Starting phenix.real_space_refine on Thu Aug 6 14:09:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8asb_15610/08_2026/8asb_15610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asb_15610/08_2026/8asb_15610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8asb_15610/08_2026/8asb_15610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asb_15610/08_2026/8asb_15610.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8asb_15610/08_2026/8asb_15610.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8asb_15610/08_2026/8asb_15610.cif" model { file = "/net/cci-nas-00/data/ceres_data/8asb_15610/08_2026/8asb_15610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asb_15610/08_2026/8asb_15610.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 873 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 9019 2.51 5 N 2529 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 17} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 381 Classifications: {'RNAv2': 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: {'RNAv2': 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: 4.12, per 1000 atoms: 0.28 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: 1.13 Conformation dependent library (CDL) restraints added in 801.8 milliseconds 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: 1.27 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: 2.44 Time building geometry restraints manager: 1.41 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 - 27.35: 8445 27.35 - 54.69: 410 54.69 - 82.03: 61 82.03 - 109.38: 5 109.38 - 136.72: 1 Dihedral angle restraints: 8922 sinusoidal: 3950 harmonic: 4972 Sorted by residual: dihedral pdb=" C4' A P 5 " pdb=" C3' A P 5 " pdb=" C2' A P 5 " pdb=" C1' A P 5 " ideal model delta sinusoidal sigma weight residual 36.34 -36.37 72.71 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' A P 17 " pdb=" C3' A P 17 " pdb=" C2' A P 17 " pdb=" C1' A P 17 " ideal model delta sinusoidal sigma weight residual 36.34 -35.82 72.16 1 3.10e+00 1.04e-01 6.93e+02 dihedral pdb=" C4' U T 21 " pdb=" C3' U T 21 " pdb=" C2' U T 21 " pdb=" C1' U T 21 " ideal model delta sinusoidal sigma weight residual 36.35 -34.86 71.20 1 3.10e+00 1.04e-01 6.77e+02 ... (remaining 8919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1817 0.056 - 0.112: 336 0.112 - 0.168: 55 0.168 - 0.224: 8 0.224 - 0.280: 52 Chirality restraints: 2268 Sorted by residual: chirality pdb=" C2' U T 21 " pdb=" C3' U T 21 " pdb=" O2' U T 21 " pdb=" C1' U T 21 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C2' G P 6 " pdb=" C3' G P 6 " pdb=" O2' G P 6 " pdb=" C1' G P 6 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C2' A P 7 " pdb=" C3' A P 7 " pdb=" O2' A P 7 " pdb=" C1' A P 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.88e+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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.690 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.253 14860 Z= 0.280 Angle : 1.005 62.020 20234 Z= 0.437 Chirality : 0.058 0.280 2268 Planarity : 0.005 0.060 2438 Dihedral : 15.299 136.722 5710 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.19), residues: 1697 helix: 0.43 (0.18), residues: 791 sheet: -0.38 (0.43), residues: 148 loop : -1.83 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1542 TYR 0.035 0.002 TYR A 202 PHE 0.037 0.002 PHE A 84 TRP 0.059 0.002 TRP A 897 HIS 0.010 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.28 (14860) covalent geometry : angle 1.00491 / 0.44 (20234) hydrogen bonds : bond 0.15393 / 10.53 ( 656) hydrogen bonds : angle 6.22677 / 4.48 ( 1919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.320 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: 0.1264 time to fit residues: 63.1192 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0970 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 990 ASN A1011 HIS A1403 HIS A1569 ASN A1604 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113750 restraints weight = 53091.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119470 restraints weight = 19487.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123104 restraints weight = 9666.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125426 restraints weight = 5691.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126881 restraints weight = 3818.679| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 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 = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14860 Z= 0.165 Angle : 0.743 11.549 20234 Z= 0.355 Chirality : 0.057 0.838 2268 Planarity : 0.005 0.061 2438 Dihedral : 10.426 138.515 2356 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.66 % Allowed : 9.16 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1697 helix: 1.09 (0.18), residues: 810 sheet: 0.14 (0.45), residues: 140 loop : -1.77 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1497 TYR 0.018 0.002 TYR A 754 PHE 0.026 0.002 PHE A1048 TRP 0.031 0.002 TRP A 897 HIS 0.011 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (14860) covalent geometry : angle 0.74256 / 0.35 (20234) hydrogen bonds : bond 0.04168 / 2.89 ( 656) hydrogen bonds : angle 4.54862 / 3.31 ( 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: 10 poor density : 363 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6851 (ppp) cc_final: 0.6299 (pmm) REVERT: A 145 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6835 (ttmm) REVERT: A 200 GLU cc_start: 0.7428 (tp30) cc_final: 0.6911 (tp30) REVERT: A 209 ASP cc_start: 0.7154 (m-30) cc_final: 0.6186 (m-30) REVERT: A 213 GLU cc_start: 