Starting phenix.real_space_refine on Sun May 3 20:25:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8asb_15610/05_2026/8asb_15610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asb_15610/05_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 { model { file = "/net/cci-nas-00/data/ceres_data/8asb_15610/05_2026/8asb_15610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asb_15610/05_2026/8asb_15610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8asb_15610/05_2026/8asb_15610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asb_15610/05_2026/8asb_15610.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 5.42, 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: 1.36 Conformation dependent library (CDL) restraints added in 1.1 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: 1.96 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: 3.26 Time building geometry restraints manager: 1.75 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: 8564 27.34 - 54.69: 406 54.69 - 82.03: 82 82.03 - 109.38: 7 109.38 - 136.72: 1 Dihedral angle restraints: 9060 sinusoidal: 4088 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 9057 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.760 Find NCS groups from input model: 0.170 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 15.701 136.722 5848 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 covalent geometry : bond 0.00566 (14860) covalent geometry : angle 0.97543 (20234) hydrogen bonds : bond 0.15393 ( 656) hydrogen bonds : angle 6.22677 ( 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 : 0.507 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: 0.1481 time to fit residues: 72.6806 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 : 0.527 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3793 r_free = 0.3793 target = 0.138791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113649 restraints weight = 53115.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119369 restraints weight = 19405.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123029 restraints weight = 9599.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125388 restraints weight = 5628.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126902 restraints weight = 3737.749| |-----------------------------------------------------------------------------| 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14860 Z= 0.152 Angle : 0.604 8.348 20234 Z= 0.312 Chirality : 0.042 0.216 2268 Planarity : 0.005 0.061 2438 Dihedral : 12.882 138.688 2494 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.53 % Allowed : 9.16 % Favored : 90.31 % 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: -0.29 (0.20), residues: 1697 helix: 1.10 (0.18), residues: 809 sheet: 0.13 (0.45), residues: 140 loop : -1.76 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1497 TYR 0.019 0.002 TYR A 754 PHE 0.027 0.002 PHE A1048 TRP 0.032 0.002 TRP A 897 HIS 0.011 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00335 (14860) covalent geometry : angle 0.60425 (20234) hydrogen bonds : bond 0.04104 ( 656) hydrogen bonds : angle 4.55469 ( 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 373 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 365 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6873 (ppp) cc_final: 0.6289 (pmm) REVERT: A 145 LYS cc_start: 0.7169 (mmtt) cc_final: 0.6824 (ttmm) REVERT: A 200 GLU cc_start: 0.7455 (tp30) cc_final: 0.6935 (tp30) REVERT: A 209 ASP cc_start: 0.7133 (m-30) cc_final: 0.6217 (m-30) REVERT: A 213 GLU cc_start: 0.6798 (mp0) cc_final: 0.6440 (mp0) REVERT: A 271 LYS cc_start: 0.7950 (ptpp) cc_final: 0.7408 (ptpp) REVERT: A 302 CYS cc_start: 0.7811 (t) cc_final: 0.7467 (t) REVERT: A 306 ASP cc_start: 0.7315 (m-30) cc_final: 0.6989 (m-30) REVERT: A 488 GLU cc_start: 0.7227 (tp30) cc_final: 0.6840 (tp30) REVERT: A 495 ASP cc_start: 0.7393 (p0) cc_final: 0.7142 (p0) REVERT: A 544 LYS cc_start: 0.8081 (mttt) cc_final: 0.7795 (mttt) REVERT: A 671 MET cc_start: 0.6639 (mmm) cc_final: 0.6375 (tpp) REVERT: A 719 SER cc_start: 0.8372 (t) cc_final: 0.8133 (t) REVERT: A 759 GLU cc_start: 0.6701 (tp30) cc_final: 0.6390 (mm-30) REVERT: A 864 VAL cc_start: 0.8186 (m) cc_final: 0.7983 (p) REVERT: A 933 GLN cc_start: 0.7505 (tm-30) cc_final: 0.7275 (tm-30) REVERT: A 964 ASN cc_start: 0.7847 (m-40) cc_final: 0.7628 (m-40) REVERT: A 1032 PHE cc_start: 0.7843 (t80) cc_final: 0.7544 (t80) REVERT: A 1064 TRP cc_start: 0.7632 (p-90) cc_final: 0.7344 (p-90) REVERT: A 1108 GLU cc_start: 0.7558 (pp20) cc_final: 0.7208 (pp20) REVERT: A 1123 GLU cc_start: 0.6913 (pp20) cc_final: 0.6518 (pp20) REVERT: A 1137 LYS cc_start: 0.8453 (mttt) cc_final: 0.8049 (mttt) REVERT: A 1141 ASP cc_start: 0.7360 (t0) cc_final: 0.7061 (t0) REVERT: A 1142 GLU cc_start: 0.7536 (tt0) cc_final: 0.7331 (tt0) REVERT: A 1182 ASN cc_start: 0.8180 (m-40) cc_final: 0.7946 (m-40) REVERT: A 1193 ARG cc_start: 0.7541 (mtp180) cc_final: 0.7283 (mtp180) REVERT: A 1223 THR cc_start: 0.7889 (m) cc_final: 0.7591 (p) REVERT: A 1227 GLU cc_start: 0.7143 (pp20) cc_final: 0.6867 (pp20) REVERT: A 1346 LYS cc_start: 0.7323 (mtpt) cc_final: 0.6981 (mtpt) REVERT: A 1514 GLU cc_start: 0.7451 (tp30) cc_final: 0.7130 (tp30) REVERT: A 1755 ASP cc_start: 0.7667 (p0) cc_final: 0.7257 (p0) REVERT: A 1845 MET cc_start: 0.5670 (ptm) cc_final: 0.5137 (ptm) outliers start: 8 outliers final: 7 residues processed: 369 average time/residue: 0.1536 time to fit residues: 76.9395 Evaluate side-chains 355 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 348 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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: 0.0170 chunk 43 optimal weight: 1.9990 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: 0.6980 chunk 31 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3774 r_free = 0.3774 target = 0.137273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111140 restraints weight = 62247.