Starting phenix.real_space_refine on Thu Aug 6 18:40:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r6w_18967/08_2026/8r6w_18967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r6w_18967/08_2026/8r6w_18967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r6w_18967/08_2026/8r6w_18967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r6w_18967/08_2026/8r6w_18967.map" model { file = "/net/cci-nas-00/data/ceres_data/8r6w_18967/08_2026/8r6w_18967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r6w_18967/08_2026/8r6w_18967.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 40 5.49 5 S 95 5.16 5 C 10315 2.51 5 N 2886 2.21 5 O 3203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 16539 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1974, 15661 Classifications: {'peptide': 1974} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1901} Chain breaks: 7 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 3} Chain: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNA': 16} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain: "T" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {'M7G': 1} Classifications: {'RNA': 3, 'undetermined': 1} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1, None: 1} Not linked: pdbres="M7G C 1 " pdbres=" A C 2 " Time building chain proxies: 3.48, per 1000 atoms: 0.21 Number of scatterers: 16539 At special positions: 0 Unit cell: (123.25, 116.45, 126.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 95 16.00 P 40 15.00 O 3203 8.00 N 2886 7.00 C 10315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 668.7 milliseconds 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 16 sheets defined 50.2% alpha, 8.6% beta 9 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.885A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.640A pdb=" N ALA A 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.566A pdb=" N PHE A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.758A pdb=" N VAL A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 149 through 160 removed outlier: 3.876A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 207 Processing helix chain 'A' and resid 220 through 234 removed outlier: 3.721A pdb=" N ILE A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.758A pdb=" N GLY A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 259 removed outlier: 4.194A pdb=" N LEU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 Processing helix chain 'A' and resid 292 through 317 Processing helix chain 'A' and resid 355 through 358 removed outlier: 3.685A pdb=" N HIS A 358 " --> pdb=" O LEU A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.635A pdb=" N LEU A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.509A pdb=" N SER A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.525A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 477 through 492 Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 512 through 534 removed outlier: 3.509A pdb=" N TRP A 517 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.999A pdb=" N THR A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.820A 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 removed outlier: 3.864A pdb=" N ARG A 642 " --> pdb=" O CYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 671 removed outlier: 4.137A pdb=" N ILE A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 685 removed outlier: 3.804A pdb=" N LYS A 685 " --> pdb=" O LYS A 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 682 through 685' Processing helix chain 'A' and resid 686 through 691 removed outlier: 3.553A pdb=" N LEU A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 686 through 691' Processing helix chain 'A' and resid 696 through 716 removed outlier: 3.801A pdb=" N VAL A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 751 removed outlier: 4.095A pdb=" N TYR A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 767 through 780 removed outlier: 4.747A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 779 " --> pdb=" O VAL A 775 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 3.985A pdb=" N PHE A 787 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 Processing helix chain 'A' and resid 824 through 839 Processing helix chain 'A' and resid 856 through 860 removed outlier: 3.792A pdb=" N LEU A 860 " --> pdb=" O ASP A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 884 removed outlier: 4.029A pdb=" N LYS A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 891 Processing helix chain 'A' and resid 892 through 902 Processing helix chain 'A' and resid 927 through 947 removed outlier: 4.230A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 963 through 973 removed outlier: 4.366A pdb=" N LEU A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 3.768A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1021 removed outlier: 3.813A pdb=" N HIS A1011 " --> pdb=" O PRO A1007 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE A1013 " --> pdb=" O LYS A1009 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1038 removed outlier: 3.603A pdb=" N HIS A1035 " --> pdb=" O ARG A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1058 removed outlier: 3.796A pdb=" N GLU A1050 " --> pdb=" O ASP A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1108 removed outlier: 3.540A pdb=" N GLU A1108 " --> pdb=" O SER A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1160 removed outlier: 4.047A pdb=" N VAL A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LYS A1157 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1163 No H-bonds generated for 'chain 'A' and resid 1161 through 1163' Processing helix chain 'A' and resid 1195 through 1201 removed outlier: 3.574A pdb=" N ALA A1201 " --> pdb=" O ARG A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1228 removed