0.6814 (mp0) cc_final: 0.6457 (mp0) REVERT: A 271 LYS cc_start: 0.7967 (ptpp) cc_final: 0.7439 (ptpp) REVERT: A 302 CYS cc_start: 0.7818 (t) cc_final: 0.7472 (t) REVERT: A 306 ASP cc_start: 0.7308 (m-30) cc_final: 0.6988 (m-30) REVERT: A 488 GLU cc_start: 0.7221 (tp30) cc_final: 0.6840 (tp30) REVERT: A 495 ASP cc_start: 0.7397 (p0) cc_final: 0.7149 (p0) REVERT: A 544 LYS cc_start: 0.8092 (mttt) cc_final: 0.7785 (mttt) REVERT: A 671 MET cc_start: 0.6616 (mmm) cc_final: 0.6358 (tpp) REVERT: A 719 SER cc_start: 0.8371 (t) cc_final: 0.8132 (t) REVERT: A 759 GLU cc_start: 0.6668 (tp30) cc_final: 0.6341 (mm-30) REVERT: A 864 VAL cc_start: 0.8199 (m) cc_final: 0.7980 (p) REVERT: A 933 GLN cc_start: 0.7505 (tm-30) cc_final: 0.7272 (tm-30) REVERT: A 964 ASN cc_start: 0.7836 (m-40) cc_final: 0.7619 (m-40) REVERT: A 1032 PHE cc_start: 0.7756 (t80) cc_final: 0.7452 (t80) REVERT: A 1064 TRP cc_start: 0.7654 (p-90) cc_final: 0.7386 (p-90) REVERT: A 1079 MET cc_start: 0.5971 (mtm) cc_final: 0.5762 (mtm) REVERT: A 1108 GLU cc_start: 0.7562 (pp20) cc_final: 0.7236 (pp20) REVERT: A 1123 GLU cc_start: 0.6930 (pp20) cc_final: 0.6526 (pp20) REVERT: A 1137 LYS cc_start: 0.8444 (mttt) cc_final: 0.8043 (mttt) REVERT: A 1141 ASP cc_start: 0.7363 (t0) cc_final: 0.7070 (t0) REVERT: A 1142 GLU cc_start: 0.7518 (tt0) cc_final: 0.7315 (tt0) REVERT: A 1182 ASN cc_start: 0.8157 (m-40) cc_final: 0.7920 (m-40) REVERT: A 1193 ARG cc_start: 0.7540 (mtp180) cc_final: 0.7280 (mtp180) REVERT: A 1223 THR cc_start: 0.7887 (m) cc_final: 0.7592 (p) REVERT: A 1227 GLU cc_start: 0.7138 (pp20) cc_final: 0.6871 (pp20) REVERT: A 1346 LYS cc_start: 0.7338 (mtpt) cc_final: 0.7019 (mtpt) REVERT: A 1381 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6546 (tm-30) REVERT: A 1514 GLU cc_start: 0.7456 (tp30) cc_final: 0.7134 (tp30) REVERT: A 1755 ASP cc_start: 0.7682 (p0) cc_final: 0.7304 (p0) REVERT: A 1845 MET cc_start: 0.5668 (ptm) cc_final: 0.5139 (ptm) outliers start: 10 outliers final: 9 residues processed: 367 average time/residue: 0.1394 time to fit residues: 69.9843 Evaluate side-chains 354 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 345 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 1122 ILE Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1601 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.0060 chunk 43 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3793 r_free = 0.3793 target = 0.138628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112455 restraints weight = 62177.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118501 restraints weight = 21605.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122365 restraints weight = 10464.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124808 restraints weight = 6038.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126481 restraints weight = 3991.454| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14860 Z= 0.143 Angle : 0.651 9.739 20234 Z= 0.317 Chirality : 0.050 0.560 2268 Planarity : 0.004 0.056 2438 Dihedral : 10.396 145.543 2354 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.73 % Allowed : 11.02 % Favored : 88.25 % 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: -0.16 (0.20), residues: 1697 helix: 1.26 (0.19), residues: 811 sheet: -0.09 (0.44), residues: 148 loop : -1.72 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1542 TYR 0.017 0.002 TYR A 754 PHE 0.036 0.002 PHE A 82 TRP 0.025 0.001 TRP A 897 HIS 0.010 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14860) covalent geometry : angle 0.65078 / 0.32 (20234) hydrogen bonds : bond 0.03761 / 2.58 ( 656) hydrogen bonds : angle 4.30752 / 3.13 ( 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 366 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 357 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6838 (ppp) cc_final: 0.6371 (pmm) REVERT: A 125 VAL cc_start: 0.8370 (t) cc_final: 0.8143 (t) REVERT: A 135 ILE cc_start: 0.8526 (mm) cc_final: 0.8045 (tp) REVERT: A 145 LYS cc_start: 0.7219 (mmtt) cc_final: 0.6911 (ttmm) REVERT: A 179 SER cc_start: 0.7990 (m) cc_final: 0.7353 (t) REVERT: A 200 GLU cc_start: 0.7482 (tp30) cc_final: 0.6969 (tp30) REVERT: A 209 ASP cc_start: 0.7111 (m-30) cc_final: 0.6287 (m-30) REVERT: A 239 GLU cc_start: 0.7409 (pp20) cc_final: 0.7176 (pp20) REVERT: A 271 LYS cc_start: 0.8015 (ptpp) cc_final: 0.7472 (ptpp) REVERT: A 302 CYS cc_start: 0.7842 (t) cc_final: 0.7529 (t) REVERT: A 306 ASP cc_start: 0.7328 (m-30) cc_final: 0.6959 (m-30) REVERT: A 488 GLU cc_start: 0.7221 (tp30) cc_final: 0.6893 (tp30) REVERT: A 489 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7519 (tttt) REVERT: A 495 ASP cc_start: 0.7474 (p0) cc_final: 0.7257 (p0) REVERT: A 544 LYS cc_start: 0.7960 (mttt) cc_final: 0.7743 (mttt) REVERT: A 618 ASN cc_start: 0.7522 (m-40) cc_final: 0.7271 (m110) REVERT: A 707 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6986 (mp) REVERT: A 719 SER cc_start: 0.8389 (t) cc_final: 0.8154 (t) REVERT: A 759 GLU cc_start: 0.6763 (tp30) cc_final: 0.6451 (mm-30) REVERT: A 933 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 964 ASN cc_start: 0.7851 (m-40) cc_final: 0.7586 (m-40) REVERT: A 1052 MET cc_start: 0.7326 (mmt) cc_final: 0.7116 (mmt) REVERT: A 1064 TRP cc_start: 0.7675 (p-90) cc_final: 0.7415 (p-90) REVERT: A 1079 MET cc_start: 0.6133 (mtm) cc_final: 0.5817 (mtm) REVERT: A 1087 SER cc_start: 0.8367 (m) cc_final: 0.8128 (m) REVERT: A 1108 GLU cc_start: 0.7543 (pp20) cc_final: 0.7219 (pp20) REVERT: A 1137 LYS cc_start: 0.8448 (mttt) cc_final: 0.8029 (mttt) REVERT: A 1141 ASP cc_start: 0.7391 (t0) cc_final: 