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117215 restraints weight = 21512.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121015 restraints weight = 10357.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123500 restraints weight = 5998.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125098 restraints weight = 3939.517| |-----------------------------------------------------------------------------| 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 = 0.36 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 = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14860 Z= 0.161 Angle : 0.582 7.208 20234 Z= 0.302 Chirality : 0.042 0.213 2268 Planarity : 0.004 0.056 2438 Dihedral : 12.821 141.795 2492 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.93 % Allowed : 10.68 % Favored : 88.39 % 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: -0.21 (0.20), residues: 1697 helix: 1.20 (0.19), residues: 811 sheet: -0.15 (0.44), residues: 148 loop : -1.73 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1542 TYR 0.016 0.002 TYR A1348 PHE 0.036 0.002 PHE A 82 TRP 0.025 0.002 TRP A 897 HIS 0.009 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00357 (14860) covalent geometry : angle 0.58211 (20234) hydrogen bonds : bond 0.03912 ( 656) hydrogen bonds : angle 4.34491 ( 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 378 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 366 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6464 (mm) REVERT: A 113 VAL cc_start: 0.7799 (t) cc_final: 0.7590 (p) REVERT: A 125 VAL cc_start: 0.8401 (t) cc_final: 0.8188 (t) REVERT: A 135 ILE cc_start: 0.8531 (mm) cc_final: 0.8033 (tp) REVERT: A 145 LYS cc_start: 0.7250 (mmtt) cc_final: 0.6977 (ttmm) REVERT: A 179 SER cc_start: 0.8045 (m) cc_final: 0.7420 (t) REVERT: A 200 GLU cc_start: 0.7521 (tp30) cc_final: 0.7001 (tp30) REVERT: A 209 ASP cc_start: 0.7141 (m-30) cc_final: 0.6351 (m-30) REVERT: A 239 GLU cc_start: 0.7430 (pp20) cc_final: 0.7202 (pp20) REVERT: A 271 LYS cc_start: 0.8026 (ptpp) cc_final: 0.7507 (ptpp) REVERT: A 302 CYS cc_start: 0.7851 (t) cc_final: 0.7533 (t) REVERT: A 306 ASP cc_start: 0.7340 (m-30) cc_final: 0.6979 (m-30) REVERT: A 488 GLU cc_start: 0.7231 (tp30) cc_final: 0.6867 (tp30) REVERT: A 489 LYS cc_start: 0.7783 (ttmt) cc_final: 0.7527 (tttt) REVERT: A 495 ASP cc_start: 0.7505 (p0) cc_final: 0.7300 (p0) REVERT: A 618 ASN cc_start: 0.7530 (m-40) cc_final: 0.7255 (m110) REVERT: A 707 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6991 (mp) REVERT: A 719 SER cc_start: 0.8399 (t) cc_final: 0.7732 (p) REVERT: A 912 LYS cc_start: 0.8620 (ttmm) cc_final: 0.8345 (ttmm) REVERT: A 933 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 964 ASN cc_start: 0.7847 (m-40) cc_final: 0.7578 (m-40) REVERT: A 1012 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7060 (ttp80) REVERT: A 1052 MET cc_start: 0.7334 (mmt) cc_final: 0.7128 (mmt) REVERT: A 1064 TRP cc_start: 0.7743 (p-90) cc_final: 0.7453 (p-90) REVERT: A 1108 GLU cc_start: 0.7539 (pp20) cc_final: 0.7207 (pp20) REVERT: A 1137 LYS cc_start: 0.8444 (mttt) cc_final: 0.8013 (mttt) REVERT: A 1141 ASP cc_start: 0.7420 (t0) cc_final: 0.7171 (t0) REVERT: A 1142 GLU cc_start: 0.7550 (tt0) cc_final: 0.7349 (tt0) REVERT: A 1182 ASN cc_start: 0.8220 (m-40) cc_final: 0.7982 (m-40) REVERT: A 1193 ARG cc_start: 0.7602 (mtp180) cc_final: 0.7340 (mtp180) REVERT: A 1216 GLU cc_start: 0.7112 (pt0) cc_final: 0.6853 (pt0) REVERT: A 1223 THR cc_start: 0.7940 (m) cc_final: 0.7602 (p) REVERT: A 1227 GLU cc_start: 0.7227 (pp20) cc_final: 0.6926 (pp20) REVERT: A 1346 LYS cc_start: 0.7334 (mtpt) cc_final: 0.6970 (mtpt) REVERT: A 1514 GLU cc_start: 0.7304 (tp30) cc_final: 0.6967 (tp30) REVERT: A 1755 ASP cc_start: 0.7794 (p0) cc_final: 0.7405 (p0) REVERT: A 1845 MET cc_start: 0.5709 (ptm) cc_final: 0.5392 (ptm) outliers start: 12 outliers final: 5 residues processed: 367 average time/residue: 0.1526 time to fit residues: 76.0735 Evaluate side-chains 366 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 359 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 3.9990 chunk 83 optimal weight: 0.7980 chunk 41 optimal weight: 0.0570 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 165 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112878 restraints weight = 57119.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118825 restraints weight = 20365.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122563 restraints weight = 9917.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124985 restraints weight = 5760.