556 (m-40) REVERT: A 1032 PHE cc_start: 0.7850 (t80) cc_final: 0.7555 (t80) REVERT: A 1064 TRP cc_start: 0.7426 (p-90) cc_final: 0.7171 (p-90) REVERT: A 1108 GLU cc_start: 0.7636 (pp20) cc_final: 0.7175 (pp20) REVERT: A 1123 GLU cc_start: 0.7027 (pp20) cc_final: 0.6588 (pp20) REVERT: A 1141 ASP cc_start: 0.7166 (t0) cc_final: 0.6722 (t0) REVERT: A 1182 ASN cc_start: 0.7904 (m-40) cc_final: 0.7698 (m-40) REVERT: A 1227 GLU cc_start: 0.7116 (pp20) cc_final: 0.6844 (pp20) REVERT: A 1610 SER cc_start: 0.8037 (m) cc_final: 0.7810 (m) REVERT: A 1845 MET cc_start: 0.5366 (ptm) cc_final: 0.4717 (ptm) outliers start: 1 outliers final: 1 residues processed: 358 average time/residue: 0.1518 time to fit residues: 75.3229 Evaluate side-chains 334 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0970 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 990 ASN A1011 HIS A1569 ASN A1604 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113711 restraints weight = 53185.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119468 restraints weight = 19473.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123101 restraints weight = 9593.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125479 restraints weight = 5606.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126959 restraints weight = 3724.702| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14860 Z= 0.152 Angle : 0.604 8.279 20234 Z= 0.312 Chirality : 0.042 0.218 2268 Planarity : 0.005 0.061 2438 Dihedral : 8.432 137.495 2356 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.53 % Allowed : 9.09 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.30 (0.20), residues: 1697 helix: 1.09 (0.18), residues: 810 sheet: 0.12 (0.45), residues: 140 loop : -1.77 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1497 TYR 0.018 0.002 TYR A 754 PHE 0.026 0.002 PHE A1048 TRP 0.031 0.001 TRP A 897 HIS 0.011 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (14860) covalent geometry : angle 0.60424 / 0.31 (20234) hydrogen bonds : bond 0.04146 / 2.88 ( 656) hydrogen bonds : angle 4.57062 / 3.32 ( 1919) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 364 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6860 (ppp) cc_final: 0.6281 (pmm) REVERT: A 145 LYS cc_start: 0.7113 (mmtt) cc_final: 0.6758 (ttmm) REVERT: A 200 GLU cc_start: 0.7462 (tp30) cc_final: 0.6951 (tp30) REVERT: A 209 ASP cc_start: 0.7145 (m-30) cc_final: 0.6342 (m-30) REVERT: A 271 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7421 (ptpp) REVERT: A 302 CYS cc_start: 0.7816 (t) cc_final: 0.7469 (t) REVERT: A 306 ASP cc_start: 0.7309 (m-30) cc_final: 0.6988 (m-30) REVERT: A 488 GLU cc_start: 0.7222 (tp30) cc_final: 0.6834 (tp30) REVERT: A 495 ASP cc_start: 0.7396 (p0) cc_final: 0.7142 (p0) REVERT: A 544 LYS cc_start: 0.8082 (mttt) cc_final: 0.7860 (mttt) REVERT: A 671 MET cc_start: 0.6642 (mmm) cc_final: 0.6377 (tpp) REVERT: A 719 SER cc_start: 0.8349 (t) cc_final: 0.8108 (t) REVERT: A 759 GLU cc_start: 0.6707 (tp30) cc_final: 0.6389 (mm-30) REVERT: A 864 VAL cc_start: 0.8186 (m) cc_final: 0.7983 (p) REVERT: A 933 GLN cc_start: 0.7500 (tm-30) cc_final: 0.7268 (tm-30) REVERT: A 964 ASN cc_start: 0.7845 (m-40) cc_final: 0.7624 (m-40) REVERT: A 1032 PHE cc_start: 0.7840 (t80) cc_final: 0.7543 (t80) REVERT: A 1064 TRP cc_start: 0.7626 (p-90) cc_final: 0.7343 (p-90) REVERT: A 1108 GLU cc_start: 0.7561 (pp20) cc_final: 0.7209 (pp20) REVERT: A 1123 GLU cc_start: 0.6918 (pp20) cc_final: 0.6517 (pp20) REVERT: A 1137 LYS cc_start: 0.8454 (mttt) cc_final: 0.8047 (mttt) REVERT: A 1141 ASP cc_start: 0.7356 (t0) cc_final: 0.7060 (t0) REVERT: A 1142 GLU cc_start: 0.7530 (tt0) cc_final: 0.7324 (tt0) REVERT: A 1182 ASN cc_start: 0.8179 (m-40) cc_final: 0.7937 (m-40) REVERT: A 1193 ARG cc_start: 0.7552 (mtp180) cc_final: 0.7294 (mtp180) REVERT: A 1223 THR cc_start: 0.7888 (m) cc_final: 0.7582 (p) REVERT: A 1227 GLU cc_start: 0.7139 (pp20) cc_final: 0.6872 (pp20) REVERT: A 1346 LYS cc_start: 0.7324 (mtpt) cc_final: 0.6978 (mtpt) REVERT: A 1381 GLU cc_start: 0.6739 (tm-30) cc_final: 0.6539 (tm-30) REVERT: A 1514 GLU cc_start: 0.7446 (tp30) cc_final: 0.7127 (tp30) REVERT: A 1755 ASP cc_start: 0.7662 (p0) cc_final: 0.7256 (p0) REVERT: A 1845 MET cc_start: 0.5686 (ptm) cc_final: 0.5162 (ptm) outliers start: 8 outliers final: 7 residues processed: 368 average time/residue: 0.1613 time to fit residues: 81.0897 Evaluate side-chains 351 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 344 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 135 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 GLN A1292 ASN A1569 ASN ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111584 restraints weight = 62118.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.117678 restraints weight = 21415.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121495 restraints weight = 10292.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123916 restraints weight = 5933.