Starting phenix.real_space_refine on Thu Aug 6 18:01:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8asd_15614/08_2026/8asd_15614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asd_15614/08_2026/8asd_15614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8asd_15614/08_2026/8asd_15614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asd_15614/08_2026/8asd_15614.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8asd_15614/08_2026/8asd_15614.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8asd_15614/08_2026/8asd_15614.cif" model { file = "/net/cci-nas-00/data/ceres_data/8asd_15614/08_2026/8asd_15614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asd_15614/08_2026/8asd_15614.cif" } resolution = 2.6 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= 0.000 sd= 0.007 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 784 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 46 5.49 5 Mg 3 5.21 5 S 84 5.16 5 C 9631 2.51 5 N 2717 2.21 5 O 3050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 15531 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 14524 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1826, 14496 Classifications: {'peptide': 1826} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1756} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1826, 14496 Classifications: {'peptide': 1826} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1756} Chain breaks: 3 bond proxies already assigned to first conformer: 14761 Chain: "T" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 366 Classifications: {'RNAv2': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain breaks: 1 Chain: "G" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 151 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 40 Unusual residues: {' MG': 3, '2KH': 1} Classifications: {'undetermined': 4, 'water': 8} Link IDs: {None: 11} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A1452 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A1452 " occ=0.50 Time building chain proxies: 5.49, per 1000 atoms: 0.35 Number of scatterers: 15531 At special positions: 0 Unit cell: (98.6, 124.1, 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 84 16.00 P 46 15.00 Mg 3 11.99 O 3050 8.00 N 2717 7.00 C 9631 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: 1.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 18 sheets defined 53.6% alpha, 12.3% beta 8 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 71 through 76 removed outlier: 4.806A pdb=" N TYR A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.558A pdb=" N THR A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.751A pdb=" N GLU A 97 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 98 " --> pdb=" O LEU A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 98' Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.143A pdb=" N ASP A 107 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 removed outlier: 3.850A pdb=" N LEU A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix removed outlier: 3.901A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 209 Processing helix chain 'A' and resid 217 through 234 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: 3.839A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.830A pdb=" N ASP A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.516A pdb=" N TYR A 408 " --> pdb=" O LYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.743A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 447 removed outlier: 3.839A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 477 through 492 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.653A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 602 through 611 removed outlier: 4.225A pdb=" N THR A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 627 Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 656 through 671 removed outlier: 3.551A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 682 through 689 removed outlier: 4.209A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 767 through 780 removed outlier: 3.926A pdb=" N TYR A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 Processing helix chain 'A' and resid 824 through 840 removed outlier: 3.554A pdb=" N ASN A 828 " --> pdb=" O GLN A 824 " (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 864 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 888 through 904 removed outlier: 3.707A pdb=" N GLY A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 945 