Starting phenix.real_space_refine on Fri Nov 21 01:53:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bax_44413/11_2025/9bax_44413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bax_44413/11_2025/9bax_44413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bax_44413/11_2025/9bax_44413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bax_44413/11_2025/9bax_44413.map" model { file = "/net/cci-nas-00/data/ceres_data/9bax_44413/11_2025/9bax_44413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bax_44413/11_2025/9bax_44413.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 276 5.16 5 C 27142 2.51 5 N 7058 2.21 5 O 7624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42100 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 522 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "B" Number of atoms: 13842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1724, 13842 Classifications: {'peptide': 1724} Link IDs: {'PCIS': 1, 'PTRANS': 86, 'TRANS': 1636} Chain breaks: 23 Chain: "F" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4676 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 570} Chain breaks: 5 Chain: "G" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2010 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 236} Chain breaks: 4 Restraints were copied for chains: H, A, D, E Time building chain proxies: 25.70, per 1000 atoms: 0.61 Number of scatterers: 42100 At special positions: 0 Unit cell: (271.04, 195.58, 127.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 276 16.00 O 7624 8.00 N 7058 7.00 C 27142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 1.9 seconds 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10068 Finding SS restraints... Secondary structure from input PDB file: 274 helices and 10 sheets defined 72.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'C' and resid 727 through 736 removed outlier: 3.626A pdb=" N LEU C 731 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 736 " --> pdb=" O LYS C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 4.409A pdb=" N GLU C 746 " --> pdb=" O GLU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 787 removed outlier: 3.736A pdb=" N ALA C 764 " --> pdb=" O PHE C 760 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE C 786 " --> pdb=" O LEU C 782 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG C 787 " --> pdb=" O GLU C 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 3.701A pdb=" N VAL B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.687A pdb=" N VAL B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.554A pdb=" N ILE B 86 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 removed outlier: 3.741A pdb=" N VAL B 96 " --> pdb=" O HIS B 92 " (cutoff:3.500A) Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 127 through 146 Processing helix chain 'B' and resid 149 through 170 Processing helix chain 'B' and resid 176 through 193 removed outlier: 4.619A pdb=" N ILE B 184 " --> pdb=" O CYS B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.644A pdb=" N ALA B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.547A pdb=" N LEU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.974A pdb=" N PHE B 301 " --> pdb=" O PRO B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 301' Processing helix chain 'B' and resid 325 through 340 removed outlier: 3.566A pdb=" N LEU B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 359 removed outlier: 3.543A pdb=" N ASN B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.527A pdb=" N LEU B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 412 removed outlier: 3.621A pdb=" N VAL B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 412 " --> pdb=" O ASN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 448 removed outlier: 3.931A pdb=" N ALA B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 467 removed outlier: 3.658A pdb=" N LYS B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 496 Processing helix chain 'B' and resid 499 through 513 Proline residue: B 505 - end of helix removed outlier: 3.933A pdb=" N PHE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 563 through 584 removed outlier: 3.780A pdb=" N VAL B 583 " --> pdb=" O ALA B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 601 Processing helix chain 'B' and resid 612 through 627 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.816A pdb=" N ILE B 637 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 652 No H-bonds generated for 'chain 'B' and resid 650 through 652' Processing helix chain 'B' and resid 653 through 665 removed outlier: 3.750A pdb=" N ILE B 657 " --> pdb=" O ASP B 653 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 658 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS B 662 " --> pdb=" O ASP B 658 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 663 " --> pdb=" O GLN B 659 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE B 665 " --> pdb=" O GLY B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 686 Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' Processing helix chain 'B' and resid 705 through 718 removed outlier: 3.591A pdb=" N ILE B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 741 Processing helix chain 'B' and resid 770 through 779 removed outlier: 3.797A pdb=" N ILE B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 806 removed outlier: 3.641A pdb=" N GLN B 792 " --> pdb=" O LYS B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 830 removed outlier: 3.802A pdb=" N TYR B 820 " --> pdb=" O PRO B 816 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 823 " --> pdb=" O TRP B 819 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS B 824 " --> pdb=" O TYR B 820 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 826 " --> pdb=" O GLY B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 845 Processing helix chain 'B' and resid 858 through 873 Processing helix chain 'B' and resid 875 through 883 Processing helix chain 'B' and resid 886 through 907 removed outlier: 3.517A pdb=" N SER B 890 " --> pdb=" O ASP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 921 removed outlier: 3.518A pdb=" N MET B 916 " --> pdb=" O PHE B 913 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 917 " --> pdb=" O GLN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 928 removed outlier: 3.508A pdb=" N ASP B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 952 Processing helix chain 'B' and resid 957 through 974 removed outlier: 4.088A pdb=" N GLU B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 973 " --> pdb=" O GLN B 969 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 974 " --> pdb=" O PHE B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 977 No H-bonds generated for 'chain 'B' and resid 975 through 977' Processing helix chain 'B' and resid 980 through 997 removed outlier: 3.762A pdb=" N ARG B 984 " --> pdb=" O LYS B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1001 Processing helix chain 'B' and resid 1005 through 1021 Processing helix chain 'B' and resid 1046 through 1072 removed outlier: 3.542A pdb=" N ARG B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG B1060 " --> pdb=" O ASP B1056 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N CYS B1061 " --> pdb=" O PHE B1057 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY B1062 " --> pdb=" O ALA B1058 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP B1071 " --> pdb=" O GLU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1084 removed outlier: 3.854A pdb=" N THR B1076 " --> pdb=" O ALA B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1093 removed outlier: 3.836A pdb=" N TRP B1090 " --> pdb=" O LYS B1086 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B1091 " --> pdb=" O HIS B1087 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B1092 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1107 removed outlier: 3.649A pdb=" N ALA B1101 " --> pdb=" O HIS B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1111 Processing helix chain 'B' and resid 1136 through 1157 removed outlier: 3.512A pdb=" N MET B1140 " --> pdb=" O TYR B1136 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B1156 " --> pdb=" O GLU B1152 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B1157 " --> pdb=" O VAL B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1184 Processing helix chain 'B' and resid 1185 through 1202 removed outlier: 3.658A pdb=" N SER B1202 " --> pdb=" O ALA B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1216 removed outlier: 3.582A pdb=" N LEU B1211 " --> pdb=" O ASP B1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1221 Processing helix chain 'B' and resid 1224 through 1241 Processing helix chain 'B' and resid 1244 through 1263 removed outlier: 3.535A pdb=" N PHE B1248 " --> pdb=" O VAL B1244 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B1263 " --> pdb=" O THR B1259 " (cutoff:3.500A) Processing helix chain 'B' and resid 1275 through 1279 removed outlier: 3.776A pdb=" N ALA B1279 " --> pdb=" O PRO B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1294 through 1310 removed outlier: 3.614A pdb=" N TRP B1298 " --> pdb=" O PRO B1294 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B1299 " --> pdb=" O HIS B1295 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP B1300 " --> pdb=" O TYR B1296 " (cutoff:3.500A) Processing helix chain 'B' and resid 1315 through 1326 Processing helix chain 'B' and resid 1342 through 1345 Processing helix chain 'B' and resid 1346 through 1362 Processing helix chain 'B' and resid 1369 through 1384 removed outlier: 3.503A pdb=" N ASP B1384 " --> pdb=" O SER B1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1388 removed outlier: 4.123A pdb=" N CYS B1388 " --> pdb=" O TYR B1385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1385 through 1388' Processing helix chain 'B' and resid 1400 through 1416 Processing helix chain 'B' and resid 1478 through 1508 removed outlier: 3.889A pdb=" N ARG B1488 " --> pdb=" O TYR B1484 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN B1508 " --> pdb=" O ILE B1504 " (cutoff:3.500A) Processing helix chain 'B' and resid 1518 through 1533 removed outlier: 3.767A pdb=" N GLU B1522 " --> pdb=" O ASP B1518 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1551 removed outlier: 3.564A pdb=" N VAL B1544 " --> pdb=" O TRP B1540 " (cutoff:3.500A) Processing helix chain 'B' and resid 1551 through 1557 Processing helix chain 'B' and resid 1566 through 1579 Processing helix chain 'B' and resid 1580 through 1583 removed outlier: 3.664A pdb=" N VAL B1583 " --> pdb=" O PRO B1580 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1580 through 1583' Processing helix chain 'B' and resid 1585 through 1590 removed outlier: 3.528A pdb=" N ALA B1589 " --> pdb=" O ASP B1585 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B1590 " --> pdb=" O VAL B1586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1585 through 1590' Processing helix chain 'B' and resid 1591 through 1593 No H-bonds generated for 'chain 'B' and resid 1591 through 1593' Processing helix chain 'B' and resid 1616 through 1622 removed outlier: 3.506A pdb=" N SER B1622 " --> pdb=" O PRO B1618 " (cutoff:3.500A) Processing