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125539 restraints weight = 3920.693| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14860 Z= 0.150 Angle : 0.575 7.240 20234 Z= 0.298 Chirality : 0.042 0.211 2268 Planarity : 0.004 0.056 2438 Dihedral : 8.402 141.123 2354 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.06 % Allowed : 10.48 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.20), residues: 1697 helix: 1.23 (0.19), residues: 811 sheet: -0.11 (0.44), residues: 148 loop : -1.71 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1542 TYR 0.016 0.002 TYR A 668 PHE 0.037 0.002 PHE A 82 TRP 0.026 0.001 TRP A 897 HIS 0.010 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (14860) covalent geometry : angle 0.57501 / 0.30 (20234) hydrogen bonds : bond 0.03801 / 2.61 ( 656) hydrogen bonds : angle 4.30921 / 3.14 ( 1919) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 366 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 87 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6550 (mm) REVERT: A 113 VAL cc_start: 0.7792 (t) cc_final: 0.7572 (p) REVERT: A 125 VAL cc_start: 0.8408 (t) cc_final: 0.8179 (t) REVERT: A 135 ILE cc_start: 0.8522 (mm) cc_final: 0.8033 (tp) REVERT: A 145 LYS cc_start: 0.7233 (mmtt) cc_final: 0.6959 (ttmm) REVERT: A 179 SER cc_start: 0.8045 (m) cc_final: 0.7391 (t) REVERT: A 200 GLU cc_start: 0.7523 (tp30) cc_final: 0.6992 (tp30) REVERT: A 209 ASP cc_start: 0.7170 (m-30) cc_final: 0.6248 (m-30) REVERT: A 213 GLU cc_start: 0.6986 (mp0) cc_final: 0.6582 (mp0) REVERT: A 239 GLU cc_start: 0.7425 (pp20) cc_final: 0.7193 (pp20) REVERT: A 245 PHE cc_start: 0.7753 (m-80) cc_final: 0.7532 (m-10) REVERT: A 271 LYS cc_start: 0.8020 (ptpp) cc_final: 0.7493 (ptpp) REVERT: A 302 CYS cc_start: 0.7849 (t) cc_final: 0.7541 (t) REVERT: A 306 ASP cc_start: 0.7334 (m-30) cc_final: 0.6974 (m-30) REVERT: A 488 GLU cc_start: 0.7228 (tp30) cc_final: 0.6866 (tp30) REVERT: A 489 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7524 (tttt) REVERT: A 495 ASP cc_start: 0.7497 (p0) cc_final: 0.7269 (p0) REVERT: A 707 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6983 (mp) REVERT: A 719 SER cc_start: 0.8371 (t) cc_final: 0.8131 (t) REVERT: A 848 MET cc_start: 0.7352 (mmm) cc_final: 0.6961 (mmm) REVERT: A 863 GLU cc_start: 0.7212 (mp0) cc_final: 0.7007 (mp0) REVERT: A 912 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8332 (ttmm) REVERT: A 933 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 964 ASN cc_start: 0.7844 (m-40) cc_final: 0.7581 (m-40) REVERT: A 1012 ARG cc_start: 0.7432 (ttp80) cc_final: 0.7068 (ttp80) REVERT: A 1052 MET cc_start: 0.7335 (mmt) cc_final: 0.7090 (mmt) REVERT: A 1064 TRP cc_start: 0.7720 (p-90) cc_final: 0.7425 (p-90) REVERT: A 1108 GLU cc_start: 0.7535 (pp20) cc_final: 0.7211 (pp20) REVERT: A 1137 LYS cc_start: 0.8438 (mttt) cc_final: 0.8016 (mttt) REVERT: A 1141 ASP cc_start: 0.7417 (t0) cc_final: 0.7098 (t0) REVERT: A 1142 GLU cc_start: 0.7537 (tt0) cc_final: 0.7331 (tt0) REVERT: A 1182 ASN cc_start: 0.8226 (m-40) cc_final: 0.7976 (m-40) REVERT: A 1193 ARG cc_start: 0.7602 (mtp180) cc_final: 0.7337 (mtp180) REVERT: A 1216 GLU cc_start: 0.7103 (pt0) cc_final: 0.6842 (pt0) REVERT: A 1223 THR cc_start: 0.7892 (m) cc_final: 0.7559 (p) REVERT: A 1227 GLU cc_start: 0.7216 (pp20) cc_final: 0.6915 (pp20) REVERT: A 1346 LYS cc_start: 0.7325 (mtpt) cc_final: 0.6963 (mtpt) REVERT: A 1514 GLU cc_start: 0.7307 (tp30) cc_final: 0.6970 (tp30) REVERT: A 1755 ASP cc_start: 0.7786 (p0) cc_final: 0.7393 (p0) REVERT: A 1845 MET cc_start: 0.5684 (ptm) cc_final: 0.5380 (ptm) outliers start: 14 outliers final: 5 residues processed: 368 average time/residue: 0.1591 time to fit residues: 80.4632 Evaluate side-chains 361 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 354 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS A 618 ASN ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1349 GLN A1353 ASN A1569 ASN ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112582 restraints weight = 57062.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118473 restraints weight = 20323.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122163 restraints weight = 9932.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124583 restraints weight = 5820.