0.7147 (t0) REVERT: A 1182 ASN cc_start: 0.8198 (m-40) cc_final: 0.7945 (m-40) REVERT: A 1193 ARG cc_start: 0.7580 (mtp180) cc_final: 0.7262 (mtp180) REVERT: A 1216 GLU cc_start: 0.7100 (pt0) cc_final: 0.6846 (pt0) REVERT: A 1223 THR cc_start: 0.7900 (m) cc_final: 0.7561 (p) REVERT: A 1227 GLU cc_start: 0.7198 (pp20) cc_final: 0.6864 (pp20) REVERT: A 1346 LYS cc_start: 0.7353 (mtpt) cc_final: 0.7026 (mtpt) REVERT: A 1514 GLU cc_start: 0.7312 (tp30) cc_final: 0.6898 (tp30) REVERT: A 1755 ASP cc_start: 0.7749 (p0) cc_final: 0.7366 (p0) REVERT: A 1845 MET cc_start: 0.5745 (ptm) cc_final: 0.5368 (ptm) outliers start: 9 outliers final: 5 residues processed: 358 average time/residue: 0.1334 time to fit residues: 66.1638 Evaluate side-chains 360 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 354 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 910 LEU 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: 0.2980 chunk 83 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 131 optimal weight: 0.0870 chunk 111 optimal weight: 0.9980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS ** A 185 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114207 restraints weight = 56974.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120130 restraints weight = 20435.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123836 restraints weight = 9984.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126225 restraints weight = 5833.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127761 restraints weight = 3873.159| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14860 Z= 0.117 Angle : 0.615 9.832 20234 Z= 0.301 Chirality : 0.048 0.415 2268 Planarity : 0.004 0.055 2438 Dihedral : 10.297 155.087 2354 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.39 % Allowed : 12.61 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1697 helix: 1.43 (0.19), residues: 804 sheet: -0.01 (0.45), residues: 146 loop : -1.68 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1422 TYR 0.017 0.001 TYR A 861 PHE 0.016 0.001 PHE A1048 TRP 0.021 0.001 TRP A 897 HIS 0.008 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (14860) covalent geometry : angle 0.61530 / 0.30 (20234) hydrogen bonds : bond 0.03360 / 2.29 ( 656) hydrogen bonds : angle 4.17971 / 3.04 ( 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 378 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 359 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8549 (mm) cc_final: 0.8053 (tp) REVERT: A 145 LYS cc_start: 0.7267 (mmtt) cc_final: 0.7051 (ttmm) REVERT: A 179 SER cc_start: 0.7918 (m) cc_final: 0.7349 (t) REVERT: A 200 GLU cc_start: 0.7481 (tp30) cc_final: 0.6850 (tp30) REVERT: A 209 ASP cc_start: 0.7100 (m-30) cc_final: 0.6131 (m-30) REVERT: A 213 GLU cc_start: 0.6921 (mp0) cc_final: 0.6555 (mp0) REVERT: A 271 LYS cc_start: 0.7968 (ptpp) cc_final: 0.7418 (ptpp) REVERT: A 306 ASP cc_start: 0.7324 (m-30) cc_final: 0.6931 (m-30) REVERT: A 488 GLU cc_start: 0.7236 (tp30) cc_final: 0.6884 (tp30) REVERT: A 719 SER cc_start: 0.8320 (t) cc_final: 0.8098 (t) REVERT: A 756 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7299 (tttp) REVERT: A 759 GLU cc_start: 0.6686 (tp30) cc_final: 0.6405 (mm-30) REVERT: A 848 MET cc_start: 0.7380 (mmm) cc_final: 0.6978 (mmm) REVERT: A 864 VAL cc_start: 0.8159 (p) cc_final: 0.7942 (t) REVERT: A 933 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 964 ASN cc_start: 0.7834 (m-40) cc_final: 0.7559 (m-40) REVERT: A 1052 MET cc_start: 0.7346 (mmt) cc_final: 0.7107 (mmt) REVERT: A 1064 TRP cc_start: 0.7622 (p-90) cc_final: 0.7362 (p-90) REVERT: A 1079 MET cc_start: 0.6159 (mtm) cc_final: 0.5926 (mtm) REVERT: A 1108 GLU cc_start: 0.7579 (pp20) cc_final: 0.7218 (pp20) REVERT: A 1123 GLU cc_start: 0.6753 (pp20) cc_final: 0.6418 (pp20) REVERT: A 1137 LYS cc_start: 0.8442 (mttt) cc_final: 0.7995 (mttt) REVERT: A 1141 ASP cc_start: 0.7376 (t0) cc_final: 0.7091 (t0) REVERT: A 1182 ASN cc_start: 0.8208 (m-40) cc_final: 0.7910 (m-40) REVERT: A 1193 ARG cc_start: 0.7541 (mtp180) cc_final: 0.7224 (mtp180) REVERT: A 1223 THR cc_start: 0.7838 (m) cc_final: 0.7528 (p) REVERT: A 1227 GLU cc_start: 0.7197 (pp20) cc_final: 0.6861 (pp20) REVERT: A 1417 SER cc_start: 0.8038 (p) cc_final: 0.7756 (p) REVERT: A 1443 MET cc_start: 0.7627 (mtt) cc_final: 0.7350 (mtm) REVERT: A 1514 GLU cc_start: 0.7252 (tp30) cc_final: 0.6869 (tp30) REVERT: A 1755 ASP cc_start: 0.7727 (p0) cc_final: 0.7386 (p0) REVERT: A 1845 MET cc_start: 0.5679 (ptm) cc_final: 0.5282 (ptm) outliers start: 19 outliers final: 13 residues processed: 362 average time/residue: 0.1367 time to fit residues: 68.2441 Evaluate side-chains 365 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 351 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1268 ASP 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: 4.9990 chunk 112 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 GLN A1292 ASN A1364 GLN A1569 ASN ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109482 restraints weight = 51633.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115083 restraints weight = 19342.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118680 restraints weight = 9712.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120944 restraints weight = 5750.