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126528 restraints weight = 3804.241| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14860 Z= 0.123 Angle : 0.552 7.119 20234 Z= 0.287 Chirality : 0.041 0.296 2268 Planarity : 0.004 0.055 2438 Dihedral : 12.693 142.354 2492 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.53 % Allowed : 12.74 % Favored : 85.73 % 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: -0.04 (0.20), residues: 1697 helix: 1.37 (0.19), residues: 804 sheet: 0.30 (0.45), residues: 139 loop : -1.72 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1407 TYR 0.017 0.001 TYR A 861 PHE 0.027 0.002 PHE A 245 TRP 0.029 0.001 TRP A 897 HIS 0.007 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00279 (14860) covalent geometry : angle 0.55194 (20234) hydrogen bonds : bond 0.03453 ( 656) hydrogen bonds : angle 4.22744 ( 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 386 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 365 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.5631 (OUTLIER) cc_final: 0.5362 (t80) REVERT: A 113 VAL cc_start: 0.7802 (t) cc_final: 0.7593 (p) REVERT: A 135 ILE cc_start: 0.8542 (mm) cc_final: 0.8043 (tp) REVERT: A 145 LYS cc_start: 0.7406 (mmtt) cc_final: 0.7026 (ttmm) REVERT: A 179 SER cc_start: 0.7961 (m) cc_final: 0.7385 (t) REVERT: A 200 GLU cc_start: 0.7520 (tp30) cc_final: 0.6884 (tp30) REVERT: A 209 ASP cc_start: 0.7048 (m-30) cc_final: 0.5745 (m-30) REVERT: A 213 GLU cc_start: 0.6867 (mp0) cc_final: 0.6197 (mp0) REVERT: A 271 LYS cc_start: 0.8021 (ptpp) cc_final: 0.7468 (ptpp) REVERT: A 306 ASP cc_start: 0.7321 (m-30) cc_final: 0.6946 (m-30) REVERT: A 410 ARG cc_start: 0.7751 (mtt-85) cc_final: 0.7521 (mtt-85) REVERT: A 488 GLU cc_start: 0.7228 (tp30) cc_final: 0.6955 (tp30) REVERT: A 719 SER cc_start: 0.8355 (t) cc_final: 0.8112 (t) REVERT: A 864 VAL cc_start: 0.8172 (p) cc_final: 0.7961 (t) REVERT: A 897 TRP cc_start: 0.8353 (t-100) cc_final: 0.8135 (t-100) REVERT: A 933 GLN cc_start: 0.7596 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 964 ASN cc_start: 0.7840 (m-40) cc_final: 0.7556 (m-40) REVERT: A 1012 ARG cc_start: 0.7367 (ttp80) cc_final: 0.6987 (ttp80) REVERT: A 1052 MET cc_start: 0.7339 (mmt) cc_final: 0.7088 (mmt) REVERT: A 1064 TRP cc_start: 0.7661 (p-90) cc_final: 0.7386 (p-90) REVERT: A 1108 GLU cc_start: 0.7569 (pp20) cc_final: 0.7200 (pp20) REVERT: A 1137 LYS cc_start: 0.8467 (mttt) cc_final: 0.8024 (mttt) REVERT: A 1141 ASP cc_start: 0.7413 (t0) cc_final: 0.7133 (t0) REVERT: A 1142 GLU cc_start: 0.7514 (tt0) cc_final: 0.7293 (tt0) REVERT: A 1182 ASN cc_start: 0.8191 (m-40) cc_final: 0.7868 (m-40) REVERT: A 1193 ARG cc_start: 0.7554 (mtp180) cc_final: 0.7242 (mtp180) REVERT: A 1223 THR cc_start: 0.7879 (m) cc_final: 0.7571 (p) REVERT: A 1227 GLU cc_start: 0.7226 (pp20) cc_final: 0.6875 (pp20) REVERT: A 1417 SER cc_start: 0.8083 (p) cc_final: 0.7794 (p) REVERT: A 1443 MET cc_start: 0.7630 (mtt) cc_final: 0.7338 (mtm) REVERT: A 1514 GLU cc_start: 0.7233 (tp30) cc_final: 0.6659 (tp30) REVERT: A 1755 ASP cc_start: 0.7777 (p0) cc_final: 0.7430 (p0) REVERT: A 1845 MET cc_start: 0.5669 (ptm) cc_final: 0.5352 (ptm) outliers start: 21 outliers final: 11 residues processed: 368 average time/residue: 0.1534 time to fit residues: 76.7401 Evaluate side-chains 371 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 359 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 99 PHE 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: 1.9990 chunk 112 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.136620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111862 restraints weight = 51490.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117370 restraints weight = 19504.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120855 restraints weight = 9776.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122932 restraints weight = 5806.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124497 restraints weight = 3988.429| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14860 Z= 0.180 Angle : 0.591 7.375 20234 Z= 0.308 Chirality : 0.043 0.239 2268 Planarity : 0.004 0.055 2438 Dihedral : 12.731 141.615 2492 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.66 % Allowed : 13.80 % Favored : 84.54 % 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: -0.13 (0.20), residues: 1697 helix: 1.31 (0.19), residues: 814 sheet: -0.15 (0.44), residues: 147 loop : -1.74 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1542 TYR 0.025 0.002 TYR A 754 PHE 0.037 0.002 PHE A 82 TRP 0.025 0.002 TRP A 897 HIS 0.012 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00400 (14860) covalent geometry : angle 0.59051 (20234) hydrogen bonds : bond 0.03900 ( 656) hydrogen bonds : angle 4.28324 ( 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 397 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 374 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7064 (pmm) cc_final: 0.6826 (pmm) REVERT: A 99 PHE cc_start: 0.6017 (OUTLIER) cc_final: 0.5686 (t80) REVERT: A 113 VAL cc_start: 0.7875 (t) cc_final: 0.7645 (p) REVERT: A 135 ILE cc_start: 0.8550 (mm) cc_final: 0.8032 (tp) REVERT: A 179 SER cc_start: 0.8071 (m) cc_final: 0.7475 (t) REVERT: A 185 GLN cc_start: 0.7372 (mp10) cc_final: 0.7110 (mp10) REVERT: A 200 GLU cc_start: 0.7543 (tp30) cc_final: 0.6657 (tp30) REVERT: A 209 ASP cc_start: 0.7119 (m-30) cc_final: 0.5597 (m-30) REVERT: A 213 GLU cc_start: 0.6911 (mp0) cc_final: 0.6160 (mp0) REVERT: A 271 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7476 (ptpp) REVERT: A 302 CYS