helix chain 'B' and resid 1623 through 1625 No H-bonds generated for 'chain 'B' and resid 1623 through 1625' Processing helix chain 'B' and resid 1631 through 1643 removed outlier: 3.534A pdb=" N ARG B1643 " --> pdb=" O VAL B1639 " (cutoff:3.500A) Processing helix chain 'B' and resid 1646 through 1653 removed outlier: 3.778A pdb=" N ILE B1650 " --> pdb=" O PRO B1646 " (cutoff:3.500A) Processing helix chain 'B' and resid 1653 through 1660 removed outlier: 3.818A pdb=" N ILE B1657 " --> pdb=" O TYR B1653 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B1658 " --> pdb=" O ILE B1654 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B1659 " --> pdb=" O PRO B1655 " (cutoff:3.500A) Processing helix chain 'B' and resid 1667 through 1680 Processing helix chain 'B' and resid 1681 through 1695 removed outlier: 3.510A pdb=" N HIS B1685 " --> pdb=" O GLN B1681 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR B1693 " --> pdb=" O TRP B1689 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B1694 " --> pdb=" O ASN B1690 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B1695 " --> pdb=" O MET B1691 " (cutoff:3.500A) Processing helix chain 'B' and resid 1708 through 1720 removed outlier: 3.522A pdb=" N THR B1720 " --> pdb=" O VAL B1716 " (cutoff:3.500A) Processing helix chain 'B' and resid 1725 through 1749 removed outlier: 4.485A pdb=" N VAL B1744 " --> pdb=" O LYS B1740 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER B1745 " --> pdb=" O ILE B1741 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA B1746 " --> pdb=" O THR B1742 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B1749 " --> pdb=" O SER B1745 " (cutoff:3.500A) Processing helix chain 'B' and resid 1754 through 1768 removed outlier: 3.567A pdb=" N LYS B1758 " --> pdb=" O GLY B1754 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B1768 " --> pdb=" O ALA B1764 " (cutoff:3.500A) Processing helix chain 'B' and resid 1814 through 1821 Processing helix chain 'B' and resid 1856 through 1876 Processing helix chain 'B' and resid 1904 through 1913 Processing helix chain 'B' and resid 1915 through 1925 Processing helix chain 'B' and resid 1929 through 1954 removed outlier: 3.851A pdb=" N GLN B1933 " --> pdb=" O THR B1929 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B1945 " --> pdb=" O ARG B1941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1997 through 2004 removed outlier: 3.567A pdb=" N VAL B2001 " --> pdb=" O THR B1997 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET B2004 " --> pdb=" O MET B2000 " (cutoff:3.500A) Processing helix chain 'B' and resid 2010 through 2028 removed outlier: 3.594A pdb=" N ARG B2028 " --> pdb=" O TYR B2024 " (cutoff:3.500A) Processing helix chain 'B' and resid 2030 through 2040 removed outlier: 3.842A pdb=" N VAL B2034 " --> pdb=" O TYR B2030 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B2040 " --> pdb=" O SER B2036 " (cutoff:3.500A) Processing helix chain 'B' and resid 2052 through 2060 Processing helix chain 'B' and resid 2066 through 2081 removed outlier: 3.916A pdb=" N CYS B2081 " --> pdb=" O VAL B2077 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 154 removed outlier: 3.986A pdb=" N LEU F 138 " --> pdb=" O PRO F 134 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS F 154 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 196 Processing helix chain 'F' and resid 217 through 233 removed outlier: 4.379A pdb=" N ALA F 225 " --> pdb=" O GLY F 221 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 247 Processing helix chain 'F' and resid 254 through 269 Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.668A pdb=" N TYR F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 342 removed outlier: 3.507A pdb=" N GLU F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG F 341 " --> pdb=" O SER F 337 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP F 342 " --> pdb=" O MET F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 375 removed outlier: 4.158A pdb=" N ARG F 375 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 389 removed outlier: 3.584A pdb=" N LEU F 382 " --> pdb=" O GLN F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 392 No H-bonds generated for 'chain 'F' and resid 390 through 392' Processing helix chain 'F' and resid 396 through 411 removed outlier: 3.838A pdb=" N TRP F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 410 " --> pdb=" O SER F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 427 Processing helix chain 'F' and resid 431 through 443 Processing helix chain 'F' and resid 448 through 461 removed outlier: 3.564A pdb=" N VAL F 461 " --> pdb=" O THR F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 486 removed outlier: 3.548A pdb=" N THR F 485 " --> pdb=" O SER F 481 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP F 486 " --> pdb=" O LEU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 511 removed outlier: 3.568A pdb=" N GLU F 494 " --> pdb=" O ARG F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 528 removed outlier: 3.761A pdb=" N ALA F 518 " --> pdb=" O ASP F 514 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE F 527 " --> pdb=" O LEU F 523 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER F 528 " --> pdb=" O GLN F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 545 removed outlier: 3.654A pdb=" N ALA F 534 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 562 removed outlier: 3.544A pdb=" N LEU F 552 " --> pdb=" O ASP F 548 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER F 560 " --> pdb=" O ALA F 556 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA F 561 " --> pdb=" O LEU F 557 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN F 562 " --> pdb=" O LEU F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 579 removed outlier: 3.588A pdb=" N ALA F 568 " --> pdb=" O HIS F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 removed outlier: 3.671A pdb=" N LEU F 595 " --> pdb=" O LYS F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 617 removed outlier: 3.824A pdb=" N ALA F 602 " --> pdb=" O GLY F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 708 removed outlier: 3.547A pdb=" N GLY F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 711 through 723 Processing helix chain 'F' and resid 729 through 744 removed outlier: 3.802A pdb=" N LEU F 733 " --> pdb=" O SER F 729 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY F 744 " --> pdb=" O ALA F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 758 removed outlier: 3.540A pdb=" N ARG F 751 " --> pdb=" O ASP F 747 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 776 removed outlier: 3.802A pdb=" N GLN F 776 " --> pdb=" O LEU F 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 794 Processing helix chain 'F' and resid 797 through 810 removed outlier: 3.677A pdb=" N TRP F 801 " --> pdb=" O ALA F 797 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 810 " --> pdb=" O GLU F 806 " (cutoff:3.500A) Processing helix chain 'F' and resid 813 through 829 removed outlier: 3.538A pdb=" N ALA F 829 " --> pdb=" O LEU F 825 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 839 Processing helix chain 'G' and resid 8 through 17 Processing helix chain 'G' and resid 36 through 46 Processing helix chain 'G' and resid 52 through 63 Processing helix chain 'G' and resid 68 through 76 removed outlier: 4.037A pdb=" N LEU G 72 " --> pdb=" O GLU G 68 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE G 74 " --> pdb=" O GLN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 90 removed outlier: 3.581A pdb=" N LEU G 82 " --> pdb=" O PHE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 114 Processing helix chain 'G' and resid 176 through 189 Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.740A pdb=" N LEU G 200 " --> pdb=" O PRO G 196 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG G 209 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N CYS G 211 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 222 removed outlier: 4.230A pdb=" N HIS G 219 " --> pdb=" O TYR G 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 248 removed outlier: 4.041A pdb=" N PHE G 246 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA G 247 " --> pdb=" O GLY G 243 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 271 Processing helix chain 'G' and resid 272 through 284 removed outlier: 3.528A pdb=" N ALA G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 727 through 736 removed outlier: 3.626A pdb=" N LEU H 731 " --> pdb=" O THR H 727 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP H 736 " --> pdb=" O LYS H 732 " (cutoff:3.500A) Processing helix chain 'H' and resid 742 through 756 removed outlier: 4.408A pdb=" N GLU H 746 " --> pdb=" O GLU H 742 " (cutoff:3.500A) Processing helix chain 'H' and resid 760 through 787 removed outlier: 3.737A pdb=" N ALA H 764 " --> pdb=" O PHE H 760 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA H 765 " --> pdb=" O GLU H 761 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE H 786 " --> pdb=" O LEU H 782 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG H 787 " --> pdb=" O GLU H 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.701A pdb=" N VAL A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 removed outlier: 3.688A pdb=" N VAL A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.554A pdb=" N ILE A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 106 removed outlier: 3.741A pdb=" N VAL A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 127 through 146 Processing helix chain 'A' and resid 149 through 170 Processing helix chain 'A' and resid 176 through 193 removed outlier: 4.617A pdb=" N ILE A 184 " --> pdb=" O CYS A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.645A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.547A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.974A pdb=" N PHE A 301 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 301' Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.566A pdb=" N LEU A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.542A pdb=" N ASN A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 385 removed outlier: 3.527A pdb=" N LEU A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 412 removed outlier: 3.621A pdb=" N VAL A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 412 " --> pdb=" O ASN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 448 removed outlier: 3.930A pdb=" N ALA A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 467 removed outlier: 3.659A pdb=" N LYS A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 496 Processing helix chain 'A' and resid 499 through 513 Proline residue: A 505 - end of helix removed outlier: 3.933A pdb=" N PHE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 Processing helix chain 'A' and resid 563 through 584 removed outlier: 3.780A pdb=" N VAL A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 601 Processing helix chain 'A' and resid 612 through 627 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.815A pdb=" N ILE A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 652 No H-bonds generated for 'chain 'A' and resid 650 through 652' Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.749A pdb=" N ILE A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP A 658 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 663 " --> pdb=" O GLN A 659 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 686 Processing helix chain 'A' and resid 702 through 704 No H-bonds generated for 'chain 'A' and resid 702 through 704' Processing helix chain 'A' and resid 705 through 718 removed outlier: 3.592A pdb=" N ILE A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 741 Processing helix chain 'A' and resid 770 through 779 removed outlier: 3.796A pdb=" N ILE A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 806 removed outlier: 3.641A pdb=" N GLN A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 830 removed outlier: 3.802A pdb=" N TYR A 820 " --> pdb=" O PRO A 816 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 823 " --> pdb=" O TRP A 819 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS A 824 " --> pdb=" O TYR A 820 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 845 Processing helix chain 'A' and resid 858 through 873 Processing helix chain 'A' and resid 875 through 883 Processing helix chain 'A' and resid 886 through 907 removed outlier: 3.518A pdb=" N SER A 890 " --> pdb=" O ASP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 921 removed outlier: 3.518A pdb=" N MET A 916 " --> pdb=" O PHE A 913 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 917 " --> pdb=" O GLN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 928 removed outlier: 3.507A pdb=" N ASP A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 952 Processing helix chain 'A' and resid 957 through 974 removed outlier: 4.087A pdb=" N GLU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 973 " --> pdb=" O GLN A 969 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 977 No H-bonds generated for 'chain 'A' and resid 975 through 977' Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.762A pdb=" N ARG A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1001 Processing helix chain 'A' and resid 1005 through 1021 Processing helix chain 'A' and resid 1046 through 1072 removed outlier: 3.542A pdb=" N ARG A1050 " --> pdb=" O THR A1046 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N CYS A1061 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY A1062 " --> pdb=" O ALA A1058 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1084 removed outlier: 3.854A pdb=" N THR A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1093 removed outlier: 3.836A pdb=" N TRP A1090 " --> pdb=" O LYS A1086 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A1091 " --> pdb=" O HIS A1087 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A1092 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1107 removed outlier: 3.648A pdb=" N ALA A1101 " --> pdb=" O HIS A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1111 Processing helix chain 'A' and resid 1136 through 1157 removed outlier: 3.512A pdb=" N MET A1140 " --> pdb=" O TYR A1136 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A1157 " --> pdb=" O VAL A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1184 Processing helix chain 'A' and resid 1185 through 1202 removed outlier: 3.657A pdb=" N SER A1202 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1216 removed outlier: 3.583A pdb=" N LEU A1211 " --> pdb=" O ASP A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 Processing helix chain 'A' and resid 1224 through 1241 Processing helix chain 'A' and resid 1244 through 1263 removed outlier: 3.534A pdb=" N PHE A1248 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1279 removed outlier: 3.775A pdb=" N ALA A1279 " --> pdb=" O PRO A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1310 removed outlier: 3.614A pdb=" N TRP A1298 " --> pdb=" O PRO A1294 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A1299 " --> pdb=" O HIS A1295 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A1300 " --> pdb=" O TYR A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1326 Processing helix chain 'A' and resid 1342 through 1345 Processing helix chain 'A' and resid 1346 through 1362 Processing helix chain 'A' and resid 1369 through 1384 removed outlier: 3.503A pdb=" N ASP A1384 " --> pdb=" O SER A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1388 removed outlier: 4.122A pdb=" N CYS A1388 " --> pdb=" O TYR A1385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1385 through 1388' Processing helix chain 'A' and resid 1400 through 1416 Processing helix chain 'A' and resid 1478 through 1508 removed outlier: 3.889A pdb=" N ARG A1488 " --> pdb=" O TYR A1484 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A1508 " --> pdb=" O ILE A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1533 removed outlier: 3.767A pdb=" N GLU A1522 " --> pdb=" O ASP A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1551 removed outlier: 3.564A pdb=" N VAL A1544 " --> pdb=" O TRP A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1557 Processing helix chain 'A' and resid 1566 through 1579 Processing helix chain 'A' and resid 1580 through 1583 removed outlier: 3.664A pdb=" N VAL A1583 " --> pdb=" O PRO A1580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1580 through 1583' Processing helix chain 'A' and resid 1585 through 1590 removed outlier: 3.527A pdb=" N ALA A1589 " --> pdb=" O ASP A1585 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A1590 " --> pdb=" O VAL A1586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1585 through 1590' Processing helix chain 'A' and resid 1591 through 1593 No H-bonds generated for 'chain 'A' and resid 1591 through 1593' Processing helix chain 'A' and resid 1616 through 1622 removed outlier: 3.507A pdb=" N SER A1622 " --> pdb=" O PRO A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1625 No H-bonds generated for 'chain 'A' and resid 1623 through 1625' Processing helix chain 'A' and resid 1631 through 1643 removed outlier: 3.533A pdb=" N ARG A1643 " --> pdb=" O VAL A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1653 removed outlier: 3.778A pdb=" N ILE A1650 " --> pdb=" O PRO A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1660 removed outlier: 3.818A pdb=" N ILE A1657 " --> pdb=" O TYR A1653 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A1658 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A1659 " --> pdb=" O PRO A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 Processing helix chain 'A' and resid 1681 through 1695 removed outlier: 3.509A pdb=" N HIS A1685 " --> pdb=" O GLN A1681 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A1693 " --> pdb=" O TRP A1689 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A1694 " --> pdb=" O ASN A1690 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A1695 " --> pdb=" O MET A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1720 removed outlier: 3.522A pdb=" N THR A1720 " --> pdb=" O VAL A1716 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1749 removed outlier: 4.485A pdb=" N VAL A1744 " --> pdb=" O LYS A1740 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER A1745 " --> pdb=" O ILE A1741 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA A1746 " --> pdb=" O THR A1742 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A1749 " --> pdb=" O SER A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1768 removed outlier: 3.566A pdb=" N LYS A1758 " --> pdb=" O GLY A1754 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A1768 " --> pdb=" O ALA A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1821 Processing helix chain 'A' and resid 1856 through 1876 Processing helix chain 'A' and resid 1904 through 1913 Processing helix chain 'A' and resid 1915 through 1925 Processing helix chain 'A' and resid 1929 through 1954 removed outlier: 3.850A pdb=" N GLN A1933 " --> pdb=" O THR A1929 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A1945 " --> pdb=" O ARG A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2004 removed outlier: 3.568A pdb=" N VAL A2001 " --> pdb=" O THR A1997 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A2004 " --> pdb=" O MET A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2028 removed outlier: 3.594A pdb=" N ARG A2028 " --> pdb=" O TYR A2024 " (cutoff:3.500A) Processing helix chain 'A' and resid 2030 through 2040 removed outlier: 3.841A pdb=" N VAL A2034 " --> pdb=" O TYR A2030 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A2040 " --> pdb=" O SER A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2060 Processing helix chain 'A' and resid 2066 through 2081 removed outlier: 3.917A pdb=" N CYS A2081 " --> pdb=" O VAL A2077 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 154 removed outlier: 3.987A pdb=" N LEU D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 196 Processing helix chain 'D' and resid 217 through 233 removed outlier: 4.379A pdb=" N ALA D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 247 Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.669A pdb=" N TYR D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 342 removed outlier: 3.507A pdb=" N GLU D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG D 341 " --> pdb=" O SER D 337 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP D 342 " --> pdb=" O MET D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 375 removed outlier: 4.158A pdb=" N ARG D 375 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 389 removed outlier: 3.584A pdb=" N LEU D 382 " --> pdb=" O GLN D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 392 No H-bonds generated for 'chain 'D' and resid 390 through 392' Processing helix chain 'D' and resid 396 through 411 removed outlier: 3.837A pdb=" N TRP D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 427 Processing helix chain 'D' and resid 431 through 443 Processing helix chain 'D' and resid 448 through 461 removed outlier: 3.564A pdb=" N VAL D 461 " --> pdb=" O THR D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 486 removed outlier: 3.548A pdb=" N THR D 485 " --> pdb=" O SER D 481 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 511 removed outlier: 3.568A pdb=" N GLU D 494 " --> pdb=" O ARG D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 528 removed outlier: 3.761A pdb=" N ALA D 518 " --> pdb=" O ASP D 514 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 545 removed outlier: 3.655A pdb=" N ALA D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 562 removed outlier: 3.544A pdb=" N LEU D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA D 561 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 579 removed outlier: 3.588A pdb=" N ALA D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 removed outlier: 3.672A pdb=" N LEU D 595 " --> pdb=" O LYS D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 617 removed outlier: 3.824A pdb=" N ALA D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 708 removed outlier: 3.546A pdb=" N GLY D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 723 Processing helix chain 'D' and resid 729 through 744 removed outlier: 3.802A pdb=" N LEU D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY D 744 " --> pdb=" O ALA