removed outlier: 4.050A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 964 removed outlier: 4.075A pdb=" N ILE A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 974 Processing helix chain 'A' and resid 994 through 1006 removed outlier: 3.927A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.693A 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: 3.548A pdb=" N ALA A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1038 Processing helix chain 'A' and resid 1046 through 1057 removed outlier: 3.692A 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 1153 removed outlier: 3.610A pdb=" N VAL A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.800A 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: 4.253A pdb=" N TRP A1198 " --> pdb=" O PRO A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1228 removed outlier: 3.559A pdb=" N ARG A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A1224 " --> pdb=" O ASN A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 Processing helix chain 'A' and resid 1257 through 1267 removed outlier: 3.630A 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: 4.179A pdb=" N ALA A1284 " --> pdb=" O PRO A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1300 removed outlier: 3.612A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1315 removed outlier: 3.687A pdb=" N LYS A1305 " --> pdb=" O ASP A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1336 Processing helix chain 'A' and resid 1344 through 1354 removed outlier: 3.948A pdb=" N TYR A1348 " --> pdb=" O ASP A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1368 Processing helix chain 'A' and resid 1369 through 1373 Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1392 through 1401 Processing helix chain 'A' and resid 1404 through 1411 Processing helix chain 'A' and resid 1412 through 1414 No H-bonds generated for 'chain 'A' and resid 1412 through 1414' Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1437 through 1448 Processing helix chain 'A' and resid 1449 through 1452 removed outlier: 3.588A pdb=" N AHIS A1452 " --> pdb=" O ALA A1449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1449 through 1452' Processing helix chain 'A' and resid 1457 through 1465 Processing helix chain 'A' and resid 1467 through 1479 Processing helix chain 'A' and resid 1512 through 1523 Processing helix chain 'A' and resid 1530 through 1545 Processing helix chain 'A' and resid 1551 through 1559 Processing helix chain 'A' and resid 1563 through 1572 removed outlier: 3.528A pdb=" N PHE A1567 " --> pdb=" O SER A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1604 Processing helix chain 'A' and resid 1626 through 1638 removed outlier: 3.540A pdb=" N MET A1635 " --> pdb=" O HIS A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1657 removed outlier: 3.616A pdb=" N GLU A1648 " --> pdb=" O GLU A1644 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A1649 " --> pdb=" O TYR A1645 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A1650 " --> pdb=" O LYS A1646 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A1651 " --> pdb=" O LEU A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1681 Processing helix chain 'A' and resid 1687 through 1696 Processing helix chain 'A' and resid 1757 through 1773 removed outlier: 3.750A pdb=" N ASP A1771 " --> pdb=" O ARG A1767 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1772 " --> pdb=" O LEU A1768 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 5.881A pdb=" N GLY A 15 " --> pdb=" O VAL A 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 25 removed outlier: 7.449A pdb=" N GLY A 168 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 124 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A 170 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU A 126 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL A 172 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.569A pdb=" N ILE A 49 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 411 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: 6.059A pdb=" N MET A 906 " --> pdb=" O LYS A1025 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N MET A1027 " --> pdb=" O MET A 906 " (cutoff:3.500A) removed outlier: 7.248A 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: 7.195A pdb=" N ASN A 979 " --> pdb=" O VAL A1176 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A1176 " --> pdb=" O ASN A 979 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN A 981 " --> pdb=" O ASN