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126220 restraints weight = 3842.613| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14860 Z= 0.129 Angle : 0.554 7.316 20234 Z= 0.287 Chirality : 0.041 0.294 2268 Planarity : 0.004 0.055 2438 Dihedral : 8.293 141.140 2354 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.39 % Allowed : 12.74 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.03 (0.20), residues: 1697 helix: 1.35 (0.19), residues: 811 sheet: 0.28 (0.45), residues: 139 loop : -1.71 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1407 TYR 0.017 0.002 TYR A 754 PHE 0.023 0.002 PHE A 99 TRP 0.032 0.001 TRP A 897 HIS 0.008 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14860) covalent geometry : angle 0.55393 / 0.29 (20234) hydrogen bonds : bond 0.03505 / 2.40 ( 656) hydrogen bonds : angle 4.20101 / 3.06 ( 1919) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 368 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 VAL cc_start: 0.7799 (t) cc_final: 0.7579 (p) REVERT: A 135 ILE cc_start: 0.8549 (mm) cc_final: 0.8022 (tp) REVERT: A 145 LYS cc_start: 0.7392 (mmtt) cc_final: 0.7050 (ttmm) REVERT: A 179 SER cc_start: 0.7964 (m) cc_final: 0.7420 (t) REVERT: A 200 GLU cc_start: 0.7529 (tp30) cc_final: 0.6906 (tp30) REVERT: A 209 ASP cc_start: 0.7048 (m-30) cc_final: 0.5734 (m-30) REVERT: A 213 GLU cc_start: 0.6909 (mp0) cc_final: 0.6233 (mp0) REVERT: A 271 LYS cc_start: 0.8000 (ptpp) cc_final: 0.7460 (ptpp) REVERT: A 302 CYS cc_start: 0.7852 (t) cc_final: 0.7506 (t) REVERT: A 306 ASP cc_start: 0.7332 (m-30) cc_final: 0.6970 (m-30) REVERT: A 410 ARG cc_start: 0.7751 (mtt-85) cc_final: 0.7516 (mtt-85) REVERT: A 488 GLU cc_start: 0.7233 (tp30) cc_final: 0.6957 (tp30) REVERT: A 495 ASP cc_start: 0.7484 (p0) cc_final: 0.7277 (p0) REVERT: A 719 SER cc_start: 0.8364 (t) cc_final: 0.8124 (t) REVERT: A 848 MET cc_start: 0.7374 (mmm) cc_final: 0.6999 (mmm) REVERT: A 864 VAL cc_start: 0.8162 (p) cc_final: 0.7936 (t) REVERT: A 897 TRP cc_start: 0.8356 (t-100) cc_final: 0.8083 (t-100) REVERT: A 964 ASN cc_start: 0.7840 (m-40) cc_final: 0.7564 (m-40) REVERT: A 1052 MET cc_start: 0.7317 (mmt) cc_final: 0.7065 (mmt) REVERT: A 1064 TRP cc_start: 0.7673 (p-90) cc_final: 0.7399 (p-90) REVERT: A 1108 GLU cc_start: 0.7562 (pp20) cc_final: 0.7197 (pp20) REVERT: A 1137 LYS cc_start: 0.8446 (mttt) cc_final: 0.7988 (mttt) REVERT: A 1141 ASP cc_start: 0.7447 (t0) cc_final: 0.7195 (t0) REVERT: A 1142 GLU cc_start: 0.7519 (tt0) cc_final: 0.7291 (tt0) REVERT: A 1182 ASN cc_start: 0.8215 (m-40) cc_final: 0.7903 (m-40) REVERT: A 1193 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7161 (mtp180) REVERT: A 1223 THR cc_start: 0.7865 (m) cc_final: 0.7545 (p) REVERT: A 1227 GLU cc_start: 0.7221 (pp20) cc_final: 0.6884 (pp20) REVERT: A 1346 LYS cc_start: 0.7368 (mtpt) cc_final: 0.6973 (mtpt) REVERT: A 1417 SER cc_start: 0.8085 (p) cc_final: 0.7786 (p) REVERT: A 1443 MET cc_start: 0.7638 (mtt) cc_final: 0.7331 (mtm) REVERT: A 1514 GLU cc_start: 0.7234 (tp30) cc_final: 0.6649 (tp30) REVERT: A 1725 TRP cc_start: 0.7218 (t60) cc_final: 0.6939 (t60) REVERT: A 1755 ASP cc_start: 0.7784 (p0) cc_final: 0.7427 (p0) REVERT: A 1845 MET cc_start: 0.5682 (ptm) cc_final: 0.5368 (ptm) outliers start: 19 outliers final: 12 residues processed: 371 average time/residue: 0.1591 time to fit residues: 80.8372 Evaluate side-chains 372 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 360 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 111 optimal weight: 0.0770 chunk 114 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 933 GLN ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN A1364 GLN A1569 ASN ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110779 restraints weight = 51531.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116279 restraints weight = 19574.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119770 restraints weight = 9843.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122005 restraints weight = 5842.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123456 restraints weight = 3979.089| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14860 Z= 0.223 Angle : 0.606 7.078 20234 Z= 0.317 Chirality : 0.044 0.234 2268 Planarity : 0.004 0.055 2438 Dihedral : 8.441 140.030 2354 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.79 % Allowed : 13.60 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.24 (0.20), residues: 1697 helix: 1.23 (0.19), residues: 812 sheet: -0.27 (0.44), residues: 147 loop : -1.78 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1542 TYR 0.024 0.002 TYR A 754 PHE 0.033 0.002 PHE A 82 TRP 0.024 0.002 TRP A 897 HIS 0.028 0.002 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (14860) covalent geometry : angle 0.60590 / 0.32 (20234) hydrogen bonds : bond 0.04157 / 2.87 ( 656) hydrogen bonds : angle 4.35838 / 3.18 ( 1919) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 373 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7061 (pmm) cc_final: 0.6855 (pmm) REVERT: A 9 ARG cc_start: 0.7687 (ptp-170) cc_final: 0.7240 (ptp-170) REVERT: A 113 VAL cc_start: 0.7866 (t) cc_final: 0.7635 (p) REVERT: A 135 ILE cc_start: 0.8540 (mm) cc_final: 0.8026 (tp) REVERT: A 179 SER cc_start: 0.8130 (m) cc_final: 0.7501 (t) REVERT: A 200 GLU cc_start: 0.7563 (tp30) cc_final: 0.6718 (tp30) REVERT: A 209 ASP cc_start: 0.7163 (m-30) cc_final: 0.6256 (m-30) REVERT: A 213 GLU cc_start: 0.6989 (mp0) cc_final: 0.6496 (mp0) REVERT: A 271 LYS cc_start: 0.8057 (ptpp) cc_final: 0.7518 (ptpp) REVERT: A 302 CYS cc_start: 0.7866 (t) cc_final: 0.7510 (t) REVERT: A 306 ASP cc_start: 0.7351 (m-30) cc_final: 0.6979 (m-30) REVERT: A 488 GLU cc_start: 0.7275 (tp30) cc_final: 0.6864 (tp30) REVERT: A 489 LYS cc_start: 0.7802 (tttt) cc_final: 0.7554 (ttmt) REVERT: A 543 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.7799 (tt) REVERT: A 661 GLU cc_start: 0.6982 (tp30) cc_final: 0.6769 (mm-30) REVERT: A 719 SER cc_start: 0.8438 (t) cc_final: 0.7788 (p) REVERT: A 864 VAL cc_start: 0.8191 (p) cc_final: 0.7978 (t) REVERT: A 1010 PHE cc_start: 0.7572 (m-10) cc_final: 0.6884 (m-10) REVERT: A 1052 MET cc_start: 0.7330 (mmt) cc_final: 0.7060 (mmt) REVERT: A 1064 TRP cc_start: 0.7769 (p-90) cc_final: 0.7547 (p-90) REVERT: A 1108 GLU cc_start: 0.7556 (pp20) cc_final: 0.7162 (pp20) REVERT: A 1137 LYS cc_start: 0.8453 (mttt) cc_final: 0.8005 (mttt) REVERT: A 1141 ASP cc_start: 0.7487 (t0) cc_final: 0.7213 (t0) REVERT: A 1142 GLU cc_start: 0.7540 (tt0) cc_final: 0.7329 (tt0) REVERT: A 1182 ASN cc_start: 0.8196 (m-40) cc_final: 0.7951 (m-40) REVERT: A 1193 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7229 (mtp180) REVERT: A 1216 GLU cc_start: 0.7057 (pt0) cc_final: 0.6855 (pt0) REVERT: A 1223 THR cc_start: 0.7942 (m) cc_final: 0.7630 (p) REVERT: A 1227 GLU cc_start: 0.7343 (pp20) cc_final: 0.7024 (pp20) REVERT: A 1346 LYS cc_start: 0.7358 (mtpt) cc_final: 0.6973 (mtpt) REVERT: A 1417 SER cc_start: 0.8204 (p) cc_final: 0.7884 (p) REVERT: A 1443 MET cc_start: 0.7637 (mtt) cc_final: 0.7345 (mtm) REVERT: A 1465 PHE cc_start: 0.7344 (m-10) cc_final: 0.7130 (m-10) REVERT: A 1725 TRP cc_start: 0.7252 (t60) cc_final: 0.6863 (t60) REVERT: A 1755 ASP cc_start: 0.7850 (p0) cc_final: 0.7510 (p0) outliers start: 25 outliers final: 13 residues processed: 382 average time/residue: 0.1652 time to fit residues: 86.1397 Evaluate side-chains 372 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 358 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 ASN ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110900 restraints weight = 63266.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116880 restraints weight = 22284.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120609 restraints weight = 10761.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123076 restraints weight = 6263.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124625 restraints weight = 4137.818| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14860 Z= 0.152 Angle : 0.576 7.666 20234 Z= 0.301 Chirality : 0.042 0.217 2268 Planarity : 0.004 0.055 2438 Dihedral : 8.400 140.511 2354 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.66 % Allowed : 14.60 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.20), residues: 1697 helix: 1.29 (0.19), residues: 813 sheet: 0.07 (0.44), residues: 139 loop : -1.83 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1407 TYR 0.018 0.002 TYR A 754 PHE 0.035 0.002 PHE A 82 TRP 0.036 0.001 TRP A 897 HIS 0.012 0.001 HIS A1011 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14860) covalent geometry : angle 0.57554 / 0.30 (20234) hydrogen bonds : bond 0.03687 / 2.53 ( 656) hydrogen bonds : angle 4.28384 / 3.12 ( 1919) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 364 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7658 (ptp-170) cc_final: 0.7252 (ptp-170) REVERT: A 113 VAL cc_start: 0.7866 (t) cc_final: 0.7605 (p) REVERT: A 135 ILE cc_start: 0.8532 (mm) cc_final: 0.8014 (tp) REVERT: A 179 SER cc_start: 0.8081 (m) cc_final: 0.7500 (t) REVERT: A 200 GLU cc_start: 0.7481 (tp30) cc_final: 0.6801 (tp30) REVERT: A 209 ASP cc_start: 0.7092 (m-30) cc_final: 0.5771 (m-30) REVERT: A 213 GLU cc_start: 0.6980 (mp0) cc_final: 0.6257 (mp0) REVERT: A 271 LYS cc_start: 0.8043 (ptpp) cc_final: 0.7479 (ptpp) REVERT: A 302 CYS cc_start: 0.7868 (t) cc_final: 0.7469 (t) REVERT: A 306 ASP cc_start: 0.7345 (m-30) cc_final: 0.6956 (m-30) REVERT: A 488 GLU cc_start: 0.7241 (tp30) cc_final: 0.6916 (tp30) REVERT: A 543 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7882 (tt) REVERT: A 719 SER cc_start: 0.8452 (t) cc_final: 0.7778 (p) REVERT: A 830 GLU cc_start: 0.6759 (tt0) cc_final: 0.6512 (tt0) REVERT: A 864 VAL cc_start: 0.8183 (p) cc_final: 0.7963 (t) REVERT: A 884 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8101 (ttmm) REVERT: A 887 MET cc_start: 0.6989 (tmm) cc_final: 0.6345 (tmm) REVERT: A 897 TRP cc_start: 0.8350 (t-100) cc_final: 0.8095 (t-100) REVERT: A 956 ARG cc_start: 0.7401 (ptp90) cc_final: 0.7129 (ptp90) REVERT: A 1010 PHE cc_start: 0.7486 (m-10) cc_final: 0.6882 (m-10) REVERT: A 1052 MET cc_start: 0.7313 (mmt) cc_final: 0.7050 (mmt) REVERT: A 1064 TRP cc_start: 0.7773 (p-90) cc_final: 0.7540 (p-90) REVERT: A 1108 GLU cc_start: 0.7582 (pp20) cc_final: 0.7221 (pp20) REVERT: A 1135 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7479 (ttp-170) REVERT: A 1137 LYS cc_start: 0.8425 (mttt) cc_final: 0.8005 (mttt) REVERT: A 1141 ASP cc_start: 0.7485 (t0) cc_final: 0.7209 (t0) REVERT: A 