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122471 restraints weight = 3904.485| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 14860 Z= 0.284 Angle : 0.723 13.304 20234 Z= 0.361 Chirality : 0.053 0.408 2268 Planarity : 0.005 0.056 2438 Dihedral : 10.655 177.827 2354 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.79 % Allowed : 13.07 % Favored : 85.14 % 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: -0.40 (0.20), residues: 1697 helix: 1.08 (0.18), residues: 811 sheet: -0.38 (0.43), residues: 148 loop : -1.84 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1542 TYR 0.028 0.002 TYR A 754 PHE 0.034 0.002 PHE A 82 TRP 0.033 0.002 TRP A 897 HIS 0.031 0.002 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.28 (14860) covalent geometry : angle 0.72308 / 0.36 (20234) hydrogen bonds : bond 0.04618 / 3.17 ( 656) hydrogen bonds : angle 4.50491 / 3.28 ( 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 410 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 385 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7719 (ptp-170) cc_final: 0.7479 (ptp-110) REVERT: A 128 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8128 (m) REVERT: A 135 ILE cc_start: 0.8549 (mm) cc_final: 0.8035 (tp) REVERT: A 179 SER cc_start: 0.8170 (m) cc_final: 0.7542 (t) REVERT: A 200 GLU cc_start: 0.7635 (tp30) cc_final: 0.6806 (tp30) REVERT: A 209 ASP cc_start: 0.7198 (m-30) cc_final: 0.5967 (m-30) REVERT: A 213 GLU cc_start: 0.7005 (mp0) cc_final: 0.6328 (mp0) REVERT: A 271 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7554 (ptpp) REVERT: A 302 CYS cc_start: 0.7867 (t) cc_final: 0.7486 (t) REVERT: A 306 ASP cc_start: 0.7358 (m-30) cc_final: 0.6970 (m-30) REVERT: A 466 ASN cc_start: 0.7944 (p0) cc_final: 0.7650 (p0) REVERT: A 473 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7041 (mtm-85) REVERT: A 488 GLU cc_start: 0.7260 (tp30) cc_final: 0.6869 (tp30) REVERT: A 489 LYS cc_start: 0.7774 (tttt) cc_final: 0.7557 (ttmt) REVERT: A 543 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7772 (tt) REVERT: A 686 MET cc_start: 0.7076 (mtp) cc_final: 0.6490 (mmm) REVERT: A 719 SER cc_start: 0.8458 (t) cc_final: 0.7791 (p) REVERT: A 897 TRP cc_start: 0.8374 (t-100) cc_final: 0.8167 (t-100) REVERT: A 964 ASN cc_start: 0.7861 (m-40) cc_final: 0.7635 (m110) REVERT: A 1009 LYS cc_start: 0.8513 (pttm) cc_final: 0.7796 (pttm) REVERT: A 1010 PHE cc_start: 0.7582 (m-10) cc_final: 0.6925 (m-10) REVERT: A 1012 ARG cc_start: 0.7384 (ttp80) cc_final: 0.6987 (ttp80) REVERT: A 1052 MET cc_start: 0.7449 (mmt) cc_final: 0.7106 (mmt) REVERT: A 1064 TRP cc_start: 0.7854 (p-90) cc_final: 0.7610 (p-90) REVERT: A 1079 MET cc_start: 0.6252 (mtm) cc_final: 0.5943 (mtm) REVERT: A 1108 GLU cc_start: 0.7560 (pp20) cc_final: 0.7199 (pp20) REVERT: A 1137 LYS cc_start: 0.8415 (mttt) cc_final: 0.8001 (mttt) REVERT: A 1141 ASP cc_start: 0.7544 (t0) cc_final: 0.7255 (t0) REVERT: A 1182 ASN cc_start: 0.8130 (m-40) cc_final: 0.7920 (m-40) REVERT: A 1193 ARG cc_start: 0.7583 (mtp180) cc_final: 0.7309 (mtp180) REVERT: A 1216 GLU cc_start: 0.7121 (pt0) cc_final: 0.6914 (pt0) REVERT: A 1223 THR cc_start: 0.8002 (m) cc_final: 0.7673 (p) REVERT: A 1227 GLU cc_start: 0.7361 (pp20) cc_final: 0.7071 (pp20) REVERT: A 1264 MET cc_start: 0.6598 (mtp) cc_final: 0.6297 (mtt) REVERT: A 1346 LYS cc_start: 0.7456 (mtpt) cc_final: 0.7094 (mtpt) REVERT: A 1417 SER cc_start: 0.8233 (p) cc_final: 0.7935 (p) REVERT: A 1443 MET cc_start: 0.7647 (mtt) cc_final: 0.7400 (mtm) REVERT: A 1465 PHE cc_start: 0.7377 (m-10) cc_final: 0.7144 (m-10) REVERT: A 1514 GLU cc_start: 0.7182 (tp30) cc_final: 0.6955 (tp30) REVERT: A 1725 TRP cc_start: 0.7242 (t60) cc_final: 0.6858 (t60) REVERT: A 1755 ASP cc_start: 0.7910 (p0) cc_final: 0.7576 (p0) outliers start: 25 outliers final: 16 residues processed: 394 average time/residue: 0.1393 time to fit residues: 75.6451 Evaluate side-chains 386 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 368 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 128 SER 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 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 881 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 870 HIS ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 HIS ** 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 = 0.3775 r_free = 0.3775 target = 0.137337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111075 restraints weight = 63241.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117220 restraints weight = 21763.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121085 restraints weight = 10457.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123490 restraints weight = 6029.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125157 restraints weight = 3982.647| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 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 = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14860 Z= 0.151 Angle : 0.650 12.673 20234 Z= 0.322 Chirality : 0.049 0.345 2268 Planarity : 0.004 0.058 2438 Dihedral : 10.684 179.856 2354 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.46 % Allowed : 15.13 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1697 helix: 1.25 (0.19), residues: 811 sheet: -0.31 (0.44), residues: 147 loop : -1.82 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1422 TYR 0.018 0.002 TYR A 754 PHE 0.035 0.002 PHE A 82 TRP 0.029 0.001 TRP A 897 HIS 0.010 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (14860) covalent geometry : angle 0.64987 / 0.32 (20234) hydrogen bonds : bond 0.03701 / 2.53 ( 656) hydrogen bonds : angle 4.32147 / 3.14 ( 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 392 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 372 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7264 (pmm) cc_final: 0.7006 (pmm) REVERT: A 9 ARG cc_start: 0.7693 (ptp-170) cc_final: 0.7292 (ptp-170) REVERT: A 128 SER cc_start: 0.8515 (p) cc_final: 0.8075 (m) REVERT: A 135 ILE cc_start: 0.8548 (mm) cc_final: 0.8015 (tp) REVERT: A 179 SER cc_start: 0.8061 (m) cc_final: 0.7512 (t) REVERT: A 200 GLU cc_start: 0.7518 (tp30) cc_final: 0.6847 (tp30) REVERT: A 209 ASP cc_start: 0.7118 (m-30) cc_final: 0.6209 (m-30) REVERT: A 213 GLU cc_start: 0.6961 (mp0) cc_final: 0.6502 (mp0) REVERT: A 271 LYS cc_start: 0.8061 (ptpp) cc_final: 0.7488 (ptpp) REVERT: A 302 CYS cc_start: 0.7850 (t) cc_final: 0.7453 (t) REVERT: A 306 ASP cc_start: 0.7338 (m-30) cc_final: 0.6949 (m-30) REVERT: A 466 ASN cc_start: 0.7906 (p0) cc_final: 0.7605 (p0) REVERT: A 488 GLU cc_start: 0.7254 (tp30) cc_final: 0.6852 (tp30) REVERT: A 686 MET cc_start: 0.6901 (mtp) cc_final: 0.6331 (mmm) REVERT: A 719 SER cc_start: 0.8466 (t) cc_final: 0.7761 (p) REVERT: A 887 MET cc_start: 0.6962 (tmm) cc_final: 0.6319 (tmm) REVERT: A 964 ASN cc_start: 0.7850 (m-40) cc_final: 0.7638 (m-40) REVERT: A 990 ASN cc_start: 0.7503 (OUTLIER) cc_final: 0.7245 (m-40) REVERT: A 1010 PHE cc_start: 0.7341 (m-10) cc_final: 0.6861 (m-10) REVERT: A 1052 MET cc_start: 0.7404 (mmt) cc_final: 0.7086 (mmt) REVERT: A 1064 TRP cc_start: 0.7806 (p-90) cc_final: 0.7535 (p-90) REVERT: A 1079 MET cc_start: 0.6259 (mtm) cc_final: 0.5965 (mtm) REVERT: A 1108 GLU cc_start: 0.7572 (pp20) cc_final: 0.7215 (pp20) REVERT: A 1135 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7269 (ttt-90) REVERT: A 1137 LYS cc_start: 0.8453 (mttt) cc_final: 0.8006 (mttt) REVERT: A 1141 ASP cc_start: 0.7514 (t0) cc_final: 0.7197 (t0) REVERT: A 1182 ASN cc_start: 0.8168 (m-40) cc_final: 0.7899 (m-40) REVERT: A 1193 ARG cc_start: 0.7540 (mtp180) cc_final: 0.7187 (mtp180) REVERT: A 1223 THR cc_start: 0.7945 (m) cc_final: 0.7631 (p) REVERT: A 1227 GLU cc_start: 0.7307 (pp20) cc_final: 0.7033 (pp20) REVERT: A 1278 MET cc_start: 0.8045 (mmm) cc_final: 0.7697 (tpp) REVERT: A 1417 SER cc_start: 0.8139 (p) cc_final: 0.7889 (p) REVERT: A 1443 MET cc_start: 0.7631 (mtt) cc_final: 0.7308 (mtm) REVERT: A 1514 GLU cc_start: 0.7126 (tp30) cc_final: 0.6864 (tp30) REVERT: A 1755 ASP cc_start: 0.7875 (p0) cc_final: 0.7537 (p0) outliers start: 20 outliers final: 10 residues processed: 378 average time/residue: 0.1289 time to fit residues: 67.2319 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 : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 451 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1135 ARG Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 144 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 116 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 GLN ** 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 = 0.3770 r_free = 0.3770 target = 0.136888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111542 restraints weight = 53124.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117330 restraints weight = 19541.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120981 restraints weight = 9674.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123304 restraints weight = 5687.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124715 restraints weight = 3825.034| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- 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 = 0.33 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 = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14860 Z= 0.169 Angle : 0.659 12.077 20234 Z= 0.327 Chirality : 0.049 0.321 2268 Planarity : 0.004 0.058 2438 Dihedral : 10.692 179.385 2354 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.53 % Allowed : 15.73 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1697 helix: 1.26 (0.19), residues: 810 sheet: -0.33 (0.44), residues: 147 loop : -1.83 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1422 TYR 0.013 0.001 TYR A1348 PHE 0.037 0.002 PHE A 82 TRP 0.042 0.002 TRP A 897 HIS 0.011 0.001 HIS A1011 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (14860) covalent geometry : angle 0.65915 / 0.33 (20234) hydrogen bonds : bond 0.03816 / 2.60 ( 656) hydrogen bonds : angle 4.30929 / 3.13 ( 1919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 363 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7728 (ptp-170) cc_final: 0.7453 (ptp-110) REVERT: A 128 SER cc_start: 0.8415 (p) cc_final: 0.8050 (m) REVERT: A 135 ILE cc_start: 0.8537 (mm) cc_final: 0.8054 (tp) REVERT: A 179 SER cc_start: 0.8086 (m) cc_final: 0.7459 (t) REVERT: A 200 GLU cc_start: 0.7500 (tp30) cc_final: 0.6817 (tp30) REVERT: A 209 ASP cc_start: 0.7093 (m-30) cc_final: 0.6264 (m-30) REVERT: A 213 GLU cc_start: 0.6958 (mp0) cc_final: 0.6671 (mp0) REVERT: A 271 LYS cc_start: 0.8048 (ptpp) cc_final: 0.7474 (ptpp) REVERT: A 302 CYS cc_start: 0.7854 (t) cc_final: 0.7455 (t) REVERT: A 306 ASP cc_start: 0.7334 (m-30) cc_final: 0.6957 (m-30) REVERT: A 488 GLU cc_start: 0.7215 (tp30) cc_final: 0.6781 (tp30) REVERT: A 671 MET cc_start: 0.6680 (mmm) cc_final: 0.6383 (tpt) REVERT: A 686 MET cc_start: 0.6864 (mtp) cc_final: 0.6328 (mmm) REVERT: A 719 SER cc_start: 0.8451 (t) cc_final: 0.7682 (p) REVERT: A 884 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8160 (ttmm) REVERT: A 887 MET cc_start: 0.6932 (tmm) cc_final: 0.6277 (tmm) REVERT: A 897 TRP cc_start: 0.8352 (t-100) cc_final: 0.8118 (t-100) REVERT: A 964 ASN cc_start: 0.7849 (m-40) cc_final: 0.7629 (m110) REVERT: A 1010 PHE cc_start: 0.7337 (m-10) cc_final: 0.6793 (m-10) REVERT: A 1020 MET cc_start: 0.8123 (ptt) cc_final: 0.7815 (ptm) REVERT: A 1052 MET cc_start: 0.7396 (mmt) cc_final: 0.7190 (mtp) REVERT: A 1064 TRP cc_start: 