D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 758 removed outlier: 3.540A pdb=" N ARG D 751 " --> pdb=" O ASP D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 776 removed outlier: 3.802A pdb=" N GLN D 776 " --> pdb=" O LEU D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 794 Processing helix chain 'D' and resid 797 through 810 removed outlier: 3.678A pdb=" N TRP D 801 " --> pdb=" O ALA D 797 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA D 810 " --> pdb=" O GLU D 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 829 removed outlier: 3.539A pdb=" N ALA D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'E' and resid 8 through 17 Processing helix chain 'E' and resid 36 through 46 Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 68 through 76 removed outlier: 4.036A pdb=" N LEU E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 90 removed outlier: 3.580A pdb=" N LEU E 82 " --> pdb=" O PHE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 114 Processing helix chain 'E' and resid 176 through 189 Processing helix chain 'E' and resid 196 through 211 removed outlier: 3.741A pdb=" N LEU E 200 " --> pdb=" O PRO E 196 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS E 211 " --> pdb=" O CYS E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 222 removed outlier: 4.230A pdb=" N HIS E 219 " --> pdb=" O TYR E 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 248 removed outlier: 4.042A pdb=" N PHE E 246 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA E 247 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 271 Processing helix chain 'E' and resid 272 through 284 removed outlier: 3.527A pdb=" N ALA E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 68 through 70 removed outlier: 6.391A pdb=" N PHE B 68 " --> pdb=" O TYR B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 1032 through 1033 Processing sheet with id=AA3, first strand: chain 'B' and resid 1782 through 1787 removed outlier: 7.253A pdb=" N LYS B1808 " --> pdb=" O LEU B1785 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE B1787 " --> pdb=" O LYS B1806 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N LYS B1806 " --> pdb=" O ILE B1787 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B1850 " --> pdb=" O GLY B1894 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS B1893 " --> pdb=" O THR B1889 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1964 through 1965 Processing sheet with id=AA5, first strand: chain 'G' and resid 123 through 125 removed outlier: 7.433A pdb=" N LEU G 123 " --> pdb=" O TYR G 162 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR G 162 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE G 125 " --> pdb=" O VAL G 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 68 through 70 removed outlier: 6.390A pdb=" N PHE A 68 " --> pdb=" O TYR A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1032 through 1033 Processing sheet with id=AA8, first strand: chain 'A' and resid 1782 through 1787 removed outlier: 7.253A pdb=" N LYS A1808 " --> pdb=" O LEU A1785 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE A1787 " --> pdb=" O LYS A1806 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LYS A1806 " --> pdb=" O ILE A1787 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A1850 " --> pdb=" O GLY A1894 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS A1893 " --> pdb=" O THR A1889 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1964 through 1965 Processing sheet with id=AB1, first strand: chain 'E' and resid 123 through 125 removed outlier: 7.432A pdb=" N LEU E 123 " --> pdb=" O TYR E 162 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR E 162 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 125 " --> pdb=" O VAL E 160 " (cutoff:3.500A) 2479 hydrogen bonds defined for protein. 7341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.66 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13462 1.34 - 1.46: 9465 1.46 - 1.58: 19633 1.58 - 1.70: 0 1.70 - 1.81: 430 Bond restraints: 42990 Sorted by residual: bond pdb=" C ASP A1417 " pdb=" O ASP A1417 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.34e-02 5.57e+03 2.02e+00 bond pdb=" C ASP B1417 " pdb=" O ASP B1417 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.34e-02 5.57e+03 1.98e+00 bond pdb=" C ILE A 612 " pdb=" N PRO A 613 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 9.28e-01 bond pdb=" C ILE A 771 " pdb=" N PRO A 772 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.36e-02 5.41e+03 8.93e-01 bond pdb=" C ILE B 612 " pdb=" N PRO B 613 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 8.87e-01 ... (remaining 42985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 57447 1.84 - 3.69: 566 3.69 - 5.53: 97 5.53 - 7.38: 42 7.38 - 9.22: 8 Bond angle restraints: 58160 Sorted by residual: angle pdb=" N LYS B1419 " pdb=" CA LYS B1419 " pdb=" C LYS B1419 " ideal model delta sigma weight residual 114.09 104.87 9.22 1.55e+00 4.16e-01 3.54e+01 angle pdb=" N LYS A1419 " pdb=" CA LYS A1419 " pdb=" C LYS A1419 " ideal model delta sigma weight residual 114.09 104.91 9.18 1.55e+00 4.16e-01 3.51e+01 angle pdb=" C LYS A1418 " pdb=" N LYS A1419 " pdb=" CA LYS A1419 " ideal model delta sigma weight residual 121.44 128.12 -6.68 1.59e+00 3.96e-01 1.76e+01 angle pdb=" C LYS B1418 " pdb=" N LYS B1419 " pdb=" CA LYS B1419 " ideal model delta sigma weight residual 121.44 128.07 -6.63 1.59e+00 3.96e-01 1.74e+01 angle pdb=" CA LYS A1419 " pdb=" C LYS A1419 " pdb=" N TYR A1420 " ideal model delta sigma weight residual 119.07 115.22 3.85 1.23e+00 6.61e-01 9.82e+00 ... (remaining 58155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 24519 18.00 - 35.99: 1259 35.99 - 53.99: 220 53.99 - 71.98: 34 71.98 - 89.98: 22 Dihedral angle restraints: 26054 sinusoidal: 10584 harmonic: 15470 Sorted by residual: dihedral pdb=" CA ASP E 115 " pdb=" C ASP E 115 " pdb=" N LYS E 116 " pdb=" CA LYS E 116 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP G 115 " pdb=" C ASP G 115 " pdb=" N LYS G 116 " pdb=" CA LYS G 116 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA THR E 193 " pdb=" C THR E 193 " pdb=" N TYR E 194 " pdb=" CA TYR E 194 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 26051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4381 0.028 - 0.056: 1451 0.056 - 0.085: 522 0.085 - 0.113: 190 0.113 - 0.141: 40 Chirality restraints: 6584 Sorted by residual: chirality pdb=" CA LEU E 79 " pdb=" N LEU E 79 " pdb=" C LEU E 79 " pdb=" CB LEU E 79 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA LEU G 79 " pdb=" N LEU G 79 " pdb=" C LEU G 79 " pdb=" CB LEU G 79 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL D 133 " pdb=" N VAL D 133 " pdb=" C VAL D 133 " pdb=" CB VAL D 133 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 6581 not shown) Planarity restraints: 7338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 348 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO F 349 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 349 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 349 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 348 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO D 349 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 349 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 349 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 391 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO A 392 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.020 5.00e-02 4.00e+02 ... (remaining 7335 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1952 2.73 - 3.27: 44200 3.27 - 3.82: 68468 3.82 - 4.36: 71946 4.36 - 4.90: 125245 Nonbonded interactions: 311811 Sorted by model distance: nonbonded pdb=" OD1 ASN B1372 " pdb=" OH TYR B1485 " model vdw 2.190 3.040 nonbonded pdb=" OD1 ASN A1372 " pdb=" OH TYR A1485 " model vdw 2.190 3.040 nonbonded pdb=" O LEU D 222 " pdb=" NH2 ARG D 241 " model vdw 2.206 3.120 nonbonded pdb=" O LEU F 222 " pdb=" NH2 ARG F 241 " model vdw 2.206 3.120 nonbonded pdb=" OH TYR E 86 " pdb=" N GLY E 99 " model vdw 2.235 3.120 ... (remaining 311806 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: 0.09 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'A' } ncs_group { reference = chain 'F' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.430 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: 0.040 Extract box with map and model: 0.970 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 56.130 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.002 0.034 42990 Z= 0.097 Angle : 0.503 9.219 58160 Z= 0.253 Chirality : 0.035 0.141 6584 Planarity : 0.003 0.042 7338 Dihedral : 11.256 89.978 15986 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 1.17 % Allowed : 7.55 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.71 (0.12), residues: 5120 helix: 2.29 (0.09), residues: 3436 sheet: 1.13 (0.70), residues: 62 loop : -1.51 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1733 TYR 0.016 0.001 TYR B1484 PHE 0.011 0.001 PHE A 64 TRP 0.007 0.001 TRP G 84 HIS 0.008 0.001 HIS G 58 Details of bonding type rmsd covalent geometry : bond 0.00184 (42990) covalent geometry : angle 0.50290 (58160) hydrogen bonds : bond 0.13823 ( 2479) hydrogen bonds : angle 4.10168 ( 7341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 454 time to evaluate : 1.701 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: 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: symmetry clash revert: symmetry clash REVERT: B 200 MET cc_start: 0.8239 (mmm) cc_final: 0.7538 (tpp) REVERT: B 385 LEU cc_start: 0.9418 (mp) cc_final: 0.8877 (tp) REVERT: B 634 MET cc_start: 0.8729 (mpp) cc_final: 0.8512 (mpp) REVERT: B 950 MET cc_start: 0.9035 (tmm) cc_final: 0.8785 (tmm) REVERT: B 1010 MET cc_start: 0.7996 (ppp) cc_final: 0.7684 (ppp) REVERT: B 1031 TYR cc_start: 0.9340 (m-80) cc_final: 0.9012 (m-80) REVERT: B 1063 MET cc_start: 0.8481 (tmm) cc_final: 0.8216 (tmm) REVERT: B 1172 MET cc_start: 0.8623 (mmm) cc_final: 0.8294 (ttp) REVERT: B 1414 MET cc_start: 0.9497 (tpp) cc_final: 0.9252 (tpt) REVERT: B 1916 MET cc_start: 0.8796 (mtp) cc_final: 0.8538 (mmm) REVERT: B 2002 MET cc_start: 0.9266 (tmm) cc_final: 0.9042 (tmm) REVERT: F 381 MET cc_start: 0.8985 (mmm) cc_final: 0.8664 (tpt) REVERT: F 476 LEU cc_start: 0.9279 (tp) cc_final: 0.9051 (tt) REVERT: F 558 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9106 (mm) REVERT: F 578 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8326 (tp30) REVERT: F 728 MET cc_start: 0.8797 (mmt) cc_final: 0.8534 (mmp) REVERT: G 73 GLN cc_start: 0.8472 (mt0) cc_final: 0.7590 (tm-30) REVERT: A 162 HIS cc_start: 0.9280 (m-70) cc_final: 0.9031 (m90) REVERT: A 200 MET cc_start: 0.8776 (mmm) cc_final: 0.8383 (mmt) REVERT: A 380 MET cc_start: 0.9354 (ppp) cc_final: 0.9054 (ppp) REVERT: A 444 LEU cc_start: 0.9192 (tp) cc_final: 0.8791 (pp) REVERT: A 445 MET cc_start: 0.8364 (ptp) cc_final: 0.7875 (ptm) REVERT: A 807 PHE cc_start: 0.9084 (m-10) cc_final: 0.8853 (m-10) REVERT: A 909 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8823 (t0) REVERT: A 1010 MET cc_start: 0.8320 (ppp) cc_final: 0.7992 (ppp) REVERT: A 1036 ASP cc_start: 0.8795 (m-30) cc_final: 0.8402 (t0) REVERT: A 1063 MET cc_start: 0.8493 (tmm) cc_final: 0.8232 (tmm) REVERT: A 1172 MET cc_start: 0.9049 (mmm) cc_final: 0.8785 (tmm) REVERT: A 1173 MET cc_start: 0.8968 (mmt) cc_final: 0.8720 (mmt) REVERT: A 1199 MET cc_start: 0.9341 (tmm) cc_final: 0.9079 (tmm) REVERT: A 1221 MET cc_start: 0.9007 (ttt) cc_final: 0.8755 (ttt) REVERT: A 1258 MET cc_start: 0.9195 (tmm) cc_final: 0.8815 (tmm) REVERT: A 1627 MET cc_start: 0.9472 (mtp) cc_final: 0.9177 (mtm) REVERT: A 1740 LYS cc_start: 0.9358 (mmtm) cc_final: 0.8951 (ttpt) REVERT: A 1964 MET cc_start: 0.7633 (tpt) cc_final: 0.7311 (tpt) REVERT: A 1965 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8156 (tt) REVERT: A 2002 MET cc_start: 0.8923 (tmm) cc_final: 0.8640 (tmm) REVERT: A 2008 MET cc_start: 0.7878 (pmm) cc_final: 0.7610 (mmm) REVERT: D 257 LEU cc_start: 0.9268 (mm) cc_final: 0.8919 (tp) REVERT: D 279 TRP cc_start: 0.9055 (p90) cc_final: 0.8841 (p90) REVERT: D 767 MET cc_start: 0.8690 (mtm) cc_final: 0.8138 (ptm) REVERT: E 137 HIS cc_start: 0.8029 (t70) cc_final: 0.7770 (t70) REVERT: E 229 ARG cc_start: 0.5910 (ptm160) cc_final: 0.5220 (mtt180) REVERT: E 262 ASP cc_start: 0.8899 (m-30) cc_final: 0.8636 (m-30) outliers start: 54 outliers final: 9 residues processed: 502 average time/residue: 0.2524 time to fit residues: 210.2632 Evaluate side-chains 326 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 313 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 913 PHE Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 913 PHE Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 0.6980 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN B 766 ASN B1029 GLN ** B1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1170 ASN B1304 GLN B1325 GLN B1539 GLN B1631 HIS B1681 GLN B1685 HIS B1690 ASN F 188 GLN F 276 GLN F 524 GLN F 545 GLN F 611 GLN G 49 GLN G 70 GLN G 218 GLN G 219 HIS A 91 GLN A1026 HIS ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN A1170 ASN A1304 GLN A1325 GLN A1539 GLN A1631 HIS A1685 HIS A1690 ASN D 188 GLN D 276 GLN D 515 HIS D 611 GLN E 49 GLN E 58 HIS E 70 GLN ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.071093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048294 restraints weight = 246618.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.049678 restraints weight = 123147.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050591 restraints weight = 81376.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051119 restraints weight = 62787.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051514 restraints weight = 53658.262| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 42990 Z= 0.207 Angle : 0.659 10.035 58160 Z= 0.330 Chirality : 0.040 0.224 6584 Planarity : 0.004 0.068 7338 Dihedral : 4.568 61.029 5691 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.47 % Favored : 94.51 % Rotamer: Outliers : 2.21 % Allowed : 9.96 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.68 (0.12), residues: 5120 helix: 2.25 (0.09), residues: 3472 sheet: 1.23 (0.73), residues: 62 loop : -1.58 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 748 TYR 0.022 0.002 TYR D 579 PHE 0.028 0.002 PHE E 63 TRP 0.020 0.002 TRP B1990 HIS 0.010 0.001 HIS E 58 Details of bonding type rmsd covalent geometry : bond 0.00461 (42990) covalent geometry : angle 0.65875 (58160) hydrogen bonds : bond 0.04563 ( 2479) hydrogen bonds : angle 3.94984 ( 7341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 341 time to evaluate : 1.752 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 TYR cc_start: 0.7646 (p90) cc_final: 0.7145 (p90) REVERT: B 200 MET cc_start: 0.7957 (mmm) cc_final: 0.7611 (tpp) REVERT: B 334 ASN cc_start: 0.9440 (t0) cc_final: 0.9188 (m-40) REVERT: B 385 LEU cc_start: 0.9482 (mp) cc_final: 0.8954 (tp) REVERT: B 402 PHE cc_start: 0.9521 (m-80) cc_final: 0.8792 (m-80) REVERT: B 634 MET cc_start: 0.8981 (mpp) cc_final: 0.8743 (mpp) REVERT: B 805 MET cc_start: 0.8766 (tpp) cc_final: 0.8535 (tpp) REVERT: B 916 MET cc_start: 0.8291 (tpp) cc_final: 0.8047 (tpp) REVERT: B 950 MET cc_start: 0.9194 (tmm) cc_final: 0.8915 (tmm) REVERT: B 1063 MET cc_start: 0.8471 (tmm) cc_final: 0.8191 (tmm) REVERT: B 1414 MET cc_start: 0.9511 (tpp) cc_final: 0.9211 (tpt) REVERT: B 1417 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8337 (t0) REVERT: B 1575 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9147 (tt) REVERT: B 1671 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8371 (pp20) REVERT: F 578 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8434 (tp30) REVERT: G 63 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8642 (m-10) REVERT: G 184 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8185 (pp) REVERT: A 162 HIS cc_start: 0.9233 (m-70) cc_final: 0.9008 (m-70) REVERT: A 200 MET cc_start: 0.8952 (mmm) cc_final: 0.8536 (mmt) REVERT: A 377 MET cc_start: 0.9642 (mmm) cc_final: 0.9402 (mmm) REVERT: A 380 MET cc_start: 0.9439 (ppp) cc_final: 0.9160 (ppp) REVERT: A 807 PHE cc_start: 0.9045 (m-10) cc_final: 0.8739 (m-10) REVERT: A 1010 MET cc_start: 0.8547 (ppp) cc_final: 0.8189 (ppp) REVERT: A 1063 MET cc_start: 0.8405 (tmm) cc_final: 0.8160 (tmm) REVERT: A 1173 MET cc_start: 0.9185 (mmt) cc_final: 0.8403 (mmt) REVERT: A 1199 MET cc_start: 0.9353 (tmm) cc_final: 0.9026 (tmm) REVERT: A 1258 MET cc_start: 0.9221 (tmm) cc_final: 0.8796 (tmm) REVERT: A 1296 TYR cc_start: 0.8483 (t80) cc_final: 0.8268 (t80) REVERT: A 1539 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: A 1965 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8292 (tt) REVERT: A 2002 MET cc_start: 0.8978 (tmm) cc_final: 0.8695 (tmm) REVERT: A 2017 MET cc_start: 0.9168 (tpp) cc_final: 0.8647 (tpt) REVERT: D 257 LEU cc_start: 0.9302 (mm) cc_final: 0.8968 (tp) REVERT: D 279 TRP cc_start: 0.9095 (p90) cc_final: 0.8853 (p90) REVERT: D 789 ASP cc_start: 0.9358 (m-30) cc_final: 0.9141 (m-30) REVERT: E 60 LEU cc_start: 0.9455 (mt) cc_final: 0.9005 (mm) REVERT: E 64 TYR cc_start: 0.8237 (m-80) cc_final: 0.7775 (m-80) REVERT: E 75 THR cc_start: 0.7744 (p) cc_final: 0.7523 (t) REVERT: E 137 HIS cc_start: 0.8281 (t70) cc_final: 0.7860 (t70) REVERT: E 229 ARG cc_start: 0.6284 (ptm160) cc_final: 0.5363 (mtt180) REVERT: E 262 ASP cc_start: 0.9316 (m-30) cc_final: 0.8969 (m-30) outliers start: 102 outliers final: 39 residues processed: 423 average time/residue: 0.2333 time to fit residues: 169.2605 Evaluate side-chains 342 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 296 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 1260 VAL Chi-restraints excluded: chain B residue 1308 ILE Chi-restraints excluded: chain B residue 1417 ASP Chi-restraints excluded: chain B residue 1539 GLN Chi-restraints excluded: chain B residue 1556 VAL Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1594 VAL Chi-restraints excluded: chain B residue 1611 CYS Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1755 ASP Chi-restraints excluded: chain B residue 1761 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1663 TYR Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 237 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 499 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 183 optimal weight: 0.0980 chunk 143 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 494 optimal weight: 0.4980 chunk 402 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 508 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 184 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN B 766 ASN B1114 ASN B1295 HIS B1325 GLN B1527 ASN B1539 GLN B1694 ASN B1739 ASN A 732 ASN A1096 GLN A1694 ASN D 170 GLN D 545 GLN E 218 GLN E 219 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.072671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.049938 restraints weight = 244456.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051383 restraints weight = 120607.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.052332 restraints weight = 79117.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052938 restraints weight = 60867.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.053313 restraints weight = 51691.581| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 42990 Z= 0.106 Angle : 0.565 12.945 58160 Z= 0.273 Chirality : 0.037 0.158 6584 Planarity : 0.003 0.050 7338 Dihedral : 4.133 65.669 5679 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 1.95 % Allowed : 11.05 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.84 (0.13), residues: 5120 helix: 2.35 (0.09), residues: 3482 sheet: 2.93 (0.89), residues: 42 loop : -1.52 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 221 TYR 0.015 0.001 TYR B 670 PHE 0.024 0.001 PHE C 760 TRP 0.020 0.001 TRP E 12 HIS 0.010 0.001 HIS E 58 Details of bonding type rmsd covalent geometry : bond 0.00221 (42990) covalent geometry : angle 0.56500 (58160) hydrogen bonds : bond 0.03757 ( 2479) hydrogen bonds : angle 3.51789 ( 7341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 313 time to evaluate : 1.788 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.9183 (ttp80) cc_final: 0.8799 (ttp80) REVERT: B 83 ILE cc_start: 0.9377 (tp) cc_final: 0.9141 (mt) REVERT: B 197 TYR cc_start: 0.7608 (p90) cc_final: 0.7135 (p90) REVERT: B 200 MET cc_start: 0.8040 (mmm) cc_final: 0.7679 (tpp) REVERT: B 334 ASN cc_start: 0.9453 (t0) cc_final: 0.9189 (m-40) REVERT: B 385 LEU cc_start: 0.9466 (mp) cc_final: 0.8990 (tp) REVERT: B 402 PHE cc_start: 0.9430 (m-80) cc_final: 0.8793 (m-80) REVERT: B 805 MET cc_start: 0.8743 (tpp) cc_final: 0.8527 (tpp) REVERT: B 916 MET cc_start: 0.8390 (tpp) cc_final: 0.8123 (tpp) REVERT: B 950 MET cc_start: 0.9183 (tmm) cc_final: 0.8961 (tmm) REVERT: B 1010 MET cc_start: 0.8096 (ppp) cc_final: 0.7878 (ppp) REVERT: B 1063 MET cc_start: 0.8459 (tmm) cc_final: 0.8151 (tmm) REVERT: B 1414 MET cc_start: 0.9536 (tpp) cc_final: 0.9264 (tpt) REVERT: B 1417 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8133 (t0) REVERT: B 1671 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8319 (pp20) REVERT: B 2065 MET cc_start: 0.8530 (mtp) cc_final: 0.7831 (ttm) REVERT: F 269 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9131 (mt) REVERT: F 578 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8338 (tp30) REVERT: G 184 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8169 (pp) REVERT: A 162 HIS cc_start: 0.9253 (m-70) cc_final: 0.9039 (m-70) REVERT: A 200 MET cc_start: 0.8967 (mmm) cc_final: 0.8555 (mmt) REVERT: A 377 MET cc_start: 0.9599 (mmm) cc_final: 0.9392 (mmm) REVERT: A 380 MET cc_start: 0.9445 (ppp) cc_final: 0.9103 (ppp) REVERT: A 807 PHE cc_start: 0.9020 (m-10) cc_final: 0.8685 (m-10) REVERT: A 1010 MET cc_start: 0.8496 (ppp) cc_final: 0.8136 (ppp) REVERT: A 1063 MET cc_start: 0.8396 (tmm) cc_final: 0.8140 (tmm) REVERT: A 1172 MET cc_start: 0.7631 (tmm) cc_final: 0.7417 (tmm) REVERT: A 1173 MET cc_start: 0.9135 (mmt) cc_final: 0.8732 (mmt) REVERT: A 1199 MET cc_start: 0.9378 (tmm) cc_final: 0.9012 (tmm) REVERT: A 1258 MET cc_start: 0.9194 (tmm) cc_final: 0.8803 (tmm) REVERT: A 1539 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: A 1920 PHE cc_start: 0.9571 (OUTLIER) cc_final: 0.9277 (t80) REVERT: A 1964 MET cc_start: 0.7417 (tpp) cc_final: 0.6962 (tpp) REVERT: A 1965 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8159 (tt) REVERT: A 2002 MET cc_start: 0.9021 (tmm) cc_final: 0.8747 (tmm) REVERT: A 2017 MET cc_start: 0.9082 (tpp) cc_final: 0.8561 (tpt) REVERT: D 257 LEU cc_start: 0.9304 (mm) cc_final: 0.9004 (tp) REVERT: D 279 TRP cc_start: 0.9036 (p90) cc_final: 0.8797 (p90) REVERT: D 767 MET cc_start: 0.8759 (mtm) cc_final: 0.8247 (ptm) REVERT: E 60 LEU cc_start: 0.9469 (mt) cc_final: 0.9044 (mm) REVERT: E 64 TYR cc_start: 0.8300 (m-80) cc_final: 0.7910 (m-80) REVERT: E 137 HIS cc_start: 0.8327 (t70) cc_final: 0.7912 (t70) REVERT: E 229 ARG cc_start: 0.6264 (ptm160) cc_final: 0.5389 (mtt180) REVERT: E 262 ASP cc_start: 0.9301 (m-30) cc_final: 0.9003 (m-30) outliers start: 90 outliers final: 40 residues processed: 389 average time/residue: 0.2340 time to fit residues: 155.5999 Evaluate side-chains 336 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 289 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 913 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1417 ASP Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1755 ASP Chi-restraints excluded: chain B residue 1761 CYS Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain B residue 2000 MET Chi-restraints excluded: chain F residue 186 TYR Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 731 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 913 PHE Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1328 MET Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1663 TYR Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 242 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 450 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 364 optimal weight: 6.9990 chunk 301 optimal weight: 0.2980 chunk 357 optimal weight: 6.9990 chunk 381 optimal weight: 5.9990 chunk 449 optimal weight: 10.0000 chunk 489 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN B1508 ASN F 515 HIS F 802 ASN ** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1170 ASN A1361 HIS ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1694 ASN E 218 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.073558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050004 restraints weight = 231098.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.051279 restraints weight = 121724.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.052083 restraints weight = 83345.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.052622 restraints weight = 66289.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052889 restraints weight = 57553.073| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 42990 Z= 0.171 Angle : 0.617 14.224 58160 Z= 0.303 Chirality : 0.039 0.221 6584 Planarity : 0.004 0.049 7338 Dihedral : 4.250 64.051 5679 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.37 % Favored : 94.61 % Rotamer: Outliers : 2.21 % Allowed : 11.39 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.71 (0.12), residues: 5120 helix: 2.27 (0.09), residues: 3484 sheet: 2.52 (0.84), residues: 42 loop : -1.61 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 777 TYR 0.015 0.001 TYR B 670 PHE 0.020 0.002 PHE B 591 TRP 0.025 0.001 TRP B1990 HIS 0.008 0.001 HIS G 58 Details of bonding type rmsd covalent geometry : bond 0.00384 (42990) covalent geometry : angle 0.61680 (58160) hydrogen bonds : bond 0.04380 ( 2479) hydrogen bonds : angle 3.73158 ( 7341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 303 time to evaluate : 1.767 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.9230 (ttp80) cc_final: 0.8849 (ttp80) REVERT: B 83 ILE cc_start: 0.9417 (tp) cc_final: 0.9198 (mt) REVERT: B 197 TYR cc_start: 0.7545 (p90) cc_final: 0.7154 (p90) REVERT: B 200 MET cc_start: 0.7949 (mmm) cc_final: 0.7552 (tpp) REVERT: B 334 ASN cc_start: 0.9461 (t0) cc_final: 0.9207 (m-40) REVERT: B 385 LEU cc_start: 0.9449 (mp) cc_final: 0.8970 (tp) REVERT: B 402 PHE cc_start: 0.9480 (m-80) cc_final: 0.8849 (m-80) REVERT: B 916 MET cc_start: 0.8546 (tpp) cc_final: 0.8235 (tpp) REVERT: B 1010 MET cc_start: 0.8243 (ppp) cc_final: 0.7996 (ppp) REVERT: B 1063 MET cc_start: 0.8527 (tmm) cc_final: 0.8231 (tmm) REVERT: B 1414 MET cc_start: 0.9560 (tpp) cc_final: 0.9359 (tpp) REVERT: B 1417 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8242 (t0) REVERT: B 1666 MET cc_start: 0.7571 (mmm) cc_final: 0.6868 (mmm) REVERT: B 1927 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8294 (pp20) REVERT: F 259 MET cc_start: 0.9251 (mmt) cc_final: 0.8713 (mmm) REVERT: F 347 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6905 (tpt90) REVERT: F 380 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: F 396 GLU cc_start: 0.7632 (mp0) cc_final: 0.7395 (mp0) REVERT: F 578 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8333 (tp30) REVERT: G 63 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8620 (m-10) REVERT: G 184 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8211 (pp) REVERT: G 237 MET cc_start: 0.8196 (mmm) cc_final: 0.7977 (mmm) REVERT: A 200 MET cc_start: 0.9014 (mmm) cc_final: 0.8645 (mmt) REVERT: A 377 MET cc_start: 0.9586 (mmm) cc_final: 0.9344 (mmm) REVERT: A 380 MET cc_start: 0.9465 (ppp) cc_final: 0.9158 (ppp) REVERT: A 807 PHE cc_start: 0.9072 (m-10) cc_final: 0.8753 (m-10) REVERT: A 1010 MET cc_start: 0.8642 (ppp) cc_final: 0.8255 (ppp) REVERT: A 1063 MET cc_start: 0.8414 (tmm) cc_final: 0.8147 (tmm) REVERT: A 1172 MET cc_start: 0.7672 (tmm) cc_final: 0.7395 (tmm) REVERT: A 1173 MET cc_start: 0.9175 (mmt) cc_final: 0.8708 (mmt) REVERT: A 1199 MET cc_start: 0.9416 (tmm) cc_final: 0.9053 (tmm) REVERT: A 1258 MET cc_start: 0.9238 (tmm) cc_final: 0.8748 (tmm) REVERT: A 1920 PHE cc_start: 0.9611 (OUTLIER) cc_final: 0.9310 (t80) REVERT: A 1965 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8249 (tt) REVERT: A 2002 MET cc_start: 0.8972 (tmm) cc_final: 0.8700 (tmm) REVERT: A 2017 MET cc_start: 0.9157 (tpp) cc_final: 0.8633 (tpt) REVERT: D 257 LEU cc_start: 0.9295 (mm) cc_final: 0.8988 (tp) REVERT: D 279 TRP cc_start: 0.9101 (p90) cc_final: 0.8848 (p90) REVERT: D 789 ASP cc_start: 0.9399 (m-30) cc_final: 0.9193 (m-30) REVERT: E 60 LEU cc_start: 0.9459 (mt) cc_final: 0.9021 (mt) REVERT: E 64 TYR cc_start: 0.8441 (m-80) cc_final: 0.8027 (m-80) REVERT: E 137 HIS cc_start: 0.8258 (t70) cc_final: 0.7910 (t70) REVERT: E 229 ARG cc_start: 0.6538 (ptm160) cc_final: 0.5549 (mtt180) REVERT: E 262 ASP cc_start: 0.9353 (m-30) cc_final: 0.9012 (m-30) outliers start: 102 outliers final: 55 residues processed: 392 average time/residue: 0.2388 time to fit residues: 160.3851 Evaluate side-chains 355 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 291 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1260 VAL Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1308 ILE Chi-restraints excluded: chain B residue 1417 ASP Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1594 VAL Chi-restraints excluded: chain B residue 1611 CYS Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1679 LYS Chi-restraints excluded: chain B residue 1755 ASP Chi-restraints excluded: chain B residue 1761 CYS Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain F residue 186 TYR Chi-restraints excluded: chain F residue 229 TYR Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain G residue 57 CYS Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 731 LEU Chi-restraints excluded: chain H residue 735 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1328 MET Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1663 TYR Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 242 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 328 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 373 optimal weight: 4.9990 chunk 462 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 337 optimal weight: 4.9990 chunk 461 optimal weight: 0.7980 chunk 176 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 GLN A1694 ASN E 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.071905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.049163 restraints weight = 244201.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.050580 restraints weight = 121038.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051518 restraints weight = 79745.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.052110 restraints weight = 61479.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.052456 restraints weight = 52350.440| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 42990 Z= 0.102 Angle : 0.574 12.489 58160 Z= 0.275 Chirality : 0.037 0.211 6584 Planarity : 0.003 0.053 7338 Dihedral : 4.147 66.181 5679 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.51 % Favored : 95.47 % Rotamer: Outliers : 2.00 % Allowed : 12.20 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.82 (0.12), residues: 5120 helix: 2.34 (0.09), residues: 3490 sheet: 2.88 (0.84), residues: 42 loop : -1.56 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 748 TYR 0.015 0.001 TYR B 670 PHE 0.021 0.001 PHE B 131 TRP 0.027 0.001 TRP B1990 HIS 0.016 0.001 HIS G 58 Details of bonding type rmsd covalent geometry : bond 0.00214 (42990) covalent geometry : angle 0.57363 (58160) hydrogen bonds : bond 0.03576 ( 2479) hydrogen bonds : angle 3.41684 ( 7341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 304 time to evaluate : 1.682 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.9214 (ttp80) cc_final: 0.8859 (ttp80) REVERT: B 56 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9197 (tt) REVERT: B 83 ILE cc_start: 0.9372 (tp) cc_final: 0.9156 (mt) REVERT: B 197 TYR cc_start: 0.7545 (p90) cc_final: 0.7137 (p90) REVERT: B 200 MET cc_start: 0.8034 (mmm) cc_final: 0.7701 (tpp) REVERT: B 334 ASN cc_start: 0.9448 (t0) cc_final: 0.9217 (m-40) REVERT: B 385 LEU cc_start: 0.9436 (mp) cc_final: 0.8932 (tp) REVERT: B 402 PHE cc_start: 0.9469 (m-80) cc_final: 0.8811 (m-80) REVERT: B 634 MET cc_start: 0.8996 (mpp) cc_final: 0.8723 (mpp) REVERT: B 916 MET cc_start: 0.8547 (tpp) cc_final: 0.8259 (tpp) REVERT: B 1010 MET cc_start: 0.8201 (ppp) cc_final: 0.7937 (ppp) REVERT: B 1063 MET cc_start: 0.8559 (tmm) cc_final: 0.8244 (tmm) REVERT: B 1173 MET cc_start: 0.9470 (mmp) cc_final: 0.9142 (mmp) REVERT: B 1414 MET cc_start: 0.9573 (tpp) cc_final: 0.9214 (tpt) REVERT: B 1927 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8538 (pm20) REVERT: B 2002 MET cc_start: 0.9126 (tmm) cc_final: 0.8922 (tmm) REVERT: F 259 MET cc_start: 0.9235 (mmt) cc_final: 0.8651 (mmm) REVERT: F 269 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9151 (mt) REVERT: F 396 GLU cc_start: 0.7624 (mp0) cc_final: 0.7135 (mp0) REVERT: F 578 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8245 (tp30) REVERT: G 63 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8572 (m-10) REVERT: G 184 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8138 (pp) REVERT: G 237 MET cc_start: 0.8227 (mmm) cc_final: 0.8015 (mmm) REVERT: A 200 MET cc_start: 0.9071 (mmm) cc_final: 0.8653 (mmt) REVERT: A 380 MET cc_start: 0.9441 (ppp) cc_final: 0.9141 (ppp) REVERT: A 807 PHE cc_start: 0.9067 (m-10) cc_final: 0.8737 (m-10) REVERT: A 1010 MET cc_start: 0.8611 (ppp) cc_final: 0.8219 (ppp) REVERT: A 1063 