1142 GLU cc_start: 0.7511 (tt0) cc_final: 0.7287 (tt0) REVERT: A 1182 ASN cc_start: 0.8210 (m-40) cc_final: 0.7939 (m-40) REVERT: A 1193 ARG cc_start: 0.7493 (mtp180) cc_final: 0.7151 (mtp180) REVERT: A 1223 THR cc_start: 0.7926 (m) cc_final: 0.7612 (p) REVERT: A 1227 GLU cc_start: 0.7299 (pp20) cc_final: 0.7016 (pp20) REVERT: A 1278 MET cc_start: 0.8009 (mmm) cc_final: 0.7615 (tpp) REVERT: A 1417 SER cc_start: 0.8128 (p) cc_final: 0.7871 (p) REVERT: A 1443 MET cc_start: 0.7629 (mtt) cc_final: 0.7320 (mtm) REVERT: A 1514 GLU cc_start: 0.7243 (tp30) cc_final: 0.6947 (tp30) REVERT: A 1755 ASP cc_start: 0.7821 (p0) cc_final: 0.7497 (p0) outliers start: 23 outliers final: 16 residues processed: 370 average time/residue: 0.1610 time to fit residues: 81.2223 Evaluate side-chains 376 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 358 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1750 ILE Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 144 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 61 optimal weight: 0.0570 chunk 90 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 HIS A1190 HIS A1292 ASN A1569 ASN ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111419 restraints weight = 53316.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116954 restraints weight = 19759.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120509 restraints weight = 9840.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122746 restraints weight = 5829.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124278 restraints weight = 3935.365| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14860 Z= 0.175 Angle : 0.593 7.891 20234 Z= 0.309 Chirality : 0.043 0.225 2268 Planarity : 0.004 0.055 2438 Dihedral : 8.447 140.122 2354 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.73 % Allowed : 14.80 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.25 (0.20), residues: 1697 helix: 1.23 (0.19), residues: 820 sheet: -0.39 (0.43), residues: 147 loop : -1.80 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 30 TYR 0.017 0.002 TYR A 754 PHE 0.038 0.002 PHE A 82 TRP 0.031 0.002 TRP A 897 HIS 0.011 0.001 HIS A1011 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (14860) covalent geometry : angle 0.59254 / 0.31 (20234) hydrogen bonds : bond 0.03847 / 2.64 ( 656) hydrogen bonds : angle 4.29980 / 3.13 ( 1919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 361 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7693 (ptp-170) cc_final: 0.7297 (ptp-170) REVERT: A 113 VAL cc_start: 0.7912 (t) cc_final: 0.7662 (p) REVERT: A 135 ILE cc_start: 0.8524 (mm) cc_final: 0.8047 (tp) REVERT: A 179 SER cc_start: 0.8091 (m) cc_final: 0.7482 (t) REVERT: A 194 ARG cc_start: 0.7403 (mtp180) cc_final: 0.7048 (mtt180) REVERT: A 200 GLU cc_start: 0.7525 (tp30) cc_final: 0.6832 (tp30) REVERT: A 209 ASP cc_start: 0.7077 (m-30) cc_final: 0.5569 (m-30) REVERT: A 213 GLU cc_start: 0.6981 (mp0) cc_final: 0.6216 (mp0) REVERT: A 271 LYS cc_start: 0.8065 (ptpp) cc_final: 0.7497 (ptpp) REVERT: A 302 CYS cc_start: 0.7862 (t) cc_final: 0.7483 (t) REVERT: A 306 ASP cc_start: 0.7339 (m-30) cc_final: 0.6957 (m-30) REVERT: A 488 GLU cc_start: 0.7261 (tp30) cc_final: 0.6889 (tp30) REVERT: A 719 SER cc_start: 0.8455 (t) cc_final: 0.7791 (p) REVERT: A 864 VAL cc_start: 0.8200 (p) cc_final: 0.7982 (t) REVERT: A 884 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8151 (ttmm) REVERT: A 887 MET cc_start: 0.6967 (tmm) cc_final: 0.6313 (tmm) REVERT: A 897 TRP cc_start: 0.8370 (t-100) cc_final: 0.8157 (t-100) REVERT: A 1006 MET cc_start: 0.7587 (mmm) cc_final: 0.6977 (mmm) REVERT: A 1010 PHE cc_start: 0.7542 (m-10) cc_final: 0.6764 (m-10) REVERT: A 1064 TRP cc_start: 0.7823 (p-90) cc_final: 0.7542 (p-90) REVERT: A 1108 GLU cc_start: 0.7565 (pp20) cc_final: 0.7206 (pp20) REVERT: A 1123 GLU cc_start: 0.7017 (pp20) cc_final: 0.6568 (pp20) REVERT: A 1135 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7539 (ttp-170) REVERT: A 1137 LYS cc_start: 0.8418 (mttt) cc_final: 0.8012 (mttt) REVERT: A 1141 ASP cc_start: 0.7510 (t0) cc_final: 0.7243 (t0) REVERT: A 1142 GLU cc_start: 0.7520 (tt0) cc_final: 0.7301 (tt0) REVERT: A 1182 ASN cc_start: 0.8214 (m-40) cc_final: 0.7902 (m-40) REVERT: A 1184 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6294 (mm-30) REVERT: A 1193 ARG cc_start: 0.7478 (mtp180) cc_final: 0.7076 (mtp180) REVERT: A 1223 THR cc_start: 0.7946 (m) cc_final: 0.7651 (p) REVERT: A 1227 GLU cc_start: 0.7326 (pp20) cc_final: 0.7029 (pp20) REVERT: A 1371 VAL cc_start: 0.8013 (p) cc_final: 0.7662 (t) REVERT: A 1417 SER cc_start: 0.8139 (p) cc_final: 0.7914 (p) REVERT: A 1443 MET cc_start: 0.7615 (mtt) cc_final: 0.7306 (mtm) REVERT: A 1514 GLU cc_start: 0.7250 (tp30) cc_final: 0.6956 (tp30) REVERT: A 1755 ASP cc_start: 0.7862 (p0) cc_final: 0.7547 (p0) outliers start: 24 outliers final: 19 residues processed: 369 average time/residue: 0.1507 time to fit residues: 75.7499 Evaluate side-chains 372 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 352 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1750 ILE Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 114 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 102 optimal weight: 0.0030 chunk 10 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS A 853 ASN ** A1834 ASN ** 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 = 0.3790 r_free = 0.3790 target = 0.138149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113030 restraints weight = 54802.