outlier: 4.141A pdb=" N GLN A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1251 Processing helix chain 'A' and resid 1257 through 1268 Processing helix chain 'A' and resid 1288 through 1299 removed outlier: 3.660A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1315 Processing helix chain 'A' and resid 1345 through 1355 removed outlier: 3.592A pdb=" N MET A1355 " --> pdb=" O LEU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1368 removed outlier: 3.677A pdb=" N GLN A1364 " --> pdb=" O ASP A1360 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1390 Processing helix chain 'A' and resid 1403 through 1411 removed outlier: 3.607A pdb=" N ARG A1407 " --> pdb=" O HIS A1403 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) 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 1437 through 1446 Processing helix chain 'A' and resid 1448 through 1453 removed outlier: 3.843A pdb=" N GLY A1453 " --> pdb=" O ALA A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1465 Processing helix chain 'A' and resid 1467 through 1481 removed outlier: 3.697A pdb=" N VAL A1481 " --> pdb=" O LEU A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1523 Processing helix chain 'A' and resid 1530 through 1545 Processing helix chain 'A' and resid 1551 through 1559 removed outlier: 3.675A pdb=" N THR A1555 " --> pdb=" O ASP A1551 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A1556 " --> pdb=" O PRO A1552 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A1557 " --> pdb=" O SER A1553 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1574 removed outlier: 3.769A pdb=" N VAL A1574 " --> pdb=" O PHE A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1603 removed outlier: 3.634A pdb=" N VAL A1600 " --> pdb=" O THR A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1638 removed outlier: 3.920A pdb=" N MET A1635 " --> pdb=" O HIS A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1657 Processing helix chain 'A' and resid 1670 through 1683 removed outlier: 3.611A pdb=" N LEU A1681 " --> pdb=" O LEU A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1696 Processing helix chain 'A' and resid 1757 through 1773 Processing helix chain 'A' and resid 1858 through 1868 removed outlier: 3.981A pdb=" N ALA A1862 " --> pdb=" O SER A1858 " (cutoff:3.500A) Processing helix chain 'A' and resid 1869 through 1872 removed outlier: 3.983A pdb=" N PHE A1872 " --> pdb=" O ARG A1869 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1869 through 1872' Processing helix chain 'A' and resid 1890 through 1902 Processing helix chain 'A' and resid 1913 through 1931 removed outlier: 4.196A pdb=" N ASN A1917 " --> pdb=" O ARG A1913 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN A1930 " --> pdb=" O SER A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1979 through 1983 removed outlier: 3.688A pdb=" N ASP A1983 " --> pdb=" O SER A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2004 Processing helix chain 'A' and resid 2016 through 2027 Processing helix chain 'A' and resid 2031 through 2037 Processing helix chain 'A' and resid 2044 through 2047 removed outlier: 3.750A pdb=" N GLN A2047 " --> pdb=" O ILE A2044 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2044 through 2047' Processing helix chain 'A' and resid 2048 through 2054 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 6.799A pdb=" N SER A 17 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 41 removed outlier: 4.198A pdb=" N THR A 46 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.358A pdb=" N SER A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 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 719 through 722 Processing sheet with id=AA7, first strand: chain 'A' and resid 851 through 852 Processing sheet with id=AA8, first strand: chain 'A' and resid 906 through 908 removed outlier: 5.998A pdb=" N MET A 906 " --> pdb=" O LYS A1025 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N MET A1027 " --> pdb=" O MET A 906 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE A 908 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 6.506A pdb=" N SER A 983 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL A1173 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id=AB2, first strand: chain 'A' and resid 1328 through 1329 removed outlier: 3.733A pdb=" N THR A1333 " --> pdb=" O THR A1329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1337 through 1338 removed outlier: 3.622A pdb=" N VAL A1338 " --> pdb=" O ARG A1422 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1499 through 1501 removed outlier: 3.579A pdb=" N ILE A1500 " --> pdb=" O VAL A1581 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A1581 " --> pdb=" O ILE A1500 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1699 through 1705 removed outlier: 3.520A pdb=" N LEU A1700 " --> pdb=" O VAL A1728 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A1704 " --> pdb=" O VAL A1724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A1724 " --> pdb=" O SER A1704 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY A1716 " --> pdb=" O ARG A1712 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A1712 " --> pdb=" O GLY A1716 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1699 through 1705 removed outlier: 3.520A pdb=" N LEU A1700 " --> pdb=" O VAL A1728 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A1704 " --> pdb=" O VAL A1724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A1724 " --> pdb=" O SER A1704 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A1740 " --> pdb=" O GLY A1721 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1790 through 1791 removed outlier: 3.896A pdb=" N SER A1791 " --> pdb=" O LYS A1794 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4702 1.34 - 1.45: 3030 1.45 - 1.57: 8994 1.57 - 1.69: 78 1.69 - 1.81: 154 Bond restraints: 16958 Sorted by residual: bond pdb=" N7 A C 2 " pdb=" C5 A C 2 " ideal model delta sigma weight residual 1.388 1.328 0.060 6.00e-03 2.78e+04 1.01e+02 bond pdb=" C5 A C 2 " pdb=" C6 A C 2 " ideal model delta sigma weight residual 1.406 1.333 0.073 9.00e-03 1.23e+04 6.67e+01 bond pdb=" C2 A C 2 " pdb=" N3 A C 2 " ideal model delta sigma weight residual 1.331 1.396 -0.065 9.00e-03 1.23e+04 5.16e+01 bond pdb=" C5 A C 2 " pdb=" C4 A C 2 " ideal model delta sigma weight residual 1.383 1.335 0.048 7.00e-03 2.04e+04 4.73e+01 bond pdb=" N1 A C 2 " pdb=" C2 A C 2 " ideal model delta sigma weight residual 1.339 1.396 -0.057 9.00e-03 1.23e+04 3.98e+01 ... (remaining 16953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 23042 5.73 - 11.46: 32 11.46 - 17.19: 1 17.19 - 22.93: 2 22.93 - 28.66: 2 Bond angle restraints: 23079 Sorted by residual: angle pdb=" N1 A C 2 " pdb=" C2 A C 2 " pdb=" N3 A C 2 " ideal model delta sigma weight residual 129.30 118.17 11.13 5.00e-01 4.00e+00 4.96e+02 angle pdb=" C2 A C 2 " pdb=" N3 A C 2 " pdb=" C4 A C 2 " ideal model delta sigma weight residual 110.60 120.32 -9.72 5.00e-01 4.00e+00 3.78e+02 angle pdb=" N9 A C 2 " pdb=" C8 A C 2 " pdb=" N7 A C 2 " ideal model delta sigma weight residual 113.80 108.50 5.30 5.00e-01 4.00e+00 1.12e+02 angle pdb=" C5 A C 2 " pdb=" C4 A C 2 " pdb=" N3 A C 2 " ideal model delta sigma weight residual 126.80 119.90 6.90 7.00e-01 2.04e+00 9.73e+01 angle pdb=" O1B M7G C 1 " pdb=" PB M7G C 1 " pdb=" O3B M7G C 1 " ideal model delta sigma weight residual 115.41 86.75 28.66 3.00e+00 1.11e-01 9.12e+01 ... (remaining 23074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 9796 35.34 - 70.69: 455 70.69 - 106.03: 50 106.03 - 141.37: 0 141.37 - 176.72: 5 Dihedral angle restraints: 10306 sinusoidal: 4597 harmonic: 5709 Sorted by residual: dihedral pdb=" O4' C T 19 " pdb=" C1' C T 19 " pdb=" N1 C T 19 " pdb=" C2 C T 19 " ideal model delta sinusoidal sigma weight residual 200.00 41.31 158.69 1 1.50e+01 4.44e-03 8.24e+01 dihedral pdb=" O4' U T 21 " pdb=" C1' U T 21 " pdb=" N1 U T 21 " pdb=" C2 U T 21 " ideal model delta sinusoidal sigma weight residual -128.00 48.72 -176.72 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U T 18 " pdb=" C1' U T 18 " pdb=" N1 U T 18 " pdb=" C2 U T 18 " ideal model delta sinusoidal sigma weight residual -160.00 -70.14 -89.86 1 1.50e+01 4.44e-03 4.26e+01 ... (remaining 10303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2186 0.060 - 0.120: 339 0.120 - 0.179: 58 0.179 - 0.239: 3 0.239 - 0.299: 2 Chirality restraints: 2588 Sorted by residual: chirality pdb=" C3' M7G C 1 " pdb=" C2' M7G C 1 " pdb=" C4' M7G C 1 " pdb=" O3' M7G C 1 " both_signs ideal model delta sigma weight residual False -2.51 -2.81 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C4' M7G C 1 " pdb=" C3' M7G C 1 " pdb=" C5' M7G C 1 " pdb=" O4' M7G C 1 " both_signs ideal model delta sigma weight residual False -2.46 -2.73 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C3' U T 20 " pdb=" C4' U T 20 " pdb=" O3' U T 20 " pdb=" C2' U T 20 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2585 not shown) Planarity restraints: 2795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1712 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO A1713 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A1713 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1713 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1878 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A1879 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A1879 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1879 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1006 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO A1007 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1007 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1007 " 0.026 5.00e-02 4.00e+02 ... (remaining 2792 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1907 2.75 - 3.29: 16443 3.29 - 3.83: 28683 3.83 - 4.36: 32986 4.36 - 4.90: 55653 Nonbonded interactions: 135672 Sorted by model distance: nonbonded pdb=" OP1 C P 10 " pdb=" O2' G P 11 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 132 " pdb=" OD1 ASN A 134 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A1780 " pdb=" O GLY A1803 " model vdw 2.256 3.040 nonbonded pdb=" O MET A1729 " pdb=" OG1 THR A1732 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR A 558 " pdb=" O HIS A 563 " model vdw 2.268 3.040 ... (remaining 135667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 18.230 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.004 0.124 16959 Z= 0.259 Angle : 0.810 28.656 23079 Z= 0.530 Chirality : 0.046 0.299 2588 Planarity : 0.005 0.054 2795 Dihedral : 18.961 176.716 6618 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.87 % Favored : 91.98 % Rotamer: Outliers : 9.45 % Allowed : 11.54 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.18), residues: 1958 helix: 0.30 (0.17), residues: 917 sheet: -0.32 (0.48), residues: 136 loop : -2.68 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 642 TYR 0.015 0.002 TYR A 861 PHE 0.018 0.001 PHE A 649 TRP 0.014 0.001 TRP A 520 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.25 (16958) covalent geometry : angle 0.80994 / 0.53 (23079) hydrogen bonds : bond 0.16172 / 10.82 ( 709) hydrogen bonds : angle 5.98835 / 4.33 ( 2064) Misc. bond : bond 0.07284 / 3.83 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 259 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 VAL cc_start: 0.8195 (t) cc_final: 0.7927 (m) REVERT: A 54 ASP cc_start: 0.7740 (m-30) cc_final: 0.7472 (m-30) REVERT: A 92 ASP cc_start: 0.8003 (t0) cc_final: 0.7304 (p0) REVERT: A 280 ASP cc_start: 0.8341 (t70) cc_final: 0.8033 (t0) REVERT: A 582 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7834 (mpp80) REVERT: A 651 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 653 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8276 (mm) REVERT: A 743 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8735 (tp) REVERT: A 800 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6751 (mt-10) REVERT: A 937 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: A 1018 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7839 (mt) REVERT: A 1020 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8497 (ptm) REVERT: A 1065 MET cc_start: 0.8332 (mmm) cc_final: 0.8047 (mmt) REVERT: A 1110 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6061 (t80) REVERT: A 1418 ARG cc_start: 0.8004 (tpp80) cc_final: 0.7179 (mmt180) REVERT: A 1478 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8033 (mm) REVERT: A 1489 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8553 (m) REVERT: A 1540 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8734 (ptpp) REVERT: A 1612 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: A 1690 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8299 (t0) REVERT: A 1745 ASN cc_start: 0.6742 (m-40) cc_final: 0.6380 (m-40) REVERT: A 1757 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7314 (mtp180) REVERT: A 1787 MET cc_start: 0.6021 (pmm) cc_final: 0.5622 (ptp) REVERT: A 1995 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7150 (mm-30) outliers start: 163 outliers final: 39 residues processed: 387 average time/residue: 0.1610 time to fit residues: 88.6758 Evaluate side-chains 203 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1024 LYS Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1110 TYR Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1341 TYR Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1489 VAL Chi-restraints excluded: chain A residue 1540 LYS Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1635 MET Chi-restraints excluded: chain A residue 1690 ASP Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1796 LYS Chi-restraints excluded: chain A residue 1833 LEU Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 285 HIS A 300 ASN A 426 GLN A 824 GLN A 895 GLN A 914 ASN A 916 HIS A1174 ASN A1188 HIS A1239 GLN A1280 ASN A1292 ASN ** A1452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1467 GLN A1679 ASN A1707 GLN A1776 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.085765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.069550 restraints weight = 53793.801| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.53 r_work: 0.3408 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16959 Z= 0.173 Angle : 0.650 9.712 23079 Z= 0.343 Chirality : 0.042 0.371 2588 Planarity : 0.005 0.059 2795 Dihedral : 16.642 177.159 2908 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.15 % Favored : 92.70 % Rotamer: Outliers : 4.81 % Allowed : 15.25 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.18), residues: 1958 helix: 0.61 (0.17), residues: 923 sheet: -0.41 (0.47), residues: 136 loop : -2.56 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1777 TYR 0.016 0.002 TYR A 861 PHE 0.016 0.001 PHE A 649 TRP 0.016 0.001 TRP A 335 HIS 0.012 0.001 HIS A1452 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (16958) covalent geometry : angle 0.64968 / 0.34 (23079) hydrogen bonds : bond 0.05021 / 3.31 ( 709) hydrogen bonds : angle 4.63518 / 3.33 ( 2064) Misc. bond : bond 0.00745 / 0.39 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 147 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7837 (m-30) cc_final: 0.7576 (m-30) REVERT: A 92 ASP cc_start: 0.7795 (t0) cc_final: 0.7184 (p0) REVERT: A 192 MET cc_start: 0.7674 (mtm) cc_final: 0.7141 (ptp) REVERT: A 445 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: A 653 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 710 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8135 (ttp) REVERT: A 712 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7686 (ttt-90) REVERT: A 743 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8648 (tp) REVERT: A 860 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8445 (mm) REVERT: A 1061 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: A 1065 MET cc_start: 0.8468 (mmm) cc_final: 0.8260 (mmt) REVERT: A 1418 ARG cc_start: 0.8016 (tpp80) cc_final: 0.7197 (mmt180) REVERT: A 1489 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8612 (m) REVERT: A 1612 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: A 1745 ASN cc_start: 0.6986 (m-40) cc_final: 0.6582 (m-40) REVERT: A 1757 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7229 (mtp180) REVERT: A 1919 PHE cc_start: 0.8848 (m-10) cc_final: 0.8600 (m-80) REVERT: A 1995 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7081 (mm-30) outliers start: 83 outliers final: 41 residues processed: 219 average time/residue: 0.1375 time to fit residues: 44.9266 Evaluate side-chains 174 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1341 TYR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1489 VAL Chi-restraints excluded: chain A residue 1528 LYS Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1635 MET Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1754 SER Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1828 VAL Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 12 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 116 optimal weight: 0.0040 chunk 197 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A1569 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.084049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.067663 restraints weight = 54327.235| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.55 r_work: 0.3361 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16959 Z= 0.170 Angle : 0.603 9.523 23079 Z= 0.319 Chirality : 0.041 0.375 2588 Planarity : 0.005 0.057 2795 Dihedral : 15.946 175.965 2850 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.76 % Favored : 92.08 % Rotamer: Outliers : 4.23 % Allowed : 17.16 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1958 helix: 0.80 (0.17), residues: 923 sheet: -0.66 (0.42), residues: 161 loop : -2.41 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 537 TYR 0.016 0.002 TYR A1341 PHE 0.019 0.001 PHE A 649 TRP 0.020 0.001 TRP A 335 HIS 0.009 0.001 HIS A1452 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (16958) covalent geometry : angle 0.60316 / 0.32 (23079) hydrogen bonds : bond 0.04487 / 2.94 ( 709) hydrogen bonds : angle 4.38427 / 3.13 ( 2064) Misc. bond : bond 0.00481 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 129 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7811 (m-30) cc_final: 0.7555 (m-30) REVERT: A 92 ASP cc_start: 0.7779 (t0) cc_final: 0.7221 (p0) REVERT: A 160 MET cc_start: 0.7256 (mmm) cc_final: 0.7042 (mmm) REVERT: A 445 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: A 507 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8842 (mptt) REVERT: A 710 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8125 (ttp) REVERT: A 712 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7722 (ttt-90) REVERT: A 713 ILE cc_start: 0.8750 (tt) cc_final: 0.8266 (mt) REVERT: A 848 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7878 (mpp) REVERT: A 1157 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7968 (ptpp) REVERT: A 1418 ARG cc_start: 0.7919 (tpp80) cc_final: 0.7131 (mmt180) REVERT: A 1745 ASN cc_start: 0.7245 (m-40) cc_final: 0.6872 (m-40) REVERT: A 1757 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7385 (mtm180) REVERT: A 2039 ARG cc_start: 0.7536 (tpp80) cc_final: 0.6718 (tpp80) outliers start: 73 outliers final: 46 residues processed: 191 average time/residue: 0.1324 time to fit residues: 38.1911 Evaluate side-chains 170 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1341 TYR Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1538 TRP Chi-restraints excluded: chain A residue 1578 SER Chi-restraints excluded: chain A residue 1635 MET Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1828 VAL Chi-restraints excluded: chain A residue 1833 LEU Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 166 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 6 optimal weight: 0.0670 chunk 40 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1896 HIS ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.081504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.064945 restraints weight = 54591.800| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.54 r_work: 0.3290 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 16959 Z= 0.240 Angle : 0.664 9.355 23079 Z= 0.351 Chirality : 0.044 0.384 2588 Planarity : 0.005 0.078 2795 Dihedral : 15.832 175.658 2831 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.12 % Favored : 91.73 % Rotamer: Outliers : 5.04 % Allowed : 17.68 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1958 helix: 0.68 (0.17), residues: 924 sheet: -1.17 (0.39), residues: 183 loop : -2.42 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1913 TYR 0.035 0.002 TYR A1323 PHE 0.023 0.002 PHE A 649 TRP 0.016 0.002 TRP A 335 HIS 0.007 0.002 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (16958) covalent geometry : angle 0.66365 / 0.35 (23079) hydrogen bonds : bond 0.04628 / 3.07 ( 709) hydrogen bonds : angle 4.49326 / 3.20 ( 2064) Misc. bond : bond 0.00381 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 125 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7866 (m-30) cc_final: 0.7655 (m-30) REVERT: A 92 ASP cc_start: 0.7754 (t0) cc_final: 0.7258 (p0) REVERT: A 221 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8180 (mp) REVERT: A 392 ILE cc_start: 0.9103 (mm) cc_final: 0.8851 (mm) REVERT: A 445 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: A 507 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8851 (mptt) REVERT: A 710 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8055 (ttp) REVERT: A 712 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8070 (ttt-90) REVERT: A 860 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8499 (mm) REVERT: A 883 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: A 887 MET cc_start: 0.6851 (tmm) cc_final: 0.6340 (tmm) REVERT: A 1157 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8000 (ptpp) REVERT: A 1612 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: A 1635 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7414 (mmm) REVERT: A 1741 ASP cc_start: 0.6995 (p0) cc_final: 0.6498 (t70) REVERT: A 1757 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7275 (mtp180) outliers start: 87 outliers final: 54 residues processed: 197 average time/residue: 0.1272 time to fit residues: 37.8036 Evaluate side-chains 176 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 111 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1341 TYR Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1400 SER Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1578 SER Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1635 MET Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1729 MET Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1754 SER Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1828 VAL Chi-restraints excluded: chain A residue 1833 LEU Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 174 optimal weight: 5.9990 chunk 33 optimal weight: 0.0170 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 HIS A1896 HIS ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.083590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067295 restraints weight = 53767.733| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.61 