0.7821 (p-90) cc_final: 0.7526 (p-90) REVERT: A 1079 MET cc_start: 0.6251 (mtm) cc_final: 0.5968 (mtm) REVERT: A 1105 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8234 (mmmm) REVERT: A 1108 GLU cc_start: 0.7608 (pp20) cc_final: 0.7194 (pp20) REVERT: A 1137 LYS cc_start: 0.8455 (mttt) cc_final: 0.8004 (mttt) REVERT: A 1141 ASP cc_start: 0.7531 (t0) cc_final: 0.7235 (t0) REVERT: A 1182 ASN cc_start: 0.8191 (m-40) cc_final: 0.7945 (m-40) REVERT: A 1193 ARG cc_start: 0.7497 (mtp180) cc_final: 0.7141 (mtp180) REVERT: A 1223 THR cc_start: 0.7948 (m) cc_final: 0.7629 (p) REVERT: A 1227 GLU cc_start: 0.7319 (pp20) cc_final: 0.7040 (pp20) REVERT: A 1371 VAL cc_start: 0.7970 (p) cc_final: 0.7707 (t) REVERT: A 1417 SER cc_start: 0.8134 (p) cc_final: 0.7920 (p) REVERT: A 1443 MET cc_start: 0.7655 (mtt) cc_final: 0.7329 (mtm) REVERT: A 1514 GLU cc_start: 0.7129 (tp30) cc_final: 0.6889 (tp30) REVERT: A 1755 ASP cc_start: 0.7882 (p0) cc_final: 0.7568 (p0) REVERT: A 1845 MET cc_start: 0.6081 (ptm) cc_final: 0.5841 (ptm) outliers start: 21 outliers final: 15 residues processed: 369 average time/residue: 0.1386 time to fit residues: 70.2204 Evaluate side-chains 370 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 355 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 113 VAL 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 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1409 VAL 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: 2.9990 chunk 114 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 10 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113348 restraints weight = 54740.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119036 restraints weight = 20288.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122536 restraints weight = 10026.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124830 restraints weight = 5942.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126317 restraints weight = 3995.709| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14860 Z= 0.144 Angle : 0.647 11.730 20234 Z= 0.320 Chirality : 0.048 0.293 2268 Planarity : 0.004 0.058 2438 Dihedral : 10.699 179.156 2354 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.53 % Allowed : 15.86 % 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: -0.18 (0.20), residues: 1697 helix: 1.30 (0.19), residues: 816 sheet: -0.02 (0.44), residues: 139 loop : -1.83 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1422 TYR 0.015 0.001 TYR A 474 PHE 0.042 0.002 PHE A 82 TRP 0.038 0.002 TRP A 897 HIS 0.009 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (14860) covalent geometry : angle 0.64746 / 0.32 (20234) hydrogen bonds : bond 0.03620 / 2.46 ( 656) hydrogen bonds : angle 4.25839 / 3.09 ( 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 376 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 355 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7717 (ptp-170) cc_final: 0.7378 (ptp-170) REVERT: A 128 SER cc_start: 0.8395 (p) cc_final: 0.8003 (m) REVERT: A 135 ILE cc_start: 0.8539 (mm) cc_final: 0.8034 (tp) REVERT: A 200 GLU cc_start: 0.7457 (tp30) cc_final: 0.6754 (tp30) REVERT: A 209 ASP cc_start: 0.7030 (m-30) cc_final: 0.5558 (m-30) REVERT: A 213 GLU cc_start: 0.6961 (mp0) cc_final: 0.6263 (mp0) REVERT: A 271 LYS cc_start: 0.8016 (ptpp) cc_final: 0.7426 (ptpp) REVERT: A 302 CYS cc_start: 0.7832 (t) cc_final: 0.7457 (t) REVERT: A 306 ASP cc_start: 0.7321 (m-30) cc_final: 0.6958 (m-30) REVERT: A 445 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6206 (mp0) REVERT: A 488 GLU cc_start: 0.7203 (tp30) cc_final: 0.6804 (tp30) REVERT: A 671 MET cc_start: 0.6668 (mmm) cc_final: 0.6365 (tpt) REVERT: A 686 MET cc_start: 0.6825 (mtp) cc_final: 0.6236 (mmt) REVERT: A 719 SER cc_start: 0.8450 (t) cc_final: 0.8207 (t) REVERT: A 884 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8205 (ttmm) REVERT: A 887 MET cc_start: 0.6867 (tmm) cc_final: 0.6228 (tmm) REVERT: A 897 TRP cc_start: 0.8348 (t-100) cc_final: 0.8078 (t-100) REVERT: A 914 ASN cc_start: 0.7248 (m110) cc_final: 0.7015 (m-40) REVERT: A 956 ARG cc_start: 0.7344 (ptp90) cc_final: 0.7139 (ptp90) REVERT: A 964 ASN cc_start: 0.7845 (m-40) cc_final: 0.7607 (m110) REVERT: A 1010 PHE cc_start: 0.7340 (m-10) cc_final: 0.7029 (m-10) REVERT: A 1020 MET cc_start: 0.8115 (ptt) cc_final: 0.7801 (ptm) REVERT: A 1064 TRP cc_start: 0.7789 (p-90) cc_final: 0.7518 (p-90) REVERT: A 1079 MET cc_start: 0.6323 (mtm) cc_final: 0.6101 (mtm) REVERT: A 1087 SER cc_start: 0.8367 (m) cc_final: 0.8096 (m) REVERT: A 1108 GLU cc_start: 0.7594 (pp20) cc_final: 0.7223 (pp20) REVERT: A 1135 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7513 (ttt180) REVERT: A 1137 LYS cc_start: 0.8412 (mttt) cc_final: 0.8150 (mttt) REVERT: A 1141 ASP cc_start: 0.7562 (t0) cc_final: 0.7227 (t0) REVERT: A 1182 ASN cc_start: 0.8173 (m-40) cc_final: 0.7925 (m-40) REVERT: A 1193 ARG cc_start: 0.7450 (mtp180) cc_final: 0.7097 (mtp180) REVERT: A 1223 THR cc_start: 0.7917 (m) cc_final: 0.7604 (p) REVERT: A 1227 GLU cc_start: 0.7318 (pp20) cc_final: 0.7056 (pp20) REVERT: A 1443 MET cc_start: 0.7630 (mtt) cc_final: 0.7325 (mtm) REVERT: A 1755 ASP cc_start: 0.7865 (p0) cc_final: 0.7547 (p0) outliers start: 21 outliers final: 17 residues processed: 362 average time/residue: 0.1394 time to fit residues: 69.3404 Evaluate side-chains 368 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 351 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 113 VAL 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 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1583 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: 2.9990 chunk 132 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 163 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** 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 = 0.3752 r_free = 0.3752 target = 0.135698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110650 restraints weight = 60846.