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118689 restraints weight = 20162.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122279 restraints weight = 9958.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124602 restraints weight = 5882.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126097 restraints weight = 3937.702| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14860 Z= 0.123 Angle : 0.578 8.069 20234 Z= 0.300 Chirality : 0.041 0.216 2268 Planarity : 0.004 0.054 2438 Dihedral : 8.385 140.714 2354 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.66 % Allowed : 16.06 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.11 (0.20), residues: 1697 helix: 1.34 (0.19), residues: 816 sheet: 0.09 (0.45), residues: 139 loop : -1.80 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 30 TYR 0.016 0.001 TYR A 474 PHE 0.041 0.002 PHE A 82 TRP 0.030 0.001 TRP A 897 HIS 0.009 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (14860) covalent geometry : angle 0.57803 / 0.30 (20234) hydrogen bonds : bond 0.03439 / 2.35 ( 656) hydrogen bonds : angle 4.21036 / 3.06 ( 1919) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 361 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7692 (ptp-170) cc_final: 0.7320 (ptp-170) REVERT: A 113 VAL cc_start: 0.7922 (t) cc_final: 0.7672 (p) REVERT: A 135 ILE cc_start: 0.8556 (mm) cc_final: 0.8079 (tp) REVERT: A 145 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7283 (ttmm) REVERT: A 192 MET cc_start: 0.6874 (ttp) cc_final: 0.6546 (ttp) REVERT: A 194 ARG cc_start: 0.7371 (mtp180) cc_final: 0.7008 (mtp180) REVERT: A 200 GLU cc_start: 0.7461 (tp30) cc_final: 0.6762 (tp30) REVERT: A 209 ASP cc_start: 0.6971 (m-30) cc_final: 0.6143 (m-30) REVERT: A 271 LYS cc_start: 0.8030 (ptpp) cc_final: 0.7433 (ptpp) REVERT: A 302 CYS cc_start: 0.7864 (t) cc_final: 0.7497 (t) REVERT: A 306 ASP cc_start: 0.7324 (m-30) cc_final: 0.6955 (m-30) REVERT: A 488 GLU cc_start: 0.7182 (tp30) cc_final: 0.6747 (tp30) REVERT: A 624 ARG cc_start: 0.7708 (ttt180) cc_final: 0.7285 (ttt-90) REVERT: A 719 SER cc_start: 0.8381 (t) cc_final: 0.7709 (p) REVERT: A 864 VAL cc_start: 0.8213 (p) cc_final: 0.7988 (t) REVERT: A 884 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8115 (ttmm) REVERT: A 887 MET cc_start: 0.6910 (tmm) cc_final: 0.6252 (tmm) REVERT: A 897 TRP cc_start: 0.8350 (t-100) cc_final: 0.8075 (t-100) REVERT: A 1006 MET cc_start: 0.7468 (mmm) cc_final: 0.7070 (mpp) REVERT: A 1010 PHE cc_start: 0.7466 (m-10) cc_final: 0.6973 (m-10) REVERT: A 1020 MET cc_start: 0.8116 (ptt) cc_final: 0.7846 (ptm) REVERT: A 1064 TRP cc_start: 0.7739 (p-90) cc_final: 0.7494 (p-90) REVERT: A 1108 GLU cc_start: 0.7592 (pp20) cc_final: 0.7204 (pp20) REVERT: A 1123 GLU cc_start: 0.6991 (pp20) cc_final: 0.6534 (pp20) REVERT: A 1135 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7519 (ttp-170) REVERT: A 1137 LYS cc_start: 0.8421 (mttt) cc_final: 0.7993 (mttt) REVERT: A 1141 ASP cc_start: 0.7513 (t0) cc_final: 0.7233 (t0) REVERT: A 1142 GLU cc_start: 0.7499 (tt0) cc_final: 0.7295 (tt0) REVERT: A 1182 ASN cc_start: 0.8178 (m-40) cc_final: 0.7867 (m-40) REVERT: A 1193 ARG cc_start: 0.7423 (mtp180) cc_final: 0.7075 (mtp180) REVERT: A 1219 SER cc_start: 0.8148 (t) cc_final: 0.7713 (p) REVERT: A 1223 THR cc_start: 0.7877 (m) cc_final: 0.7583 (p) REVERT: A 1227 GLU cc_start: 0.7298 (pp20) cc_final: 0.7037 (pp20) REVERT: A 1443 MET cc_start: 0.7629 (mtt) cc_final: 0.7314 (mtm) REVERT: A 1514 GLU cc_start: 0.7217 (tp30) cc_final: 0.6928 (tp30) REVERT: A 1570 PHE cc_start: 0.7687 (t80) cc_final: 0.7479 (t80) REVERT: A 1755 ASP cc_start: 0.7846 (p0) cc_final: 0.7551 (p0) outliers start: 23 outliers final: 18 residues processed: 367 average time/residue: 0.1549 time to fit residues: 77.2286 Evaluate side-chains 374 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 355 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1750 ILE Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 161 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 156 optimal weight: 0.0980 chunk 172 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS A1292 ASN ** A1834 ASN ** 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 = 0.3807 r_free = 0.3807 target = 0.141904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116600 restraints weight = 61140.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122607 restraints weight = 20488.