A1174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1178 through 1181 removed outlier: 3.689A pdb=" N PHE A1185 " --> pdb=" O VAL A1192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1338 through 1340 Processing sheet with id=AB4, first strand: chain 'A' and resid 1486 through 1488 Processing sheet with id=AB5, first strand: chain 'A' and resid 1496 through 1502 Processing sheet with id=AB6, first strand: chain 'A' and resid 1700 through 1705 removed outlier: 6.234A pdb=" N VAL A1724 " --> pdb=" O SER A1704 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N HIS A1733 " --> pdb=" O LEU A1752 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A1752 " --> pdb=" O HIS A1733 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN A1735 " --> pdb=" O ILE A1750 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE A1750 " --> pdb=" O GLN A1735 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A1737 " --> pdb=" O GLU A1748 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN A1745 " --> pdb=" O ASN A1775 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1700 through 1705 removed outlier: 6.234A pdb=" N VAL A1724 " --> pdb=" O SER A1704 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N HIS A1733 " --> pdb=" O LEU A1752 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A1752 " --> pdb=" O HIS A1733 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN A1735 " --> pdb=" O ILE A1750 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE A1750 " --> pdb=" O GLN A1735 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A1737 " --> pdb=" O GLU A1748 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU A1748 " --> pdb=" O PRO A1805 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ARG A1807 " --> pdb=" O GLU A1748 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE A1750 " --> pdb=" O ARG A1807 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A1788 " --> pdb=" O VAL A1806 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1709 through 1711 Processing sheet with id=AB9, first strand: chain 'A' and resid 1825 through 1829 removed outlier: 3.519A pdb=" N LEU A1833 " --> pdb=" O TYR A1850 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL A1837 " --> pdb=" O ASN A1846 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN A1846 " --> pdb=" O VAL A1837 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A1839 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL A1844 " --> pdb=" O ILE A1839 " (cutoff:3.500A) 743 hydrogen bonds defined for protein. 2065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2445 1.30 - 1.43: 4367 1.43 - 1.56: 8871 1.56 - 1.68: 87 1.68 - 1.81: 140 Bond restraints: 15910 Sorted by residual: bond pdb=" C3' 2KH A2104 " pdb=" C4' 2KH A2104 " ideal model delta sigma weight residual 1.550 1.300 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" N3A 2KH A2104 " pdb=" PA 2KH A2104 " ideal model delta sigma weight residual 1.933 1.701 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" N3A 2KH A2104 " pdb=" PB 2KH A2104 " ideal model delta sigma weight residual 1.890 1.702 0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" O2G 2KH A2104 " pdb=" PG 2KH A2104 " ideal model delta sigma weight residual 1.682 1.506 0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" O3G 2KH A2104 " pdb=" PG 2KH A2104 " ideal model delta sigma weight residual 1.669 1.506 0.163 2.00e-02 2.50e+03 6.63e+01 ... (remaining 15905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.44: 21686 12.44 - 24.87: 6 24.87 - 37.31: 0 37.31 - 49.75: 0 49.75 - 62.19: 2 Bond angle restraints: 21694 Sorted by residual: angle pdb=" N3A 2KH A2104 " pdb=" PA 2KH A2104 " pdb=" O2A 2KH A2104 " ideal model delta sigma weight residual 48.17 110.36 -62.19 3.00e+00 1.11e-01 4.30e+02 angle pdb=" O2G 2KH A2104 " pdb=" PG 2KH A2104 " pdb=" O3G 2KH A2104 " ideal model delta sigma weight residual 53.94 109.80 -55.86 3.00e+00 1.11e-01 3.47e+02 angle pdb=" O1A 2KH A2104 " pdb=" PA 2KH A2104 " pdb=" O2A 2KH A2104 " ideal model delta sigma weight residual 130.82 108.65 22.17 3.00e+00 1.11e-01 5.46e+01 angle pdb=" O1B 2KH A2104 " pdb=" PB 2KH A2104 " pdb=" O2B 2KH A2104 " ideal model delta sigma weight residual 130.56 110.04 20.52 3.00e+00 1.11e-01 4.68e+01 angle pdb=" O1G 2KH A2104 " pdb=" PG 2KH A2104 " pdb=" O2G 2KH A2104 " ideal model delta sigma weight residual 130.21 109.76 20.45 3.00e+00 1.11e-01 4.65e+01 ... (remaining 21689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8589 17.87 - 35.73: 716 35.73 - 53.60: 148 53.60 - 71.46: 