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116450 restraints weight = 21582.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120149 restraints weight = 10492.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122530 restraints weight = 6098.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124057 restraints weight = 4028.215| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 14860 Z= 0.230 Angle : 0.692 11.269 20234 Z= 0.346 Chirality : 0.051 0.322 2268 Planarity : 0.004 0.055 2438 Dihedral : 10.768 179.311 2354 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.53 % Allowed : 15.86 % 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: -0.35 (0.20), residues: 1697 helix: 1.14 (0.18), residues: 820 sheet: -0.48 (0.43), residues: 147 loop : -1.84 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 296 TYR 0.017 0.002 TYR A1348 PHE 0.040 0.002 PHE A 82 TRP 0.037 0.002 TRP A 897 HIS 0.012 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.23 (14860) covalent geometry : angle 0.69184 / 0.35 (20234) hydrogen bonds : bond 0.04199 / 2.88 ( 656) hydrogen bonds : angle 4.38248 / 3.18 ( 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 390 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 369 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7730 (ptp-170) cc_final: 0.7468 (ptp-110) REVERT: A 128 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8073 (m) REVERT: A 135 ILE cc_start: 0.8546 (mm) cc_final: 0.8059 (tp) REVERT: A 145 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7608 (mmtt) REVERT: A 179 SER cc_start: 0.8130 (m) cc_final: 0.7539 (t) REVERT: A 200 GLU cc_start: 0.7531 (tp30) cc_final: 0.6828 (tp30) REVERT: A 202 TYR cc_start: 0.7846 (t80) cc_final: 0.7587 (t80) REVERT: A 209 ASP cc_start: 0.7038 (m-30) cc_final: 0.5565 (m-30) REVERT: A 213 GLU cc_start: 0.6975 (mp0) cc_final: 0.6290 (mp0) REVERT: A 271 LYS cc_start: 0.8076 (ptpp) cc_final: 0.7479 (ptpp) REVERT: A 302 CYS cc_start: 0.7853 (t) cc_final: 0.7490 (t) REVERT: A 306 ASP cc_start: 0.7329 (m-30) cc_final: 0.6971 (m-30) REVERT: A 488 GLU cc_start: 0.7212 (tp30) cc_final: 0.6869 (tp30) REVERT: A 686 MET cc_start: 0.6945 (mtp) cc_final: 0.6350 (mmt) REVERT: A 719 SER cc_start: 0.8482 (t) cc_final: 0.7721 (p) REVERT: A 884 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8267 (ttmm) REVERT: A 887 MET cc_start: 0.6918 (tmm) cc_final: 0.6273 (tmm) REVERT: A 897 TRP cc_start: 0.8402 (t-100) cc_final: 0.8153 (t-100) REVERT: A 964 ASN cc_start: 0.7850 (m-40) cc_final: 0.7624 (m110) REVERT: A 1010 PHE cc_start: 0.7467 (m-10) cc_final: 0.7090 (m-10) REVERT: A 1020 MET cc_start: 0.8193 (ptt) cc_final: 0.7874 (ptm) REVERT: A 1025 LYS cc_start: 0.7928 (tppp) cc_final: 0.7677 (mtpt) REVERT: A 1064 TRP cc_start: 0.7864 (p-90) cc_final: 0.7642 (p-90) REVERT: A 1079 MET cc_start: 0.6395 (mtm) cc_final: 0.6148 (mtm) REVERT: A 1108 GLU cc_start: 0.7588 (pp20) cc_final: 0.7235 (pp20) REVERT: A 1135 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7519 (ttt180) REVERT: A 1137 LYS cc_start: 0.8382 (mttt) cc_final: 0.8113 (mttt) REVERT: A 1141 ASP cc_start: 0.7559 (t0) cc_final: 0.7268 (t0) REVERT: A 1182 ASN cc_start: 0.8116 (m-40) cc_final: 0.7878 (m-40) REVERT: A 1193 ARG cc_start: 0.7529 (mtp180) cc_final: 0.7155 (mtp180) REVERT: A 1223 THR cc_start: 0.7934 (m) cc_final: 0.7643 (p) REVERT: A 1227 GLU cc_start: 0.7351 (pp20) cc_final: 0.7096 (pp20) REVERT: A 1278 MET cc_start: 0.8031 (mmm) cc_final: 0.7750 (mmm) REVERT: A 1388 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 1443 MET cc_start: 0.7681 (mtt) cc_final: 0.7371 (mtm) REVERT: A 1467 GLN cc_start: 0.7770 (mp10) cc_final: 0.7489 (mp10) REVERT: A 1514 GLU cc_start: 0.7288 (tp30) cc_final: 0.7035 (tp30) REVERT: A 1755 ASP cc_start: 0.7911 (p0) cc_final: 0.7611 (p0) REVERT: A 1777 ARG cc_start: 0.6742 (mtt180) cc_final: 0.6529 (mmt90) outliers start: 21 outliers final: 16 residues processed: 375 average time/residue: 0.1484 time to fit residues: 76.2902 Evaluate side-chains 377 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 360 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER 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 756 LYS Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1750 ILE 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: 0.6980 chunk 133 optimal weight: 0.5980 chunk 77 optimal weight: 0.0040 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 overall best weight: 0.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113916 restraints weight = 54205.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119679 restraints weight = 19575.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123306 restraints weight = 9623.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125661 restraints weight = 5631.