r_work: 0.3350 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16959 Z= 0.117 Angle : 0.560 9.366 23079 Z= 0.295 Chirality : 0.040 0.370 2588 Planarity : 0.004 0.056 2795 Dihedral : 15.527 176.201 2825 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.30 % Favored : 92.59 % Rotamer: Outliers : 3.48 % Allowed : 19.59 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.19), residues: 1958 helix: 1.04 (0.17), residues: 921 sheet: -1.06 (0.39), residues: 183 loop : -2.38 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 164 TYR 0.014 0.001 TYR A1341 PHE 0.012 0.001 PHE A1874 TRP 0.016 0.001 TRP A 520 HIS 0.006 0.001 HIS A1255 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (16958) covalent geometry : angle 0.56002 / 0.29 (23079) hydrogen bonds : bond 0.03813 / 2.50 ( 709) hydrogen bonds : angle 4.20727 / 3.00 ( 2064) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 120 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7687 (m-30) cc_final: 0.7477 (m-30) REVERT: A 92 ASP cc_start: 0.7717 (t0) cc_final: 0.7228 (p0) REVERT: A 392 ILE cc_start: 0.9064 (mm) cc_final: 0.8837 (mm) REVERT: A 635 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7833 (mtm180) REVERT: A 710 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8044 (ttp) REVERT: A 712 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8063 (ttt-90) REVERT: A 713 ILE cc_start: 0.8833 (tt) cc_final: 0.8441 (mt) REVERT: A 860 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8495 (mm) REVERT: A 1061 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: A 1157 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7945 (ptpp) REVERT: A 1418 ARG cc_start: 0.7818 (tpp80) cc_final: 0.6988 (mmt180) REVERT: A 1741 ASP cc_start: 0.6798 (p0) cc_final: 0.6423 (t70) REVERT: A 1757 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7373 (mtm180) REVERT: A 1995 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7139 (mm-30) outliers start: 60 outliers final: 37 residues processed: 173 average time/residue: 0.1241 time to fit residues: 32.9673 Evaluate side-chains 158 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1538 TRP Chi-restraints excluded: chain A residue 1578 SER Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1754 SER Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1896 HIS ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.082567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.066354 restraints weight = 53764.265| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.53 r_work: 0.3327 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 16959 Z= 0.150 Angle : 0.569 10.635 23079 Z= 0.299 Chirality : 0.040 0.374 2588 Planarity : 0.004 0.059 2795 Dihedral : 15.313 176.141 2816 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.07 % Favored : 91.83 % Rotamer: Outliers : 3.77 % Allowed : 19.48 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 1958 helix: 1.04 (0.17), residues: 924 sheet: -1.10 (0.39), residues: 183 loop : -2.39 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1913 TYR 0.012 0.001 TYR A 861 PHE 0.014 0.001 PHE A 649 TRP 0.014 0.001 TRP A 335 HIS 0.019 0.001 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16958) covalent geometry : angle 0.56939 / 0.30 (23079) hydrogen bonds : bond 0.03919 / 2.56 ( 709) hydrogen bonds : angle 4.21846 / 3.00 ( 2064) Misc. bond : bond 0.00122 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 117 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7692 (t0) cc_final: 0.7204 (p0) REVERT: A 240 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8570 (ttt-90) REVERT: A 507 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8845 (mptt) REVERT: A 710 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8058 (ttp) REVERT: A 712 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8206 (ttt-90) REVERT: A 860 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8539 (mm) REVERT: A 1061 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: A 1157 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7916 (ptpp) REVERT: A 1334 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8553 (pp) REVERT: A 1418 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7017 (mmt180) REVERT: A 1741 ASP cc_start: 0.6876 (p0) cc_final: 0.6482 (t70) REVERT: A 1757 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7432 (mtm180) REVERT: A 1995 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7139 (mm-30) outliers start: 65 outliers final: 45 residues processed: 172 average time/residue: 0.1279 time to fit residues: 34.1294 Evaluate side-chains 165 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 110 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1538 TRP Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1635 MET Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1754 SER Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1787 MET Chi-restraints excluded: chain A residue 1793 PHE Chi-restraints excluded: chain A residue 1833 LEU Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 102 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 65 optimal weight: 0.0040 chunk 153 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 overall best weight: 2.