72 71.46 - 89.33: 20 Dihedral angle restraints: 9545 sinusoidal: 4244 harmonic: 5301 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 36.35 -37.60 73.94 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' G T 23 " pdb=" C3' G T 23 " pdb=" C2' G T 23 " pdb=" C1' G T 23 " ideal model delta sinusoidal sigma weight residual 36.35 -36.30 72.64 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' U T 22 " pdb=" C3' U T 22 " pdb=" C2' U T 22 " pdb=" C1' U T 22 " ideal model delta sinusoidal sigma weight residual 36.34 -36.20 72.54 1 3.10e+00 1.04e-01 6.99e+02 ... (remaining 9542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2128 0.069 - 0.138: 237 0.138 - 0.207: 10 0.207 - 0.276: 59 0.276 - 0.345: 5 Chirality restraints: 2439 Sorted by residual: chirality pdb=" P U T 22 " pdb=" OP1 U T 22 " pdb=" OP2 U T 22 " pdb=" O5' U T 22 " both_signs ideal model delta sigma weight residual True 2.17 2.52 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" P A T 4 " pdb=" OP1 A T 4 " pdb=" OP2 A T 4 " pdb=" O5' A T 4 " both_signs ideal model delta sigma weight residual True 2.17 2.51 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C2' U T 22 " pdb=" C3' U T 22 " pdb=" O2' U T 22 " pdb=" C1' U T 22 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2436 not shown) Planarity restraints: 2606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 549 " 0.037 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO A 550 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 550 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 550 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1505 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO A1506 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1506 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1506 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 590 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ALA A 590 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA A 590 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY A 591 " 0.010 2.00e-02 2.50e+03 ... (remaining 2603 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 145 2.60 - 3.18: 12569 3.18 - 3.75: 25000 3.75 - 4.33: 35711 4.33 - 4.90: 57121 Nonbonded interactions: 130546 Sorted by model distance: nonbonded pdb=" OP1 A E 5 " pdb="MG MG A2103 " model vdw 2.030 2.170 nonbonded pdb=" OE2 GLU A 126 " pdb="MG MG A2103 " model vdw 2.105 2.170 nonbonded pdb=" OH TYR A 286 " pdb=" OE1 GLU A 303 " model vdw 2.140 3.040 nonbonded pdb="MG MG A2102 " pdb=" O3G 2KH A2104 " model vdw 2.142 2.170 nonbonded pdb=" OD1 ASP A1127 " pdb="MG MG A2101 " model vdw 2.147 2.170 ... (remaining 130541 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 19.440 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 0.250 15910 Z= 0.289 Angle : 0.971 62.185 21694 Z= 0.428 Chirality : 0.059 0.345 2439 Planarity : 0.005 0.058 2606 Dihedral : 15.020 89.330 6125 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.27 (0.19), residues: 1824 helix: 0.66 (0.17), residues: 864 sheet: -0.27 (0.38), residues: 183 loop : -1.06 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 481 TYR 0.019 0.002 TYR A 193 PHE 0.020 0.002 PHE A1283 TRP 0.017 0.002 TRP A 520 HIS 0.006 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.29 (15910) covalent geometry : angle 0.97054 / 0.43 (21694) hydrogen bonds : bond 0.14590 / 9.77 ( 741) hydrogen bonds : angle 6.07746 / 4.41 ( 2109) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7176 (m-30) cc_final: 0.6872 (m-30) REVERT: A 1347 LYS cc_start: 0.7542 (ttpt) cc_final: 0.7338 (ttpp) REVERT: A 1463 MET cc_start: 0.7860 (mtp) cc_final: 0.7636 (mtp) REVERT: A 1535 LYS cc_start: 0.8053 (tmtt) cc_final: 0.7663 (tppp) REVERT: A 1672 MET cc_start: 0.2190 (tmm) cc_final: 0.1837 (ttp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.7113 time to fit residues: 168.4723 Evaluate side-chains 170 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 500 HIS A 742 ASN A 819 GLN A 853 ASN A1095 GLN A1204 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.113001 restraints weight = 49664.893| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.97 r_work: 0.2876 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15910 Z= 0.177 Angle : 0.737 16.827 21694 Z= 0.352 Chirality : 0.064 0.986 2439 Planarity : 0.005 0.066 2606 Dihedral : 10.092 153.607 2548 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.25 % Allowed : 7.16 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 1824 helix: 1.14 (0.17), residues: 884 sheet: -0.27 (0.37), residues: 183 loop : -0.96 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1766 TYR 0.016 0.002 TYR A 193 PHE 0.017 0.002 PHE A 911 TRP 0.014 0.002 TRP A 520 HIS 0.005 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (15910) covalent geometry : angle 0.73716 / 0.35 (21694) hydrogen bonds : bond 0.05053 / 3.35 ( 741) hydrogen bonds : angle 4.88594 / 3.58 ( 2109) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.501 Fit side-chains REVERT: A 303 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: A 389 ASP cc_start: 0.7494 (m-30) cc_final: 0.7194 (m-30) REVERT: A 1463 MET cc_start: 0.8447 (mtp) cc_final: 0.8206 (mtp) REVERT: A 1535 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7647 (tppp) outliers start: 19 outliers final: 10 residues processed: 185 average time/residue: 0.6704 time to fit residues: 135.2451 Evaluate side-chains 178 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 147 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 178 optimal weight: 0.0070 chunk 180 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 500 HIS A 742 ASN A 819 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116002 restraints weight = 53820.331| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.16 r_work: 0.2893 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15910 Z= 0.117 Angle : 0.589 9.645 21694 Z= 0.290 Chirality : 0.049 0.556 2439 Planarity : 0.004 0.037 2606 Dihedral : 10.052 169.723 2548 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.25 % Allowed : 8.47 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.57 (0.19), residues: 1824 helix: 1.60 (0.18), residues: 871 sheet: -0.07 (0.35), residues: 203 loop : -0.95 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1473 TYR 0.015 0.001 TYR A 193 PHE 0.015 0.001 PHE A 911 TRP 0.017 0.001 TRP A 520 HIS 0.004 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (15910) covalent geometry : angle 0.58928 / 0.29 (21694) hydrogen bonds : bond 0.03927 / 2.61 ( 741) hydrogen bonds : angle 4.55555 / 3.32 ( 2109) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.488 Fit side-chains REVERT: A 68 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6154 (tp) REVERT: A 252 MET cc_start: 0.8623 (ttm) cc_final: 0.8329 (ttm) REVERT: A 389 ASP cc_start: 0.7469 (m-30) cc_final: 0.7176 (m-30) REVERT: A 912 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8403 (ttmm) REVERT: A 1463 MET cc_start: 0.8427 (mtp) cc_final: 0.8144 (mtp) REVERT: A 1535 LYS cc_start: 0.8079 (tmtt) cc_final: 0.7568 (tppp) REVERT: A 1672 MET cc_start: 0.1938 (tmm) cc_final: 0.1696 (tmm) REVERT: A 1768 LEU cc_start: 0.6506 (tp) cc_final: 0.6099 (tp) outliers start: 19 outliers final: 6 residues processed: 187 average time/residue: 0.6732 time to fit residues: 137.2490 Evaluate side-chains 176 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 40 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 159 optimal weight: 0.0030 chunk 38 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 500 HIS A 742 ASN A 819 GLN A 990 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.112259 restraints weight = 45305.549| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.35 r_work: 0.2877 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15910 Z= 0.186 Angle : 0.677 10.441 21694 Z= 0.333 Chirality : 0.053 0.710 2439 Planarity : 0.005 0.063 2606 Dihedral : 10.484 169.477 2548 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.93 % Allowed : 9.46 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 1824 helix: 1.41 (0.17), residues: 872 sheet: -0.24 (0.38), residues: 183 loop : -0.98 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1473 TYR 0.017 0.002 TYR A 193 PHE 0.016 0.002 PHE A 911 TRP 0.014 0.002 TRP A 989 HIS 0.005 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (15910) covalent geometry : angle 0.67651 / 0.33 (21694) hydrogen bonds : bond 0.04917 / 3.28 ( 741) hydrogen bonds : angle 4.68156 / 3.42 ( 2109) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.6882 (tm-30) REVERT: A 211 ASP cc_start: 0.6161 (OUTLIER) cc_final: 0.5562 (t0) REVERT: A 213 GLU cc_start: 0.6253 (pt0) cc_final: 0.5915 (pt0) REVERT: A 303 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: A 389 ASP cc_start: 0.7528 (m-30) cc_final: 0.7196 (m-30) REVERT: A 1463 MET cc_start: 0.8447 (mtp) cc_final: 0.8188 (mtp) REVERT: A 1612 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5434 (mp0) REVERT: A 1672 MET cc_start: 0.2108 (tmm) cc_final: 0.1857 (tmm) REVERT: A 1768 LEU cc_start: 0.6532 (tp) cc_final: 0.6110 (tp) outliers start: 30 outliers final: 15 residues processed: 189 average time/residue: 0.7027 time to fit residues: 144.5451 Evaluate side-chains 185 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1612 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 88 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 500 HIS A 742 ASN A 819 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115313 restraints weight = 59838.785| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 4.60 r_work: 0.2863 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15910 Z= 0.124 Angle : 0.580 8.624 21694 Z= 0.288 Chirality : 0.048 0.554 2439 Planarity : 0.004 0.042 2606 Dihedral : 10.378 175.247 2548 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.31 % Allowed : 10.46 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1824 helix: 1.70 (0.18), residues: 866 sheet: -0.19 (0.38), residues: 183 loop : -0.95 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1766 TYR 0.019 0.001 TYR A 193 PHE 0.015 0.001 PHE A 911 TRP 0.017 0.001 TRP A 520 HIS 0.004 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15910) covalent geometry : angle 0.58048 / 0.29 (21694) hydrogen bonds : bond 0.03979 / 2.65 ( 741) hydrogen bonds : angle 4.48788 / 3.27 ( 2109) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.579 Fit side-chains REVERT: A 211 ASP cc_start: 0.6168 (OUTLIER) cc_final: 0.5623 (t0) REVERT: A 389 ASP cc_start: 0.7550 (m-30) cc_final: 0.7230 (m-30) REVERT: A 654 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: A 1463 MET cc_start: 0.8476 (mtp) cc_final: 0.8243 (mtp) REVERT: A 1535 LYS cc_start: 0.8058 (tmtt) cc_final: 0.7575 (tppp) REVERT: A 1672 MET cc_start: 0.1971 (tmm) cc_final: 0.1717 (tmm) REVERT: A 1768 LEU cc_start: 0.6500 (tp) cc_final: 0.6068 (tp) outliers start: 20 outliers final: 10 residues processed: 184 average time/residue: 0.7238 time to fit residues: 145.0824 Evaluate side-chains 179 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 500 HIS A 742 ASN A 819 GLN A1566 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109794 restraints weight = 50368.477| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.27 r_work: 0.2817 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15910 Z= 0.270 Angle : 0.790 10.716 21694 Z= 0.387 Chirality : 0.060 0.853 2439 Planarity : 0.005 0.084 2606 Dihedral : 10.810 170.707 2548 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.24 % Allowed : 9.96 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 1824 helix: 1.14 (0.17), residues: 885 sheet: -0.52 (0.37), residues: 183 loop : -0.99 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1712 TYR 0.017 0.002 TYR A1414 PHE 0.020 0.003 PHE A 166 TRP 0.017 0.002 TRP A 989 HIS 0.007 0.002 HIS A1035 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.27 (15910) covalent geometry : angle 0.78963 / 0.39 (21694) hydrogen bonds : bond 0.05738 / 3.83 ( 741) hydrogen bonds : angle 4.85888 / 3.55 ( 2109) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7873 (ttp-170) cc_final: 0.7593 (ttm-80) REVERT: A 26 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: A 173 SER cc_start: 0.8507 (p) cc_final: 0.8254 (p) REVERT: A 211 ASP cc_start: 0.6169 (OUTLIER) cc_final: 0.5632 (t0) REVERT: A 213 GLU cc_start: 0.6357 (pt0) cc_final: 0.6042 (pt0) REVERT: A 303 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: A 389 ASP cc_start: 0.7654 (m-30) cc_final: 0.7317 (m-30) REVERT: A 654 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: A 726 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.6167 (pmm-80) REVERT: A 1463 MET cc_start: 0.8500 (mtp) cc_final: 0.8232 (mtp) REVERT: A 1535 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7618 (tppp) REVERT: A 1612 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.5650 (mp0) REVERT: A 1768 LEU cc_start: 0.6456 (tp) cc_final: 0.6045 (tp) outliers start: 35 outliers final: 17 residues processed: 186 average time/residue: 0.7778 time to fit residues: 157.2473 Evaluate side-chains 188 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1612 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 144 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 500 HIS A 742 ASN A 819 GLN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 ASN A1566 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.114970 restraints weight = 56633.253| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 4.39 r_work: 0.2863 