MET cc_start: 0.8417 (tmm) cc_final: 0.8138 (tmm) REVERT: A 1172 MET cc_start: 0.7695 (tmm) cc_final: 0.7468 (tmm) REVERT: A 1173 MET cc_start: 0.9121 (mmt) cc_final: 0.8705 (mmt) REVERT: A 1258 MET cc_start: 0.9277 (tmm) cc_final: 0.8824 (tmm) REVERT: A 1666 MET cc_start: 0.7813 (mmm) cc_final: 0.7509 (mmm) REVERT: A 1920 PHE cc_start: 0.9610 (OUTLIER) cc_final: 0.9305 (t80) REVERT: A 1964 MET cc_start: 0.7423 (tpp) cc_final: 0.7128 (tpp) REVERT: A 1965 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8201 (tt) REVERT: A 2002 MET cc_start: 0.9024 (tmm) cc_final: 0.8762 (tmm) REVERT: A 2017 MET cc_start: 0.9084 (tpp) cc_final: 0.8570 (tpt) REVERT: D 257 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8983 (tp) REVERT: D 279 TRP cc_start: 0.9037 (p90) cc_final: 0.8775 (p90) REVERT: D 789 ASP cc_start: 0.9373 (m-30) cc_final: 0.9143 (m-30) REVERT: E 60 LEU cc_start: 0.9463 (mt) cc_final: 0.9054 (mm) REVERT: E 64 TYR cc_start: 0.8508 (m-80) cc_final: 0.8112 (m-80) REVERT: E 229 ARG cc_start: 0.6521 (ptm160) cc_final: 0.5565 (mtt180) REVERT: E 262 ASP cc_start: 0.9354 (m-30) cc_final: 0.8984 (m-30) outliers start: 92 outliers final: 47 residues processed: 385 average time/residue: 0.2333 time to fit residues: 153.3103 Evaluate side-chains 345 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 913 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1308 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1761 CYS Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain F residue 186 TYR Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain G residue 57 CYS Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 913 PHE Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1663 TYR Chi-restraints excluded: chain A residue 1694 ASN Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 242 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 65 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 490 optimal weight: 0.4980 chunk 296 optimal weight: 5.9990 chunk 349 optimal weight: 0.7980 chunk 353 optimal weight: 4.9990 chunk 302 optimal weight: 8.9990 chunk 383 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 434 optimal weight: 3.9990 chunk 432 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS B 766 ASN ** B1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1482 HIS B1539 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS E 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.070595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.047815 restraints weight = 248188.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.049193 restraints weight = 124401.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.050101 restraints weight = 82562.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.050642 restraints weight = 63978.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051022 restraints weight = 54776.137| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42990 Z= 0.147 Angle : 0.599 13.146 58160 Z= 0.290 Chirality : 0.038 0.248 6584 Planarity : 0.004 0.056 7338 Dihedral : 4.187 64.277 5679 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 2.00 % Allowed : 13.00 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.80 (0.12), residues: 5120 helix: 2.32 (0.09), residues: 3500 sheet: 2.67 (0.83), residues: 42 loop : -1.58 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 748 TYR 0.015 0.001 TYR B 670 PHE 0.027 0.001 PHE D 397 TRP 0.029 0.001 TRP B1990 HIS 0.013 0.001 HIS E 58 Details of bonding type rmsd covalent geometry : bond 0.00331 (42990) covalent geometry : angle 0.59913 (58160) hydrogen bonds : bond 0.03902 ( 2479) hydrogen bonds : angle 3.55438 ( 7341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 294 time to evaluate : 1.930 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.9226 (ttp80) cc_final: 0.8882 (ttp80) REVERT: B 83 ILE cc_start: 0.9386 (tp) cc_final: 0.9174 (mt) REVERT: B 197 TYR cc_start: 0.7566 (p90) cc_final: 0.7172 (p90) REVERT: B 200 MET cc_start: 0.7984 (mmm) cc_final: 0.7664 (tpp) REVERT: B 334 ASN cc_start: 0.9482 (t0) cc_final: 0.9230 (m-40) REVERT: B 377 MET cc_start: 0.8792 (ptt) cc_final: 0.8427 (ppp) REVERT: B 385 LEU cc_start: 0.9433 (mp) cc_final: 0.8942 (tp) REVERT: B 402 PHE cc_start: 0.9500 (m-80) cc_final: 0.8819 (m-80) REVERT: B 634 MET cc_start: 0.8981 (mpp) cc_final: 0.8725 (mpp) REVERT: B 916 MET cc_start: 0.8654 (tpp) cc_final: 0.8335 (tpp) REVERT: B 1063 MET cc_start: 0.8584 (tmm) cc_final: 0.8291 (tmm) REVERT: B 1173 MET cc_start: 0.9464 (mmp) cc_final: 0.9120 (mmp) REVERT: B 1927 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: B 1979 MET cc_start: 0.8813 (ppp) cc_final: 0.8605 (ppp) REVERT: F 259 MET cc_start: 0.9282 (mmt) cc_final: 0.8711 (mmm) REVERT: F 269 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9150 (mt) REVERT: F 396 GLU cc_start: 0.7681 (mp0) cc_final: 0.7145 (mp0) REVERT: F 578 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: G 63 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8619 (m-10) REVERT: G 184 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8142 (pp) REVERT: A 200 MET cc_start: 0.9127 (mmm) cc_final: 0.8730 (mmt) REVERT: A 380 MET cc_start: 0.9453 (ppp) cc_final: 0.9137 (ppp) REVERT: A 807 PHE cc_start: 0.9048 (m-10) cc_final: 0.8729 (m-10) REVERT: A 1010 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8225 (ppp) REVERT: A 1063 MET cc_start: 0.8429 (tmm) cc_final: 0.8174 (tmm) REVERT: A 1172 MET cc_start: 0.7737 (tmm) cc_final: 0.7484 (tmm) REVERT: A 1173 MET cc_start: 0.9130 (mmt) cc_final: 0.8693 (mmt) REVERT: A 1258 MET cc_start: 0.9291 (tmm) cc_final: 0.8840 (tmm) REVERT: A 1666 MET cc_start: 0.7907 (mmm) cc_final: 0.7707 (mmm) REVERT: A 1920 PHE cc_start: 0.9608 (OUTLIER) cc_final: 0.9289 (t80) REVERT: A 1964 MET cc_start: 0.7400 (tpp) cc_final: 0.7100 (tpp) REVERT: A 1965 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8217 (tt) REVERT: A 2002 MET cc_start: 0.9000 (tmm) cc_final: 0.8733 (tmm) REVERT: A 2017 MET cc_start: 0.9151 (tpp) cc_final: 0.8636 (tpt) REVERT: D 257 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8972 (tp) REVERT: D 279 TRP cc_start: 0.9081 (p90) cc_final: 0.8810 (p90) REVERT: E 60 LEU cc_start: 0.9472 (mt) cc_final: 0.9049 (mt) REVERT: E 64 TYR cc_start: 0.8480 (m-80) cc_final: 0.8122 (m-80) REVERT: E 229 ARG cc_start: 0.6572 (ptm160) cc_final: 0.5609 (mtt180) REVERT: E 262 ASP cc_start: 0.9358 (m-30) cc_final: 0.8994 (m-30) outliers start: 92 outliers final: 57 residues processed: 374 average time/residue: 0.2386 time to fit residues: 152.1274 Evaluate side-chains 351 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 285 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1308 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1556 VAL Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1761 CYS Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain F residue 186 TYR Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain G residue 57 CYS Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 731 LEU Chi-restraints excluded: chain H residue 735 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 913 PHE Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1328 MET Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1663 TYR Chi-restraints excluded: chain A residue 1768 VAL Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 58 HIS Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 242 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 421 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 313 optimal weight: 2.9990 chunk 456 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 360 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** B1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 811 GLN A1539 GLN A1739 ASN D 811 GLN E 58 HIS E 218 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.070059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.047295 restraints weight = 246595.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.048660 restraints weight = 124405.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.049549 restraints weight = 82630.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.050107 restraints weight = 64212.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.050413 restraints weight = 54996.340| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 42990 Z= 0.162 Angle : 0.624 15.050 58160 Z= 0.303 Chirality : 0.038 0.273 6584 Planarity : 0.004 0.056 7338 Dihedral : 4.235 65.160 5677 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 2.24 % Allowed : 13.06 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.74 (0.12), residues: 5120 helix: 2.28 (0.09), residues: 3494 sheet: 1.25 (0.71), residues: 62 loop : -1.59 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 347 TYR 0.023 0.001 TYR B 600 PHE 0.030 0.001 PHE D 397 TRP 0.028 0.001 TRP B 676 HIS 0.029 0.001 HIS E 58 Details of bonding type rmsd covalent geometry : bond 0.00364 (42990) covalent geometry : angle 0.62391 (58160) hydrogen bonds : bond 0.04130 ( 2479) hydrogen bonds : angle 3.63682 ( 7341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 297 time to evaluate : 1.878 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: symmetry clash REVERT: B 40 ARG cc_start: 0.9230 (ttp80) cc_final: 0.8910 (ttp80) REVERT: B 83 ILE cc_start: 0.9381 (tp) cc_final: 0.9163 (mt) REVERT: B 197 TYR cc_start: 0.7555 (p90) cc_final: 0.7165 (p90) REVERT: B 200 MET cc_start: 0.8041 (mmm) cc_final: 0.7708 (tpp) REVERT: B 334 ASN cc_start: 0.9486 (t0) cc_final: 0.9237 (m-40) REVERT: B 385 LEU cc_start: 0.9454 (mp) cc_final: 0.8969 (tp) REVERT: B 402 PHE cc_start: 0.9515 (m-80) cc_final: 0.8848 (m-80) REVERT: B 627 LEU cc_start: 0.9110 (mt) cc_final: 0.8893 (pp) REVERT: B 909 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8175 (t0) REVERT: B 916 MET cc_start: 0.8743 (tpp) cc_final: 0.8432 (tpp) REVERT: B 1063 MET cc_start: 0.8628 (tmm) cc_final: 0.8333 (tmm) REVERT: B 1173 MET cc_start: 0.9486 (mmp) cc_final: 0.9128 (mmp) REVERT: B 1339 MET cc_start: 0.8525 (mmm) cc_final: 0.8238 (mmm) REVERT: B 1414 MET cc_start: 0.9608 (tpp) cc_final: 0.9404 (tpt) REVERT: B 1575 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9206 (tt) REVERT: B 1671 GLU cc_start: 0.9337 (OUTLIER) cc_final: 0.8818 (tm-30) REVERT: B 1927 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8479 (pm20) REVERT: B 1979 MET cc_start: 0.8955 (ppp) cc_final: 0.8730 (ppp) REVERT: F 259 MET cc_start: 0.9318 (mmt) cc_final: 0.8779 (mmm) REVERT: F 269 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9147 (mt) REVERT: F 396 GLU cc_start: 0.7763 (mp0) cc_final: 0.7210 (mp0) REVERT: F 578 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: G 63 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8538 (m-10) REVERT: G 184 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8140 (pp) REVERT: A 380 MET cc_start: 0.9462 (ppp) cc_final: 0.9182 (ppp) REVERT: A 807 PHE cc_start: 0.9090 (m-10) cc_final: 0.8778 (m-10) REVERT: A 1010 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8277 (ppp) REVERT: A 1063 MET cc_start: 0.8437 (tmm) cc_final: 0.8166 (tmm) REVERT: A 1172 MET cc_start: 0.7791 (tmm) cc_final: 0.7541 (tmm) REVERT: A 