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126359 restraints weight = 9728.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128808 restraints weight = 5572.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130364 restraints weight = 3623.714| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14860 Z= 0.165 Angle : 0.597 8.135 20234 Z= 0.312 Chirality : 0.043 0.216 2268 Planarity : 0.004 0.055 2438 Dihedral : 8.401 140.104 2354 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.59 % Allowed : 15.93 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.20), residues: 1697 helix: 1.29 (0.19), residues: 817 sheet: 0.04 (0.45), residues: 139 loop : -1.79 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1407 TYR 0.016 0.002 TYR A 754 PHE 0.041 0.002 PHE A 82 TRP 0.028 0.002 TRP A 897 HIS 0.011 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (14860) covalent geometry : angle 0.59731 / 0.31 (20234) hydrogen bonds : bond 0.03709 / 2.55 ( 656) hydrogen bonds : angle 4.24657 / 3.09 ( 1919) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 365 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7734 (ptp-170) cc_final: 0.7362 (ptp-170) REVERT: A 81 ASP cc_start: 0.6929 (m-30) cc_final: 0.6656 (m-30) REVERT: A 113 VAL cc_start: 0.7858 (t) cc_final: 0.7622 (p) REVERT: A 135 ILE cc_start: 0.8566 (mm) cc_final: 0.8065 (tp) REVERT: A 145 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7324 (ttmm) REVERT: A 179 SER cc_start: 0.8008 (m) cc_final: 0.7417 (t) REVERT: A 192 MET cc_start: 0.6895 (ttp) cc_final: 0.6459 (ttt) REVERT: A 194 ARG cc_start: 0.7392 (mtp180) cc_final: 0.7018 (mtp180) REVERT: A 200 GLU cc_start: 0.7449 (tp30) cc_final: 0.6867 (tp30) REVERT: A 204 LYS cc_start: 0.7943 (mtmm) cc_final: 0.7714 (mtmm) REVERT: A 209 ASP cc_start: 0.6906 (m-30) cc_final: 0.6096 (m-30) REVERT: A 271 LYS cc_start: 0.8010 (ptpp) cc_final: 0.7408 (ptpp) REVERT: A 302 CYS cc_start: 0.7882 (t) cc_final: 0.7515 (t) REVERT: A 306 ASP cc_start: 0.7331 (m-30) cc_final: 0.6965 (m-30) REVERT: A 488 GLU cc_start: 0.7182 (tp30) cc_final: 0.6779 (tp30) REVERT: A 719 SER cc_start: 0.8447 (t) cc_final: 0.7779 (p) REVERT: A 864 VAL cc_start: 0.8235 (p) cc_final: 0.8003 (t) REVERT: A 884 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8190 (ttmm) REVERT: A 887 MET cc_start: 0.6899 (tmm) cc_final: 0.6240 (tmm) REVERT: A 897 TRP cc_start: 0.8377 (t-100) cc_final: 0.8122 (t-100) REVERT: A 956 ARG cc_start: 0.7394 (ptp90) cc_final: 0.7191 (ptp90) REVERT: A 1009 LYS cc_start: 0.8175 (pttm) cc_final: 0.7882 (pttm) REVERT: A 1010 PHE cc_start: 0.7548 (m-10) cc_final: 0.6550 (m-10) REVERT: A 1020 MET cc_start: 0.8109 (ptt) cc_final: 0.7873 (ptm) REVERT: A 1025 LYS cc_start: 0.7905 (tppp) cc_final: 0.7684 (mttt) REVERT: A 1064 TRP cc_start: 0.7805 (p-90) cc_final: 0.7538 (p-90) REVERT: A 1108 GLU cc_start: 0.7637 (pp20) cc_final: 0.7265 (pp20) REVERT: A 1123 GLU cc_start: 0.6998 (pp20) cc_final: 0.6555 (pp20) REVERT: A 1135 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7525 (ttp-170) REVERT: A 1137 LYS cc_start: 0.8407 (mttt) cc_final: 0.8160 (mttt) REVERT: A 1141 ASP cc_start: 0.7524 (t0) cc_final: 0.7276 (t0) REVERT: A 1142 GLU cc_start: 0.7542 (tt0) cc_final: 0.7330 (tt0) REVERT: A 1182 ASN cc_start: 0.8189 (m-40) cc_final: 0.7867 (m-40) REVERT: A 1184 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6270 (mm-30) REVERT: A 1193 ARG cc_start: 0.7476 (mtp180) cc_final: 0.7039 (mtp180) REVERT: A 1223 THR cc_start: 0.7928 (m) cc_final: 0.7620 (p) REVERT: A 1227 GLU cc_start: 0.7326 (pp20) cc_final: 0.7064 (pp20) REVERT: A 1443 MET cc_start: 0.7629 (mtt) cc_final: 0.7318 (mtm) REVERT: A 1514 GLU cc_start: 0.7222 (tp30) cc_final: 0.6943 (tp30) REVERT: A 1755 ASP cc_start: 0.7854 (p0) cc_final: 0.7542 (p0) outliers start: 22 outliers final: 18 residues processed: 371 average time/residue: 0.1532 time to fit residues: 77.2679 Evaluate side-chains 374 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 355 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 136 optimal weight: 0.8980 chunk 133 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 59 optimal weight: 0.1980 chunk 138 optimal weight: 2.9990 chunk 167 optimal weight: 0.0870 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.145002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121046 restraints weight = 54441.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.126810 restraints weight = 19128.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130427 restraints weight = 9179.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132716 restraints weight = 5269.