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15910 Z= 0.123 Angle : 0.586 8.136 21694 Z= 0.292 Chirality : 0.048 0.563 2439 Planarity : 0.004 0.039 2606 Dihedral : 10.529 175.302 2548 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.87 % Allowed : 12.08 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.48 (0.19), residues: 1824 helix: 1.56 (0.17), residues: 885 sheet: -0.36 (0.37), residues: 183 loop : -1.00 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1766 TYR 0.019 0.001 TYR A 193 PHE 0.016 0.001 PHE A 649 TRP 0.019 0.001 TRP A 520 HIS 0.004 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15910) covalent geometry : angle 0.58607 / 0.29 (21694) hydrogen bonds : bond 0.04003 / 2.66 ( 741) hydrogen bonds : angle 4.52302 / 3.30 ( 2109) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7838 (ttp-170) cc_final: 0.7559 (ttm-80) REVERT: A 26 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: A 211 ASP cc_start: 0.6087 (OUTLIER) cc_final: 0.5576 (t0) REVERT: A 213 GLU cc_start: 0.6280 (pt0) cc_final: 0.5922 (pt0) REVERT: A 389 ASP cc_start: 0.7638 (m-30) cc_final: 0.7323 (m-30) REVERT: A 654 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: A 1364 GLN cc_start: 0.8374 (mt0) cc_final: 0.8127 (mt0) REVERT: A 1463 MET cc_start: 0.8464 (mtp) cc_final: 0.8231 (mtp) REVERT: A 1535 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7609 (tppp) REVERT: A 1729 MET cc_start: 0.6691 (mtm) cc_final: 0.6485 (mtp) REVERT: A 1768 LEU cc_start: 0.6402 (tp) cc_final: 0.5941 (tp) outliers start: 13 outliers final: 8 residues processed: 179 average time/residue: 0.7540 time to fit residues: 147.2350 Evaluate side-chains 175 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 157 optimal weight: 0.3980 chunk 168 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 HIS A 742 ASN A 819 GLN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113640 restraints weight = 43821.415| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.29 r_work: 0.2904 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15910 Z= 0.139 Angle : 0.600 7.804 21694 Z= 0.298 Chirality : 0.049 0.605 2439 Planarity : 0.004 0.042 2606 Dihedral : 10.624 174.097 2548 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.25 % Allowed : 11.71 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.55 (0.19), residues: 1824 helix: 1.61 (0.17), residues: 886 sheet: -0.33 (0.37), residues: 183 loop : -0.96 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1766 TYR 0.018 0.001 TYR A 193 PHE 0.015 0.002 PHE A 911 TRP 0.015 0.001 TRP A 520 HIS 0.004 0.001 HIS A1245 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (15910) covalent geometry : angle 0.60016 / 0.30 (21694) hydrogen bonds : bond 0.04227 / 2.82 ( 741) hydrogen bonds : angle 4.51567 / 3.30 ( 2109) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7512 (ttm-80) REVERT: A 26 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: A 211 ASP cc_start: 0.6072 (OUTLIER) cc_final: 0.5562 (t0) REVERT: A 213 GLU cc_start: 0.6292 (pt0) cc_final: 0.5936 (pt0) REVERT: A 389 ASP cc_start: 0.7583 (m-30) cc_final: 0.7256 (m-30) REVERT: A 654 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: A 1463 MET cc_start: 0.8432 (mtp) cc_final: 0.8210 (mtp) REVERT: A 1535 LYS cc_start: 0.8116 (tmtt) cc_final: 0.7634 (tppp) REVERT: A 1612 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5377 (mp0) REVERT: A 1768 LEU cc_start: 0.6462 (tp) cc_final: 0.6024 (tp) outliers start: 19 outliers final: 13 residues processed: 176 average time/residue: 0.6334 time to fit residues: 121.5935 Evaluate side-chains 181 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1612 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 154 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 500 HIS A 742 ASN A 819 GLN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111926 restraints weight = 51810.825| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.23 r_work: 0.2837 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15910 Z= 0.215 Angle : 0.709 8.217 21694 Z= 0.350 Chirality : 0.055 0.763 2439 Planarity : 0.005 0.070 2606 Dihedral : 11.066 178.345 2548 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.62 % Allowed : 11.39 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.19), residues: 1824 helix: 1.32 (0.17), residues: 886 sheet: -0.53 (0.37), residues: 185 loop : -1.00 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1766 TYR 0.016 0.002 TYR A 193 PHE 0.016 0.002 PHE A 166 TRP 0.015 0.002 TRP A 989 HIS 0.006 0.001 HIS A1564 