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS A1896 HIS ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.081914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065643 restraints weight = 53613.665| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.53 r_work: 0.3310 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 16959 Z= 0.164 Angle : 0.575 9.499 23079 Z= 0.302 Chirality : 0.041 0.374 2588 Planarity : 0.004 0.056 2795 Dihedral : 15.237 176.147 2814 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.12 % Favored : 91.78 % Rotamer: Outliers : 3.83 % Allowed : 19.59 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 1958 helix: 1.03 (0.17), residues: 927 sheet: -1.10 (0.39), residues: 183 loop : -2.39 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1913 TYR 0.013 0.001 TYR A1166 PHE 0.016 0.001 PHE A 649 TRP 0.021 0.001 TRP A1547 HIS 0.009 0.001 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (16958) covalent geometry : angle 0.57547 / 0.30 (23079) hydrogen bonds : bond 0.03958 / 2.60 ( 709) hydrogen bonds : angle 4.24673 / 3.03 ( 2064) Misc. bond : bond 0.00117 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 112 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7697 (t0) cc_final: 0.7222 (p0) REVERT: A 240 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8649 (ttt-90) REVERT: A 445 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: A 507 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8845 (mptt) REVERT: A 710 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8044 (ttp) REVERT: A 712 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8251 (ttt-90) REVERT: A 860 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8540 (mm) REVERT: A 1157 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7924 (ptpp) REVERT: A 1334 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8548 (pp) REVERT: A 1418 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7076 (mmt180) REVERT: A 1741 ASP cc_start: 0.6929 (p0) cc_final: 0.6542 (t70) REVERT: A 1757 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7431 (mtm180) REVERT: A 1995 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7171 (mm-30) outliers start: 66 outliers final: 51 residues processed: 168 average time/residue: 0.1291 time to fit residues: 33.7511 Evaluate side-chains 166 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 105 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1635 MET Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1754 SER Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1787 MET Chi-restraints excluded: chain A residue 1793 PHE Chi-restraints excluded: chain A residue 1833 LEU Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Chi-restraints excluded: chain A residue 2003 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 44 optimal weight: 0.0770 chunk 141 optimal weight: 0.9980 chunk 134 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1896 HIS ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.083066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066807 restraints weight = 53940.320| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.61 r_work: 0.3337 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16959 Z= 0.114 Angle : 0.561 10.707 23079 Z= 0.293 Chirality : 0.040 0.369 2588 Planarity : 0.004 0.057 2795 Dihedral : 15.153 176.374 2814 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.71 % Favored : 92.19 % Rotamer: Outliers : 3.30 % Allowed : 20.41 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.19), residues: 1958 helix: 1.14 (0.17), residues: 926 sheet: -1.05 (0.39), residues: 183 loop : -2.37 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2039 TYR 0.013 0.001 TYR A1341 PHE 0.011 0.001 PHE A 649 TRP 0.021 0.001 TRP A1547 HIS 0.007 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (16958) covalent geometry : angle 0.56063 / 0.29 (23079) hydrogen bonds : bond 0.03659 / 2.40 ( 709) hydrogen bonds : angle 4.14486 / 2.95 ( 2064) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 114 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7699 (t0) cc_final: 0.7207 (p0) REVERT: A 143 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7551 (mtm-85) REVERT: A 346 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.6943 (tt) REVERT: A 507 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8846 (mptt) REVERT: A 710 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8019 (ttp) REVERT: A 712 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8217 (ttt-90) REVERT: A 860 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8584 (mm) REVERT: A 1067 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7820 (tppt) REVERT: A 1157 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7920 (ptpp) REVERT: A 1418 ARG cc_start: 0.7745 (tpp80) cc_final: 0.7003 (mmt180) REVERT: A 1741 ASP cc_start: 0.6942 (p0) cc_final: 0.6548 (t70) REVERT: A 1757 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7401 (mtm180) REVERT: A 1995 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7136 (mm-30) outliers start: 57 outliers final: 42 residues processed: 162 average time/residue: 0.1401 time to fit residues: 35.1989 Evaluate side-chains 160 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1067 LYS Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1538 TRP Chi-restraints excluded: chain A residue 1635 MET Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1754 SER Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1787 MET Chi-restraints excluded: chain A residue 1793 PHE Chi-restraints excluded: chain A residue 1833 LEU Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 154 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 HIS A1391 HIS A1896 HIS ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.083270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.067025 restraints weight = 53787.430| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.60 r_work: 0.3343 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16959 Z= 0.114 Angle : 0.562 10.796 23079 Z= 0.291 Chirality : 0.039 0.368 2588 Planarity : 0.004 0.056 2795 Dihedral : 15.087 176.612 2814 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.71 % Favored : 92.19 % Rotamer: Outliers : 3.25 % Allowed : 20.35 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.19), residues: 1958 helix: 1.16 (0.17), residues: 928 sheet: -1.02 (0.39), residues: 183 loop : -2.34 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2039 TYR 0.013 0.001 TYR A1341 PHE 0.011 0.001 PHE A 649 TRP 0.021 0.001 TRP A1547 HIS 0.006 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (16958) covalent geometry : angle 0.56175 / 0.29 (23079) hydrogen bonds : bond 0.03584 / 2.34 ( 709) hydrogen bonds : angle 4.10586 / 2.91 ( 2064) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 113 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7651 (t0) cc_final: 0.7155 (p0) REVERT: A 143 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7680 (mtm110) REVERT: A 346 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.6949 (tt) REVERT: A 507 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8852 (mptt) REVERT: A 635 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7770 (mtm180) REVERT: A 710 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8031 (ttp) REVERT: A 712 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8208 (ttt-90) REVERT: A 860 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8575 (mm) REVERT: A 883 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: A 1061 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: A 1157 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7895 (ptpp) REVERT: A 1418 ARG cc_start: 0.7733 (tpp80) cc_final: 0.6991 (mmt180) REVERT: A 1741 ASP cc_start: 0.6855 (p0) cc_final: 0.6502 (t70) REVERT: A 1757 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7413 (mtm180) REVERT: A 1995 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7084 (mm-30) outliers start: 56 outliers final: 40 residues processed: 160 average time/residue: 0.1337 time to fit residues: 32.6289 Evaluate side-chains 160 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1538 TRP Chi-restraints excluded: chain A residue 1635 MET Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 194 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 139 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1896 HIS ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.082383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.066162 restraints weight = 53922.541| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.55 r_work: 0.3323 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 16959 Z= 0.151 Angle : 0.586 13.562 23079 Z= 0.302 Chirality : 0.040 0.370 2588 Planarity : 0.004 0.056 2795 Dihedral : 15.062 176.513 2812 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.87 % Favored : 92.03 % Rotamer: Outliers : 3.30 % Allowed : 20.46 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1958 helix: 1.16 (0.17), residues: 927 sheet: -1.05 (0.39), residues: 182 loop : -2.37 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2039 TYR 0.011 0.001 TYR A1341 PHE 0.014 0.001 PHE A 649 TRP 0.023 0.001 TRP A1547 HIS 0.006 0.001 HIS A1255 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (16958) covalent geometry : angle 0.58597 / 0.30 (23079) hydrogen bonds : bond 0.03740 / 2.44 ( 709) hydrogen bonds : angle 4.15056 / 2.93 ( 2064) Misc. bond : bond 0.00080 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 108 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7678 (t0) cc_final: 0.7172 (p0) REVERT: A 477 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6646 (mm-30) REVERT: A 507 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8840 (mptt) REVERT: A 710 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8041 (ttp) REVERT: A 712 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8258 (ttt-90) REVERT: A 860 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8549 (mm) REVERT: A 883 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: A 1157 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7879 (ptpp) REVERT: A 1418 ARG cc_start: 0.7772 (tpp80) cc_final: 0.6950 (mmt180) REVERT: A 1741 ASP cc_start: 0.6876 (p0) cc_final: 0.6546 (t70) REVERT: A 1757 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7374 (mtm180) REVERT: A 1995 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7100 (mm-30) outliers start: 57 outliers final: 43 residues processed: 156 average time/residue: 0.1292 time to fit residues: 31.3059 Evaluate side-chains 158 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 107 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1538 TRP Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1754 SER Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1787 MET Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 33 optimal weight: 0.0020 chunk 11 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 189 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1896 HIS ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.083012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.066825 restraints weight = 53537.910| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.59 r_work: 0.3338 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16959 Z= 0.116 Angle : 0.572 13.813 23079 Z= 0.294 Chirality : 0.040 0.367 2588 Planarity : 0.004 0.057 2795 Dihedral : 15.028 176.596 2812 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.76 % Favored : 92.13 % Rotamer: Outliers : 3.13 % Allowed : 20.70 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1958 helix: 1.21 (0.17), residues: 927 sheet: -1.03 (0.39), residues: 183 loop : -2.34 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2039 TYR 0.012 0.001 TYR A1341 PHE 0.012 0.001 PHE A 649 TRP 0.020 0.001 TRP A1547 HIS 0.005 0.001 HIS A1255 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16958) covalent geometry : angle 0.57197 / 0.29 (23079) hydrogen bonds : bond 0.03592 / 2.35 ( 709) hydrogen bonds : angle 4.10030 / 2.90 ( 2064) Misc. bond : bond 0.00047 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3454.89 seconds wall clock time: 60 minutes 21.96 seconds (3621.96 seconds total)