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134190 restraints weight = 3433.648| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14860 Z= 0.112 Angle : 0.582 8.453 20234 Z= 0.302 Chirality : 0.041 0.213 2268 Planarity : 0.004 0.057 2438 Dihedral : 8.387 141.767 2354 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.26 % Allowed : 16.59 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.08 (0.20), residues: 1697 helix: 1.34 (0.19), residues: 813 sheet: 0.25 (0.46), residues: 132 loop : -1.75 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1407 TYR 0.014 0.001 TYR A 474 PHE 0.043 0.002 PHE A 82 TRP 0.031 0.002 TRP A 897 HIS 0.015 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (14860) covalent geometry : angle 0.58165 / 0.30 (20234) hydrogen bonds : bond 0.03180 / 2.17 ( 656) hydrogen bonds : angle 4.16895 / 3.03 ( 1919) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 354 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.6831 (m-30) cc_final: 0.6615 (m-30) REVERT: A 135 ILE cc_start: 0.8570 (mm) cc_final: 0.8073 (tp) REVERT: A 145 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7225 (ttmm) REVERT: A 192 MET cc_start: 0.6823 (ttp) cc_final: 0.6355 (ttt) REVERT: A 200 GLU cc_start: 0.7395 (tp30) cc_final: 0.6761 (tp30) REVERT: A 204 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7603 (mtmm) REVERT: A 209 ASP cc_start: 0.6752 (m-30) cc_final: 0.5909 (m-30) REVERT: A 271 LYS cc_start: 0.7963 (ptpp) cc_final: 0.7325 (ptpp) REVERT: A 306 ASP cc_start: 0.7320 (m-30) cc_final: 0.6927 (m-30) REVERT: A 410 ARG cc_start: 0.7735 (mtt-85) cc_final: 0.7525 (mtt90) REVERT: A 488 GLU cc_start: 0.7116 (tp30) cc_final: 0.6652 (tp30) REVERT: A 543 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 594 GLU cc_start: 0.6776 (tt0) cc_final: 0.6069 (mt-10) REVERT: A 671 MET cc_start: 0.6701 (mmm) cc_final: 0.6478 (tpt) REVERT: A 719 SER cc_start: 0.8352 (t) cc_final: 0.7699 (p) REVERT: A 887 MET cc_start: 0.6929 (tmm) cc_final: 0.6314 (tmm) REVERT: A 897 TRP cc_start: 0.8339 (t-100) cc_final: 0.8074 (t-100) REVERT: A 956 ARG cc_start: 0.7356 (ptp90) cc_final: 0.7137 (ptp90) REVERT: A 1006 MET cc_start: 0.7389 (mmm) cc_final: 0.6799 (mmm) REVERT: A 1010 PHE cc_start: 0.7272 (m-10) cc_final: 0.6996 (m-10) REVERT: A 1064 TRP cc_start: 0.7711 (p-90) cc_final: 0.7410 (p-90) REVERT: A 1087 SER cc_start: 0.8354 (m) cc_final: 0.8100 (m) REVERT: A 1108 GLU cc_start: 0.7694 (pp20) cc_final: 0.7302 (pp20) REVERT: A 1123 GLU cc_start: 0.6970 (pp20) cc_final: 0.6512 (pp20) REVERT: A 1141 ASP cc_start: 0.7531 (t0) cc_final: 0.7299 (t0) REVERT: A 1142 GLU cc_start: 0.7520 (tt0) cc_final: 0.7313 (tt0) REVERT: A 1182 ASN cc_start: 0.8155 (m-40) cc_final: 0.7808 (m-40) REVERT: A 1184 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6229 (mm-30) REVERT: A 1193 ARG cc_start: 0.7447 (mtp180) cc_final: 0.7023 (mtp180) REVERT: A 1219 SER cc_start: 0.8109 (t) cc_final: 0.7668 (p) REVERT: A 1223 THR cc_start: 0.7846 (m) cc_final: 0.7563 (p) REVERT: A 1227 GLU cc_start: 0.7307 (pp20) cc_final: 0.7034 (pp20) REVERT: A 1298 LYS cc_start: 0.8233 (mtpt) cc_final: 0.8004 (mmmt) REVERT: A 1443 MET cc_start: 0.7637 (mtt) cc_final: 0.7326 (mtm) REVERT: A 1514 GLU cc_start: 0.7167 (tp30) cc_final: 0.6896 (tp30) REVERT: A 1755 ASP cc_start: 0.7813 (p0) cc_final: 0.7512 (p0) outliers start: 17 outliers final: 12 residues processed: 356 average time/residue: 0.1487 time to fit residues: 72.2329 Evaluate side-chains 355 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 342 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 129 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 0.0270 chunk 163 optimal weight: 0.9980 chunk 144 optimal weight: 0.0770 chunk 69 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS A1292 ASN ** A1834 ASN ** 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 = 0.3804 r_free = 0.3804 target = 0.139443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113919 restraints weight = 65503.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120001 restraints weight = 22348.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123791 restraints weight = 10632.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126242 restraints weight = 6106.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127801 restraints weight = 3993.414| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14860 Z= 0.123 Angle : 0.587 8.286 20234 Z= 0.304 Chirality : 0.042 0.414 2268 Planarity : 0.004 0.056 2438 Dihedral : 8.375 141.292 2354 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.06 % Allowed : 17.19 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.01 (0.20), residues: 1697 helix: 1.39 (0.19), residues: 815 sheet: 0.21 (0.45), residues: 138 loop : -1.71 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1407 TYR 0.013 0.001 TYR A1110 PHE 0.043 0.002 PHE A 82 TRP 0.027 0.002 TRP A 897 HIS 0.014 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (14860) covalent geometry : angle 0.58737 / 0.30 (20234) hydrogen bonds : bond 0.03359 / 2.30 ( 656) hydrogen bonds : angle 4.12336 / 3.00 ( 1919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2976.29 seconds wall clock time: 52 minutes 9.11 seconds (3129.11 seconds total)