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (15910) covalent geometry : angle 0.70861 / 0.35 (21694) hydrogen bonds : bond 0.05180 / 3.46 ( 741) hydrogen bonds : angle 4.72700 / 3.45 ( 2109) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7868 (ttp-170) cc_final: 0.7554 (ttm-80) REVERT: A 26 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: A 173 SER cc_start: 0.8449 (p) cc_final: 0.8186 (p) REVERT: A 211 ASP cc_start: 0.6142 (OUTLIER) cc_final: 0.5611 (t0) REVERT: A 213 GLU cc_start: 0.6281 (pt0) cc_final: 0.5905 (pt0) REVERT: A 303 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: A 389 ASP cc_start: 0.7680 (m-30) cc_final: 0.7347 (m-30) REVERT: A 654 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: A 1463 MET cc_start: 0.8473 (mtp) cc_final: 0.8207 (mtp) REVERT: A 1535 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7816 (tptm) REVERT: A 1612 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5393 (mp0) REVERT: A 1768 LEU cc_start: 0.6464 (tp) cc_final: 0.6042 (tp) outliers start: 25 outliers final: 12 residues processed: 176 average time/residue: 0.6766 time to fit residues: 129.6997 Evaluate side-chains 177 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1612 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 32 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 113 optimal weight: 0.0070 chunk 88 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 42 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 500 HIS A 742 ASN A 819 GLN A1403 HIS A1566 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116420 restraints weight = 46624.134| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.44 r_work: 0.2952 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15910 Z= 0.104 Angle : 0.542 7.747 21694 Z= 0.271 Chirality : 0.045 0.446 2439 Planarity : 0.004 0.042 2606 Dihedral : 10.682 177.520 2548 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.87 % Allowed : 12.14 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.73 (0.20), residues: 1824 helix: 1.83 (0.18), residues: 879 sheet: -0.24 (0.35), residues: 203 loop : -0.94 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1766 TYR 0.020 0.001 TYR A 193 PHE 0.017 0.001 PHE A 649 TRP 0.024 0.001 TRP A 520 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (15910) covalent geometry : angle 0.54227 / 0.27 (21694) hydrogen bonds : bond 0.03462 / 2.30 ( 741) hydrogen bonds : angle 4.36912 / 3.18 ( 2109) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7486 (ttm-80) REVERT: A 211 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.4852 (p0) REVERT: A 389 ASP cc_start: 0.7500 (m-30) cc_final: 0.7177 (m-30) REVERT: A 654 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: A 726 ARG cc_start: 0.6515 (pmm-80) cc_final: 0.6233 (ptp-170) REVERT: A 1144 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7696 (mtp180) REVERT: A 1364 GLN cc_start: 0.8302 (mt0) cc_final: 0.8045 (mt0) REVERT: A 1463 MET cc_start: 0.8412 (mtp) cc_final: 0.8181 (mtp) REVERT: A 1535 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7570 (tppp) REVERT: A 1768 LEU cc_start: 0.6446 (tp) cc_final: 0.5994 (tp) outliers start: 13 outliers final: 8 residues processed: 179 average time/residue: 0.5911 time to fit residues: 115.6641 Evaluate side-chains 181 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1564 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 HIS A 742 ASN A 819 GLN ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112714 restraints weight = 51294.225| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.35 r_work: 0.2868 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15910 Z= 0.146 Angle : 0.603 7.547 21694 Z= 0.299 Chirality : 0.049 0.593 2439 Planarity : 0.004 0.045 2606 Dihedral : 10.812 179.499 2548 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.87 % Allowed : 11.96 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.69 (0.19), residues: 1824 helix: 1.72 (0.17), residues: 886 sheet: -0.25 (0.36), residues: 193 loop : -0.90 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1766 TYR 0.017 0.001 TYR A 193 PHE 0.015 0.002 PHE A 649 TRP 0.015 0.001 TRP A 520 HIS 0.004 0.001 HIS A1403 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (15910) covalent geometry : angle 0.60312 / 0.30 (21694) hydrogen bonds : bond 0.04234 / 2.83 ( 741) hydrogen bonds : angle 4.47004 / 3.26 ( 2109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5078.78 seconds wall clock time: 87 minutes 17.37 seconds (5237.37 seconds total)