cc_start: 0.7858 (t) cc_final: 0.7482 (t) REVERT: A 306 ASP cc_start: 0.7353 (m-30) cc_final: 0.6975 (m-30) REVERT: A 488 GLU cc_start: 0.7271 (tp30) cc_final: 0.6836 (tp30) REVERT: A 489 LYS cc_start: 0.7790 (tttt) cc_final: 0.7518 (ttmt) REVERT: A 686 MET cc_start: 0.6937 (mtp) cc_final: 0.6336 (mmm) REVERT: A 719 SER cc_start: 0.8420 (t) cc_final: 0.8191 (t) REVERT: A 864 VAL cc_start: 0.8184 (p) cc_final: 0.7974 (t) REVERT: A 964 ASN cc_start: 0.7846 (m-40) cc_final: 0.7637 (m-40) REVERT: A 1010 PHE cc_start: 0.7502 (m-10) cc_final: 0.6835 (m-10) REVERT: A 1020 MET cc_start: 0.8127 (ptt) cc_final: 0.7748 (ptm) REVERT: A 1052 MET cc_start: 0.7366 (mmt) cc_final: 0.7080 (mmt) REVERT: A 1064 TRP cc_start: 0.7742 (p-90) cc_final: 0.7469 (p-90) REVERT: A 1108 GLU cc_start: 0.7570 (pp20) cc_final: 0.7169 (pp20) REVERT: A 1137 LYS cc_start: 0.8448 (mttt) cc_final: 0.7989 (mttt) REVERT: A 1141 ASP cc_start: 0.7472 (t0) cc_final: 0.7214 (t0) REVERT: A 1142 GLU cc_start: 0.7519 (tt0) cc_final: 0.7315 (tt0) REVERT: A 1182 ASN cc_start: 0.8199 (m-40) cc_final: 0.7930 (m-40) REVERT: A 1193 ARG cc_start: 0.7531 (mtp180) cc_final: 0.7222 (mtp180) REVERT: A 1216 GLU cc_start: 0.7054 (pt0) cc_final: 0.6845 (pt0) REVERT: A 1223 THR cc_start: 0.7975 (m) cc_final: 0.7640 (p) REVERT: A 1227 GLU cc_start: 0.7310 (pp20) cc_final: 0.6968 (pp20) REVERT: A 1417 SER cc_start: 0.8172 (p) cc_final: 0.7837 (p) REVERT: A 1443 MET cc_start: 0.7623 (mtt) cc_final: 0.7331 (mtm) REVERT: A 1725 TRP cc_start: 0.7200 (t60) cc_final: 0.6801 (t60) REVERT: A 1755 ASP cc_start: 0.7803 (p0) cc_final: 0.7457 (p0) outliers start: 23 outliers final: 14 residues processed: 378 average time/residue: 0.1488 time to fit residues: 76.5096 Evaluate side-chains 381 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 366 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 99 PHE 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 721 ILE Chi-restraints excluded: chain A residue 770 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 1409 VAL Chi-restraints excluded: chain A residue 1441 LEU 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: 0.6980 chunk 85 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 933 GLN ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3782 r_free = 0.3782 target = 0.137659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111640 restraints weight = 63206.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.117594 restraints weight = 22143.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121353 restraints weight = 10720.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123824 restraints weight = 6240.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.125438 restraints weight = 4118.502| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- 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 = 0.38 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14860 Z= 0.143 Angle : 0.568 7.664 20234 Z= 0.296 Chirality : 0.042 0.237 2268 Planarity : 0.004 0.055 2438 Dihedral : 12.652 141.772 2492 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.79 % Allowed : 14.86 % Favored : 83.34 % 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: -0.09 (0.20), residues: 1697 helix: 1.37 (0.19), residues: 810 sheet: 0.16 (0.45), residues: 139 loop : -1.79 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1422 TYR 0.020 0.002 TYR A 754 PHE 0.022 0.001 PHE A 265 TRP 0.034 0.001 TRP A 897 HIS 0.011 0.001 HIS A1011 Details of bonding type rmsd covalent geometry : bond 0.00325 (14860) covalent geometry : angle 0.56770 (20234) hydrogen bonds : bond 0.03572 ( 656) hydrogen bonds : angle 4.22962 ( 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 389 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 364 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.5760 (t80) REVERT: A 113 VAL cc_start: 0.7879 (t) cc_final: 0.7629 (p) REVERT: A 135 ILE cc_start: 0.8522 (mm) cc_final: 0.8014 (tp) REVERT: A 179 SER cc_start: 0.8051 (m) cc_final: 0.7473 (t) REVERT: A 200 GLU cc_start: 0.7468 (tp30) cc_final: 0.6800 (tp30) REVERT: A 209 ASP cc_start: 0.7050 (m-30) cc_final: 0.6235 (m-30) REVERT: A 271 LYS cc_start: 0.8020 (ptpp) cc_final: 0.7457 (ptpp) REVERT: A 302 CYS cc_start: 0.7852 (t) cc_final: 0.7446 (t) REVERT: A 306 ASP cc_start: 0.7328 (m-30) cc_final: 0.6951 (m-30) REVERT: A 473 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.7037 (mtm-85) REVERT: A 488 GLU cc_start: 0.7241 (tp30) cc_final: 0.6913 (tp30) REVERT: A 543 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7870 (tt) REVERT: A 686 MET cc_start: 0.6896 (mtp) cc_final: 0.6304 (mmm) REVERT: A 719 SER cc_start: 0.8388 (t) cc_final: 0.8151 (t) REVERT: A 830 GLU cc_start: 0.6751 (tt0) cc_final: 0.6547 (tt0) REVERT: A 864 VAL cc_start: 0.8181 (p) cc_final: 0.7962 (t) REVERT: A 897 TRP cc_start: 0.8365 (t-100) cc_final: 0.8125 (t-100) REVERT: A 956 ARG cc_start: 0.7350 (ptp90) cc_final: 0.7134 (ptp90) REVERT: A 964 ASN cc_start: 0.7832 (m-40) cc_final: 0.7631 (m-40) REVERT: A 1010 PHE cc_start: 0.7462 (m-10) cc_final: 0.6876 (m-10) REVERT: A 1020 MET cc_start: 0.8113 (ptt) cc_final: 0.7735 (ptm) REVERT: A 1052 MET cc_start: 0.7314 (mmt) cc_final: 0.7075 (mmt) REVERT: A 1064 TRP cc_start: 0.7757 (p-90) cc_final: 0.7512 (p-90) REVERT: A 1108 GLU cc_start: 0.7615 (pp20) cc_final: 0.7222 (pp20) REVERT: A 1111 MET cc_start: 