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127194 restraints weight = 3749.388| |-----------------------------------------------------------------------------| 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 = 0.34 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14860 Z= 0.127 Angle : 0.655 11.483 20234 Z= 0.324 Chirality : 0.047 0.280 2268 Planarity : 0.004 0.057 2438 Dihedral : 10.752 179.086 2354 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.13 % Allowed : 16.92 % Favored : 81.95 % 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: -0.17 (0.20), residues: 1697 helix: 1.31 (0.19), residues: 815 sheet: 0.11 (0.46), residues: 132 loop : -1.84 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1422 TYR 0.020 0.001 TYR A1101 PHE 0.044 0.002 PHE A 82 TRP 0.038 0.002 TRP A 897 HIS 0.008 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (14860) covalent geometry : angle 0.65546 / 0.32 (20234) hydrogen bonds : bond 0.03456 / 2.35 ( 656) hydrogen bonds : angle 4.24245 / 3.08 ( 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 372 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 357 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7710 (ptp-170) cc_final: 0.7362 (ptp-170) REVERT: A 81 ASP cc_start: 0.6906 (m-30) cc_final: 0.6651 (m-30) REVERT: A 128 SER cc_start: 0.8383 (p) cc_final: 0.8048 (m) REVERT: A 135 ILE cc_start: 0.8574 (mm) cc_final: 0.8102 (tp) REVERT: A 142 TYR cc_start: 0.7929 (t80) cc_final: 0.7592 (t80) REVERT: A 145 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7535 (mmtt) REVERT: A 200 GLU cc_start: 0.7465 (tp30) cc_final: 0.6887 (tp30) REVERT: A 204 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7602 (mtmm) REVERT: A 209 ASP cc_start: 0.6835 (m-30) cc_final: 0.5813 (m-30) REVERT: A 213 GLU cc_start: 0.6954 (mp0) cc_final: 0.6522 (mp0) REVERT: A 271 LYS cc_start: 0.8014 (ptpp) cc_final: 0.7378 (ptpp) REVERT: A 302 CYS cc_start: 0.7840 (t) cc_final: 0.7438 (t) REVERT: A 306 ASP cc_start: 0.7316 (m-30) cc_final: 0.6941 (m-30) REVERT: A 410 ARG cc_start: 0.7736 (mtt-85) cc_final: 0.7520 (mtt90) REVERT: A 442 LYS cc_start: 0.8401 (tptm) cc_final: 0.7904 (tptm) REVERT: A 445 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6182 (mp0) REVERT: A 488 GLU cc_start: 0.7189 (tp30) cc_final: 0.6775 (tp30) REVERT: A 543 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7998 (tt) REVERT: A 671 MET cc_start: 0.6659 (mmm) cc_final: 0.6362 (tpt) REVERT: A 686 MET cc_start: 0.6797 (mtp) cc_final: 0.6268 (mmm) REVERT: A 719 SER cc_start: 0.8428 (t) cc_final: 0.7678 (p) REVERT: A 887 MET cc_start: 0.6891 (tmm) cc_final: 0.6209 (tmm) REVERT: A 889 TYR cc_start: 0.7785 (t80) cc_final: 0.7245 (t80) REVERT: A 897 TRP cc_start: 0.8371 (t-100) cc_final: 0.8063 (t-100) REVERT: A 914 ASN cc_start: 0.7188 (m110) cc_final: 0.6976 (m-40) REVERT: A 925 MET cc_start: 0.7156 (mtt) cc_final: 0.6923 (mtm) REVERT: A 964 ASN cc_start: 0.7841 (m-40) cc_final: 0.7632 (m110) REVERT: A 1010 PHE cc_start: 0.7411 (m-10) cc_final: 0.7016 (m-10) REVERT: A 1020 MET cc_start: 0.8112 (ptt) cc_final: 0.7867 (ptm) REVERT: A 1025 LYS cc_start: 0.7898 (tppp) cc_final: 0.7663 (mtpt) REVERT: A 1064 TRP cc_start: 0.7797 (p-90) cc_final: 0.7536 (p-90) REVERT: A 1087 SER cc_start: 0.8364 (m) cc_final: 0.8119 (m) REVERT: A 1108 GLU cc_start: 0.7633 (pp20) cc_final: 0.7219 (pp20) REVERT: A 1141 ASP cc_start: 0.7569 (t0) cc_final: 0.7291 (t0) REVERT: A 1182 ASN cc_start: 0.8142 (m-40) cc_final: 0.7845 (m-40) REVERT: A 1184 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6317 (mm-30) REVERT: A 1193 ARG cc_start: 0.7460 (mtp180) cc_final: 0.7050 (mtp180) REVERT: A 1219 SER cc_start: 0.8145 (t) cc_final: 0.7702 (p) REVERT: A 1223 THR cc_start: 0.7881 (m) cc_final: 0.7593 (p) REVERT: A 1227 GLU cc_start: 0.7319 (pp20) cc_final: 0.7053 (pp20) REVERT: A 1443 MET cc_start: 0.7629 (mtt) cc_final: 0.7313 (mtm) REVERT: A 1514 GLU cc_start: 0.7230 (tp30) cc_final: 0.6854 (tp30) REVERT: A 1755 ASP cc_start: 0.7888 (p0) cc_final: 0.7573 (p0) outliers start: 15 outliers final: 14 residues processed: 360 average time/residue: 0.1634 time to fit residues: 80.5417 Evaluate side-chains 366 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 351 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 522 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE 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 1583 LEU Chi-restraints excluded: chain A residue 1750 ILE Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 129 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.0030 chunk 64 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113100 restraints weight = 65240.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119144 restraints weight = 22540.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122917 restraints weight = 10802.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125369 restraints weight = 6251.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126967 restraints weight = 4118.252| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- 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 = 0.33 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14860 Z= 0.138 Angle : 0.656 11.384 20234 Z= 0.325 Chirality : 0.047 0.280 2268 Planarity : 0.004 0.057 2438 Dihedral : 10.708 178.572 2354 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.33 % Allowed : 16.92 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.20), residues: 1697 helix: 1.34 (0.19), residues: 815 sheet: 0.02 (0.45), residues: 138 loop : -1.82 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1422 TYR 0.014 0.001 TYR A 474 PHE 0.043 0.002 PHE A 82 TRP 0.035 0.002 TRP A 897 HIS 0.020 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14860) covalent geometry : angle 0.65572 / 0.32 (20234) hydrogen bonds : bond 0.03553 / 2.42 ( 656) hydrogen bonds : angle 4.23923 / 3.08 ( 1919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.28 seconds wall clock time: 46 minutes 48.07 seconds (2808.07 seconds total)