0.6309 (ptp) cc_final: 0.5952 (ptp) REVERT: A 1137 LYS cc_start: 0.8457 (mttt) cc_final: 0.8021 (mttt) REVERT: A 1141 ASP cc_start: 0.7471 (t0) cc_final: 0.7206 (t0) REVERT: A 1142 GLU cc_start: 0.7495 (tt0) cc_final: 0.7279 (tt0) REVERT: A 1182 ASN cc_start: 0.8206 (m-40) cc_final: 0.7917 (m-40) REVERT: A 1193 ARG cc_start: 0.7500 (mtp180) cc_final: 0.7159 (mtp180) REVERT: A 1223 THR cc_start: 0.7934 (m) cc_final: 0.7612 (p) REVERT: A 1227 GLU cc_start: 0.7281 (pp20) cc_final: 0.6988 (pp20) REVERT: A 1278 MET cc_start: 0.7999 (mmm) cc_final: 0.7737 (mmm) REVERT: A 1368 ASN cc_start: 0.7779 (t0) cc_final: 0.7579 (t0) REVERT: A 1371 VAL cc_start: 0.7903 (p) cc_final: 0.7678 (t) REVERT: A 1417 SER cc_start: 0.8098 (p) cc_final: 0.7851 (p) REVERT: A 1514 GLU cc_start: 0.7221 (tp30) cc_final: 0.6926 (tp30) REVERT: A 1755 ASP cc_start: 0.7795 (p0) cc_final: 0.7474 (p0) outliers start: 25 outliers final: 17 residues processed: 370 average time/residue: 0.1461 time to fit residues: 73.6781 Evaluate side-chains 373 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 354 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 99 PHE 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 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 770 MET 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 1268 ASP 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 1787 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 144 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3786 r_free = 0.3786 target = 0.137881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112819 restraints weight = 53441.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118452 restraints weight = 19924.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122005 restraints weight = 9903.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124202 restraints weight = 5852.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.125781 restraints weight = 3960.239| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14860 Z= 0.135 Angle : 0.574 8.303 20234 Z= 0.298 Chirality : 0.041 0.213 2268 Planarity : 0.004 0.054 2438 Dihedral : 12.628 141.918 2492 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.79 % Allowed : 15.26 % Favored : 82.95 % 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: -0.06 (0.20), residues: 1697 helix: 1.40 (0.19), residues: 810 sheet: 0.12 (0.45), residues: 139 loop : -1.78 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1422 TYR 0.017 0.001 TYR A 754 PHE 0.021 0.001 PHE A 265 TRP 0.029 0.001 TRP A 897 HIS 0.018 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00310 (14860) covalent geometry : angle 0.57423 (20234) hydrogen bonds : bond 0.03519 ( 656) hydrogen bonds : angle 4.20085 ( 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 381 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 356 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.6185 (OUTLIER) cc_final: 0.5821 (t80) REVERT: A 135 ILE cc_start: 0.8534 (mm) cc_final: 0.8066 (tp) REVERT: A 179 SER cc_start: 0.7975 (m) cc_final: 0.7404 (t) REVERT: A 192 MET cc_start: 0.6774 (ttp) cc_final: 0.6439 (ttp) REVERT: A 200 GLU cc_start: 0.7448 (tp30) cc_final: 0.6786 (tp30) REVERT: A 209 ASP cc_start: 0.7011 (m-30) cc_final: 0.6215 (m-30) REVERT: A 271 LYS cc_start: 0.8029 (ptpp) cc_final: 0.7453 (ptpp) REVERT: A 302 CYS cc_start: 0.7847 (t) cc_final: 0.7467 (t) REVERT: A 306 ASP cc_start: 0.7323 (m-30) cc_final: 0.6958 (m-30) REVERT: A 488 GLU cc_start: 0.7233 (tp30) cc_final: 0.6823 (tp30) REVERT: A 594 GLU cc_start: 0.6786 (tt0) cc_final: 0.6098 (mt-10) REVERT: A 671 MET cc_start: 0.6746 (mmm) cc_final: 0.6442 (tpp) REVERT: A 686 MET cc_start: 0.6882 (mtp) cc_final: 0.6318 (mmm) REVERT: A 719 SER cc_start: 0.8345 (t) cc_final: 0.7692 (p) REVERT: A 864 VAL cc_start: 0.8174 (p) cc_final: 0.7961 (t) REVERT: A 887 MET cc_start: 0.6967 (tmm) cc_final: 0.6340 (tmm) REVERT: A 897 TRP cc_start: 0.8348 (t-100) cc_final: 0.8143 (t-100) REVERT: A 956 ARG cc_start: 0.7345 (ptp90) cc_final: 0.7145 (ptp90) REVERT: A 964 ASN cc_start: 0.7855 (m-40) cc_final: 0.7613 (m-40) REVERT: A 1006 MET cc_start: 0.7492 (mmm) cc_final: 0.6938 (mmm) REVERT: A 1010 PHE cc_start: 0.7414 (m-10) cc_final: 0.6591 (m-10) REVERT: A 1020 MET cc_start: 0.8109 (ptt) cc_final: 0.7898 (ptm) REVERT: A 1052 MET cc_start: 0.7294 (mmt) cc_final: 0.7054 (mmt) REVERT: A 1064 TRP cc_start: 0.7755 (p-90) cc_final: 0.7474 (p-90) REVERT: A 1105 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8214 (mmmm) REVERT: A 1108 GLU cc_start: 0.7600 (pp20) cc_final: 0.7195 (pp20) REVERT: A 1135 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7470 (ttp-170) REVERT: A 1137 LYS cc_start: 0.8428 (mttt) cc_final: 0.8015 (mttt) REVERT: A 1141 ASP cc_start: 0.7487 (t0) cc_final: 0.7225 (t0) REVERT: A 1142 GLU cc_start: 0.7491 (tt0) cc_final: 0.7268 (tt0) REVERT: A 1182 ASN cc_start: 0.8199 (m-40) cc_final: 0.7885 (m-40) REVERT: A 1184 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6308 (mm-30) REVERT: A 1193 ARG cc_start: 0.7478 (mtp180) cc_final: 0.7079 (mtp180) REVERT: A 1223 THR cc_start: 0.7914 (m) cc_final: 0.7594 (p) REVERT: A 1227 GLU cc_start: 0.7296 (pp20) cc_final: 0.6992 (pp20) REVERT: A 1417 SER cc_start: 0.8109 (p) cc_final: 0.7887 (p) REVERT: A 1514 GLU cc_start: 0.7211 (tp30) cc_final: 0.6916 (tp30) REVERT: A 1755 ASP cc_start: 0.7795 (p0) cc_final: 0.7467 (p0) outliers start: 25 outliers final: 18 residues processed: 362 average time/residue: 0.1520 time to fit residues: 74.5554 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 : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 109 MET 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 336 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 770 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 1441 LEU 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: 0.9990 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 102 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3821 r_free = 0.3821 target = 0.142827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118222 restraints weight = 55055.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124060 restraints weight = 19444.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127729 restraints weight = 9398.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130063 restraints weight = 5383.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131475 restraints weight = 3513.156| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14860 Z= 0.133 Angle : 0.571 8.625 20234 Z= 0.297 Chirality : 0.041 0.213 2268 Planarity : 0.004 0.057 2438 Dihedral : 12.618 141.973 2492 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.59 % Allowed : 15.39 % Favored : 83.01 % 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: -0.05 (0.20), residues: 1697 helix: 1.40 (0.19), residues: 813 sheet: 0.11 (0.45), residues: 139 loop : -1.75 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1422 TYR 0.014 0.001 TYR A 861 PHE 0.029 0.002 PHE A 265 TRP 0.028 0.001 TRP A 897 HIS 0.016 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00305 (14860) covalent geometry : angle 0.57144 (20234) hydrogen bonds : bond 0.03488 ( 656) hydrogen bonds : angle 4.17498 ( 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 386 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 364 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7177 (pmm) cc_final: 0.6928 (pmm) REVERT: A 99 PHE cc_start: 0.6134 (OUTLIER) cc_final: 0.5709 (t80) REVERT: A 135 ILE cc_start: 0.8544 (mm) cc_final: 0.8065 (tp) REVERT: A 179 SER cc_start: 0.7934 (m) cc_final: 0.7378 (t) REVERT: A 200 GLU cc_start: 0.7441 (tp30) cc_final: 0.6752 (tp30) REVERT: A 209 ASP cc_start: 0.6982 (m-30) cc_final: 0.6176 (m-30) REVERT: A 271 LYS cc_start: 0.8022 (ptpp) cc_final: 0.7432 (ptpp) REVERT: A 302 CYS cc_start: 0.7859 (t) cc_final: 0.7481 (t) REVERT: A 306 ASP cc_start: 0.7328 (m-30) cc_final: 0.6950 (m-30) REVERT: A 488 GLU cc_start: 0.7200 (tp30) cc_final: 0.6763 (tp30) REVERT: A 594 GLU cc_start: 0.6802 (tt0) cc_final: 0.6107 (mt-10) REVERT: A 686 MET cc_start: 0.6914 (mtp) cc_final: 0.6402 (mmm) REVERT: A 719 SER cc_start: 0.8343 (t) cc_final: 0.7692 (p) REVERT: A 864 VAL cc_start: 0.8208 (p) cc_final: 0.7985 (t) REVERT: A 884 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8156 (ttmm) REVERT: A 887 MET cc_start: 0.6973 (tmm) cc_final: 0.6343 (tmm) REVERT: A 897 TRP cc_start: 0.8361 (t-100) cc_final: 0.8091 (t-100) REVERT: A 956 ARG cc_start: 0.7370 (ptp90) cc_final: 0.7157 (ptp90) REVERT: A 964 ASN cc_start: 0.7859 (m-40) cc_final: 0.7608 (m-40) REVERT: A 1006 MET cc_start: 0.7497 (mmm) cc_final: 0.7063 (mpp) REVERT: A 1010 PHE cc_start: 0.7436 (m-10) cc_final: 0.6762 (m-10) REVERT: A 1020 MET cc_start: 0.8101 (ptt) cc_final: 0.7750 (ptm) REVERT: A 1064 TRP cc_start: 0.7752 (p-90) cc_final: 0.7485 (p-90) REVERT: A 1087 SER cc_start: 0.8384 (m) cc_final: 0.8146 (m) REVERT: A 1105 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8228 (mmmm) REVERT: A 1108 GLU cc_start: 0.7628 (pp20) cc_final: 0.7229 (pp20) REVERT: A 1135 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7483 (ttp-170) REVERT: A 1141 ASP cc_start: 0.7517 (t0) cc_final: 0.7269 (t0) REVERT: A 1142 GLU cc_start: 0.7526 (tt0) cc_final: 0.7299 (tt0) REVERT: A 1182 ASN cc_start: 0.8200 (m-40) cc_final: 0.7896 (m-40) REVERT: A 1184 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6312 (mm-30) REVERT: A 1193 ARG cc_start: 0.7452 (mtp180) cc_final: 0.7041 (mtp180) REVERT: A 1223 THR cc_start: 0.7907 (m) cc_final: 0.7593 (p) REVERT: A 1227 GLU cc_start: 0.7313 (pp20) cc_final: 0.7020 (pp20) REVERT: A 1417 SER cc_start: 0.8122 (p) cc_final: 0.7914 (p) REVERT: A 1443 MET cc_start: 0.7652 (mtt) cc_final: 0.7354 (mtm) REVERT: A 1514 GLU cc_start: 0.7218 (tp30) cc_final: 0.6912 (tp30) REVERT: A 1755 ASP cc_start: 0.7803 (p0) cc_final: 0.7473 (p0) outliers start: 22 outliers final: 18 residues processed: 369 average time/residue: 0.1574 time to fit residues: 78.6050 Evaluate side-chains 376 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 357 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 PHE 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 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 770 MET 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 1206 SER 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 1787 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3802 r_free = 0.3802 target = 0.141455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116268 restraints weight = 61363.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122238 restraints weight = 20775.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126012 restraints weight = 9862.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128398 restraints weight = 5607.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129940 restraints weight = 3661.762| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14860 Z= 0.182 Angle : 0.604 9.033 20234 Z= 0.315 Chirality : 0.043 0.216 2268 Planarity : 0.004 0.056 2438 Dihedral : 12.651 140.977 2492 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.73 % Allowed : 15.39 % Favored : 82.88 % 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: -0.14 (0.20), residues: 1697 helix: 1.32 (0.19), residues: 814 sheet: 0.02 (0.44), residues: 139 loop : -1.79 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1422 TYR 0.015 0.002 TYR A 754 PHE 0.036 0.002 PHE A 265 TRP 0.030 0.002 TRP A1547 HIS 0.025 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00409 (14860) covalent geometry : angle 0.60357 (20234) hydrogen bonds : bond 0.03824 ( 656) hydrogen bonds : angle 4.24017 ( 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 385 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 361 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7680 (ptp-170) cc_final: 0.7434 (ptp-170) REVERT: A 99 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5839 (t80) REVERT: A 135 ILE cc_start: 0.8560 (mm) cc_final: 0.8054 (tp) REVERT: A 179 SER cc_start: 0.8013 (m) cc_final: 0.7397 (t) REVERT: A 192 MET cc_start: 0.6939 (ttp) cc_final: 0.6563 (ttp) REVERT: A 200 GLU cc_start: 0.7506 (tp30) cc_final: 0.6815 (tp30) REVERT: A 209 ASP cc_start: 0.6998 (m-30) cc_final: 0.6162 (m-30) REVERT: A 271 LYS cc_start: 0.8036 (ptpp) cc_final: 0.7418 (ptpp) REVERT: A 302 CYS cc_start: 0.7883 (t) cc_final: 0.7498 (t) REVERT: A 306 ASP cc_start: 0.7339 (m-30) cc_final: 0.6978 (m-30) REVERT: A 488 GLU cc_start: 0.7188 (tp30) cc_final: 0.6745 (tp30) REVERT: A 686 MET cc_start: 0.6986 (mtp) cc_final: 0.6395 (mmt) REVERT: A 719 SER cc_start: 0.8442 (t) cc_final: 0.7768 (p) REVERT: A 864 VAL cc_start: 0.8237 (p) cc_final: 0.8004 (t) REVERT: A 884 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8220 (ttmm) REVERT: A 887 MET cc_start: 0.6999 (tmm) cc_final: 0.6342 (tmm) REVERT: A 897 TRP cc_start: 0.8381 (t-100) cc_final: 0.8127 (t-100) REVERT: A 956 ARG cc_start: 0.7390 (ptp90) cc_final: 0.7169 (ptp90) REVERT: A 964 ASN cc_start: 0.7860 (m-40) cc_final: 0.7610 (m110) REVERT: A 1006 MET cc_start: 0.7579 (mmm) cc_final: 0.7064 (mmm) REVERT: A 1010 PHE cc_start: 0.7404 (m-10) cc_final: 0.6642 (m-10) REVERT: A 1020 MET cc_start: 0.8152 (ptt) cc_final: 0.7765 (ptm) REVERT: A 1064 TRP cc_start: 0.7814 (p-90) cc_final: 0.7539 (p-90) REVERT: A 1087 SER cc_start: 0.8396 (m) cc_final: 0.8160 (m) REVERT: A 1108 GLU cc_start: 0.7601 (pp20) cc_final: 0.7237 (pp20) REVERT: A 1135 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7549 (ttp-170) REVERT: A 1141 ASP cc_start: 0.7543 (t0) cc_final: 0.7276 (t0) REVERT: A 1142 GLU cc_start: 0.7514 (tt0) cc_final: 0.7294 (tt0) REVERT: A 1182 ASN cc_start: 0.8215 (m-40) cc_final: 0.7923 (m-40) REVERT: A 1184 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6325 (mm-30) REVERT: A 1193 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7076 (mtp180) REVERT: A 1223 THR cc_start: 0.7958 (m) cc_final: 0.7638 (p) REVERT: A 1227 GLU cc_start: 0.7348 (pp20) cc_final: 0.7066 (pp20) REVERT: A 1368 ASN cc_start: 0.7844 (t0) cc_final: 0.7572 (t0) REVERT: A 1443 MET cc_start: 0.7635 (mtt) cc_final: 0.7338 (mtm) REVERT: A 1514 GLU cc_start: 0.7256 (tp30) cc_final: 0.6955 (tp30) REVERT: A 1755 ASP cc_start: 0.7856 (p0) cc_final: 0.7530 (p0) outliers start: 24 outliers final: 20 residues processed: 368 average time/residue: 0.1574 time to fit residues: 78.2157 Evaluate side-chains 381 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 360 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 99 PHE 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 250 ILE 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 770 MET 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 1441 LEU 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: 0.5980 chunk 133 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 chunk 138 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3824 r_free = 0.3824 target = 0.143094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118387 restraints weight = 54427.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124224 restraints weight = 19081.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127938 restraints weight = 9225.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130243 restraints weight = 5280.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131683 restraints weight = 3477.436| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 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 = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2462 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= 0.130 Angle : 0.591 8.031 20234 Z= 0.306 Chirality : 0.041 0.216 2268 Planarity : 0.004 0.056 2438 Dihedral : 12.648 141.645 2492 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.53 % Allowed : 15.93 % Favored : 82.55 % 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: -0.07 (0.20), residues: 1697 helix: 1.39 (0.19), residues: 813 sheet: 0.10 (0.44), residues: 139 loop : -1.77 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1422 TYR 0.017 0.001 TYR A1110 PHE 0.038 0.002 PHE A 265 TRP 0.028 0.002 TRP A1547 HIS 0.022 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00299 (14860) covalent geometry : angle 0.59112 (20234) hydrogen bonds : bond 0.03510 ( 656) hydrogen bonds : angle 4.20438 ( 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 376 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 355 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.6924 (m-30) cc_final: 0.6657 (m-30) REVERT: A 99 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5785 (t80) REVERT: A 135 ILE cc_start: 0.8552 (mm) cc_final: 0.8073 (tp) REVERT: A 145 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7254 (ttmm) REVERT: A 192 MET cc_start: 0.6863 (ttp) cc_final: 0.6436 (ttt) REVERT: A 200 GLU cc_start: 0.7403 (tp30) cc_final: 0.6806 (tp30) REVERT: A 204 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7643 (mtmm) REVERT: A 206 ARG cc_start: 0.6971 (mtt-85) cc_final: 0.6744 (mmt180) REVERT: A 209 ASP cc_start: 0.6806 (m-30) cc_final: 0.5982 (m-30) REVERT: A 271 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7358 (ptpp) REVERT: A 302 CYS cc_start: 0.7853 (t) cc_final: 0.7490 (t) REVERT: A 306 ASP cc_start: 0.7332 (m-30) cc_final: 0.6952 (m-30) REVERT: A 488 GLU cc_start: 0.7173 (tp30) cc_final: 0.6688 (tp30) REVERT: A 489 LYS cc_start: 0.7616 (ttmt) cc_final: 0.7404 (ttmt) REVERT: A 686 MET cc_start: 0.6863 (mtp) cc_final: 0.6314 (mmt) REVERT: A 719 SER cc_start: 0.8374 (t) cc_final: 0.7698 (p) REVERT: A 864 VAL cc_start: 0.8200 (p) cc_final: 0.7980 (t) REVERT: A 884 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8234 (ttmm) REVERT: A 887 MET cc_start: 0.6924 (tmm) cc_final: 0.6278 (tmm) REVERT: A 897 TRP cc_start: 0.8359 (t-100) cc_final: 0.8158 (t-100) REVERT: A 956 ARG cc_start: 0.7362 (ptp90) cc_final: 0.7150 (ptp90) REVERT: A 964 ASN cc_start: 0.7849 (m-40) cc_final: 0.7597 (m110) REVERT: A 1010 PHE cc_start: 0.7470 (m-10) cc_final: 0.6809 (m-10) REVERT: A 1020 MET cc_start: 0.8115 (ptt) cc_final: 0.7768 (ptm) REVERT: A 1064 TRP cc_start: 0.7764 (p-90) cc_final: 0.7495 (p-90) REVERT: A 1087 SER cc_start: 0.8384 (m) cc_final: 0.8116 (m) REVERT: A 1108 GLU cc_start: 0.7636 (pp20) cc_final: 0.7225 (pp20) REVERT: A 1135 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7494 (ttp-170) REVERT: A 1141 ASP cc_start: 0.7529 (t0) cc_final: 0.7284 (t0) REVERT: A 1142 GLU cc_start: 0.7485 (tt0) cc_final: 0.7256 (tt0) REVERT: A 1182 ASN cc_start: 0.8198 (m-40) cc_final: 0.7905 (m-40) REVERT: A 1184 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6292 (mm-30) REVERT: A 1193 ARG cc_start: 0.7472 (mtp180) cc_final: 0.7027 (mtp180) REVERT: A 1219 SER cc_start: 0.8148 (t) cc_final: 0.7711 (p) REVERT: A 1223 THR cc_start: 0.7904 (m) cc_final: 0.7606 (p) REVERT: A 1227 GLU cc_start: 0.7311 (pp20) cc_final: 0.7031 (pp20) REVERT: A 1368 ASN cc_start: 0.7791 (t0) cc_final: 0.7544 (t0) REVERT: A 1443 MET cc_start: 0.7621 (mtt) cc_final: 0.7323 (mtm) REVERT: A 1514 GLU cc_start: 0.7206 (tp30) cc_final: 0.6891 (tp30) REVERT: A 1755 ASP cc_start: 0.7843 (p0) cc_final: 0.7530 (p0) outliers start: 21 outliers final: 19 residues processed: 359 average time/residue: 0.1564 time to fit residues: 75.9234 Evaluate side-chains 371 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 351 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 99 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 250 ILE 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 770 MET 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 1441 LEU 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: 5.9990 chunk 131 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 163 optimal weight: 0.0050 chunk 144 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 40.0000 chunk 64 optimal weight: 0.6980 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN ** 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 = 0.3773 r_free = 0.3773 target = 0.137654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111070 restraints weight = 64753.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117214 restraints weight = 22311.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121087 restraints weight = 10722.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123613 restraints weight = 6187.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125229 restraints weight = 4079.484| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 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 = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14860 Z= 0.158 Angle : 0.602 8.753 20234 Z= 0.314 Chirality : 0.042 0.217 2268 Planarity : 0.004 0.056 2438 Dihedral : 12.669 141.084 2492 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.46 % Allowed : 15.93 % Favored : 82.61 % 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: -0.09 (0.20), residues: 1697 helix: 1.37 (0.19), residues: 815 sheet: 0.09 (0.45), residues: 138 loop : -1.79 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1542 TYR 0.015 0.001 TYR A1110 PHE 0.037 0.002 PHE A 265 TRP 0.027 0.002 TRP A 897 HIS 0.009 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00360 (14860) covalent geometry : angle 0.60244 (20234) hydrogen bonds : bond 0.03673 ( 656) hydrogen bonds : angle 4.22572 ( 1919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2870.22 seconds wall clock time: 50 minutes 31.97 seconds (3031.97 seconds total)