1173 MET cc_start: 0.9116 (mmt) cc_final: 0.8675 (mmt) REVERT: A 1258 MET cc_start: 0.9312 (tmm) cc_final: 0.8851 (tmm) REVERT: A 1539 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: A 1920 PHE cc_start: 0.9617 (OUTLIER) cc_final: 0.9290 (t80) REVERT: A 1964 MET cc_start: 0.7371 (tpp) cc_final: 0.7078 (tpp) REVERT: A 1965 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 2002 MET cc_start: 0.9001 (tmm) cc_final: 0.8733 (tmm) REVERT: A 2017 MET cc_start: 0.9154 (tpp) cc_final: 0.8649 (tpt) REVERT: D 257 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8968 (tp) REVERT: D 279 TRP cc_start: 0.9099 (p90) cc_final: 0.8805 (p90) REVERT: E 60 LEU cc_start: 0.9473 (mt) cc_final: 0.9055 (mt) REVERT: E 64 TYR cc_start: 0.8533 (m-80) cc_final: 0.8166 (m-80) REVERT: E 229 ARG cc_start: 0.6591 (ptm160) cc_final: 0.5673 (mtt180) REVERT: E 262 ASP cc_start: 0.9374 (m-30) cc_final: 0.9009 (m-30) outliers start: 103 outliers final: 63 residues processed: 384 average time/residue: 0.2419 time to fit residues: 159.3837 Evaluate side-chains 360 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 284 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1136 TYR Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1260 VAL Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1308 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1611 CYS Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1671 GLU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1761 CYS Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain F residue 186 TYR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 775 HIS Chi-restraints excluded: chain G residue 57 CYS Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 731 LEU Chi-restraints excluded: chain H residue 735 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 913 PHE Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1328 MET Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1663 TYR Chi-restraints excluded: chain A residue 1691 MET Chi-restraints excluded: chain A residue 1768 VAL Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 72 optimal weight: 8.9990 chunk 217 optimal weight: 7.9990 chunk 283 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 273 optimal weight: 6.9990 chunk 512 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 365 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** B1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.071798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048173 restraints weight = 230774.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049392 restraints weight = 124154.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.050161 restraints weight = 86441.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.050669 restraints weight = 69553.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.050900 restraints weight = 60840.065| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 42990 Z= 0.231 Angle : 0.699 13.523 58160 Z= 0.346 Chirality : 0.040 0.229 6584 Planarity : 0.004 0.056 7338 Dihedral : 4.482 66.129 5677 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 2.11 % Allowed : 13.61 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.43 (0.12), residues: 5120 helix: 2.05 (0.09), residues: 3486 sheet: 1.14 (0.67), residues: 66 loop : -1.71 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 748 TYR 0.018 0.001 TYR A1149 PHE 0.029 0.002 PHE D 397 TRP 0.030 0.002 TRP B1990 HIS 0.009 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00512 (42990) covalent geometry : angle 0.69919 (58160) hydrogen bonds : bond 0.04930 ( 2479) hydrogen bonds : angle 3.97170 ( 7341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 293 time to evaluate : 1.785 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.9278 (ttp80) cc_final: 0.8986 (ttp80) REVERT: B 83 ILE cc_start: 0.9412 (tp) cc_final: 0.9189 (mt) REVERT: B 197 TYR cc_start: 0.7539 (p90) cc_final: 0.7191 (p90) REVERT: B 200 MET cc_start: 0.7958 (mmm) cc_final: 0.7563 (tpp) REVERT: B 334 ASN cc_start: 0.9480 (t0) cc_final: 0.9240 (m-40) REVERT: B 385 LEU cc_start: 0.9474 (mp) cc_final: 0.8967 (tp) REVERT: B 627 LEU cc_start: 0.9098 (mt) cc_final: 0.8860 (pp) REVERT: B 634 MET cc_start: 0.8964 (mpp) cc_final: 0.8599 (mpp) REVERT: B 916 MET cc_start: 0.8828 (tpp) cc_final: 0.8559 (tpp) REVERT: B 1063 MET cc_start: 0.8609 (tmm) cc_final: 0.8347 (tmm) REVERT: B 1339 MET cc_start: 0.8490 (mmm) cc_final: 0.8234 (mmm) REVERT: B 1575 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9269 (tt) REVERT: B 1671 GLU cc_start: 0.9400 (OUTLIER) cc_final: 0.8875 (tm-30) REVERT: B 1927 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: B 1964 MET cc_start: 0.6297 (mtt) cc_final: 0.5934 (mmt) REVERT: B 1979 MET cc_start: 0.8935 (ppp) cc_final: 0.8590 (ppp) REVERT: F 259 MET cc_start: 0.9323 (mmt) cc_final: 0.8823 (mmm) REVERT: F 269 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9106 (mt) REVERT: F 380 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8733 (mm-30) REVERT: F 396 GLU cc_start: 0.7932 (mp0) cc_final: 0.7387 (mp0) REVERT: F 578 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: G 184 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8141 (pp) REVERT: A 162 HIS cc_start: 0.8942 (m-70) cc_final: 0.8683 (m-70) REVERT: A 164 LEU cc_start: 0.9625 (pp) cc_final: 0.9369 (mm) REVERT: A 380 MET cc_start: 0.9483 (ppp) cc_final: 0.9225 (ppp) REVERT: A 807 PHE cc_start: 0.9033 (m-10) cc_final: 0.8722 (m-10) REVERT: A 1010 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8288 (ppp) REVERT: A 1063 MET cc_start: 0.8426 (tmm) cc_final: 0.8162 (tmm) REVERT: A 1539 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: A 1920 PHE cc_start: 0.9626 (OUTLIER) cc_final: 0.9325 (t80) REVERT: A 1964 MET cc_start: 0.7403 (tpp) cc_final: 0.7098 (tpp) REVERT: A 1965 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8180 (tt) REVERT: A 2002 MET cc_start: 0.9023 (tmm) cc_final: 0.8753 (tmm) REVERT: A 2017 MET cc_start: 0.9206 (tpp) cc_final: 0.8700 (tpt) REVERT: D 257 LEU cc_start: 0.9296 (mm) cc_final: 0.9012 (tp) REVERT: D 279 TRP cc_start: 0.9143 (p90) cc_final: 0.8817 (p90) REVERT: D 390 MET cc_start: 0.9318 (tpp) cc_final: 0.9032 (tpp) REVERT: E 60 LEU cc_start: 0.9516 (mt) cc_final: 0.9052 (mt) REVERT: E 64 TYR cc_start: 0.8528 (m-80) cc_final: 0.8107 (m-80) REVERT: E 262 ASP cc_start: 0.9369 (m-30) cc_final: 0.9032 (m-30) outliers start: 97 outliers final: 67 residues processed: 376 average time/residue: 0.2319 time to fit residues: 149.7609 Evaluate side-chains 363 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 285 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1136 TYR Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1260 VAL Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1308 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1556 VAL Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1611 CYS Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1671 GLU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1761 CYS Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain F residue 186 TYR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 775 HIS Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain H residue 731 LEU Chi-restraints excluded: chain H residue 735 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 913 PHE Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1328 MET Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1663 TYR Chi-restraints excluded: chain A residue 1691 MET Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 49 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 252 optimal weight: 0.9990 chunk 422 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 333 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 503 optimal weight: 7.9990 chunk 502 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** B1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.074011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.050521 restraints weight = 228863.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.051795 restraints weight = 121359.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.052586 restraints weight = 83674.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.053098 restraints weight = 67145.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.053332 restraints weight = 58823.999| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42990 Z= 0.146 Angle : 0.640 15.176 58160 Z= 0.309 Chirality : 0.038 0.232 6584 Planarity : 0.004 0.056 7338 Dihedral : 4.392 65.872 5677 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.04 % Favored : 94.92 % Rotamer: Outliers : 1.80 % Allowed : 14.15 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 (0.12), residues: 5120 helix: 2.18 (0.09), residues: 3482 sheet: 1.03 (0.70), residues: 62 loop : -1.68 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 748 TYR 0.031 0.001 TYR A 111 PHE 0.027 0.001 PHE D 397 TRP 0.040 0.001 TRP B 676 HIS 0.005 0.001 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00329 (42990) covalent geometry : angle 0.64012 (58160) hydrogen bonds : bond 0.04285 ( 2479) hydrogen bonds : angle 3.67682 ( 7341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 289 time to evaluate : 1.608 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.9274 (ttp80) cc_final: 0.8941 (ttp80) REVERT: B 83 ILE cc_start: 0.9412 (tp) cc_final: 0.9193 (mt) REVERT: B 197 TYR cc_start: 0.7538 (p90) cc_final: 0.7192 (p90) REVERT: B 200 MET cc_start: 0.7981 (mmm) cc_final: 0.7598 (tpp) REVERT: B 334 ASN cc_start: 0.9467 (t0) cc_final: 0.9231 (m-40) REVERT: B 385 LEU cc_start: 0.9464 (mp) cc_final: 0.8965 (tp) REVERT: B 627 LEU cc_start: 0.9067 (mt) cc_final: 0.8863 (pp) REVERT: B 916 MET cc_start: 0.8833 (tpp) cc_final: 0.8574 (tpp) REVERT: B 1063 MET cc_start: 0.8529 (tmm) cc_final: 0.8291 (tmm) REVERT: B 1339 MET cc_start: 0.8531 (mmm) cc_final: 0.8269 (mmm) REVERT: B 1414 MET cc_start: 0.9422 (tpt) cc_final: 0.9211 (tpp) REVERT: B 1575 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9237 (tt) REVERT: B 1671 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9169 (tp30) REVERT: B 1927 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: B 1979 MET cc_start: 0.8977 (ppp) cc_final: 0.8626 (ppp) REVERT: F 259 MET cc_start: 0.9348 (mmt) cc_final: 0.8861 (mmm) REVERT: F 269 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9104 (mt) REVERT: F 396 GLU cc_start: 0.7800 (mp0) cc_final: 0.7403 (mp0) REVERT: F 578 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: G 184 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8139 (pp) REVERT: A 380 MET cc_start: 0.9479 (ppp) cc_final: 0.9181 (ppp) REVERT: A 807 PHE cc_start: 0.9051 (m-10) cc_final: 0.8744 (m-10) REVERT: A 1010 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8274 (ppp) REVERT: A 1063 MET cc_start: 0.8387 (tmm) cc_final: 0.8152 (tmm) REVERT: A 1258 MET cc_start: 0.9258 (tmm) cc_final: 0.8957 (tmm) REVERT: A 1920 PHE cc_start: 0.9621 (OUTLIER) cc_final: 0.9344 (t80) REVERT: A 1964 MET cc_start: 0.7427 (tpp) cc_final: 0.7128 (tpp) REVERT: A 1965 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8190 (tt) REVERT: A 2002 MET cc_start: 0.9030 (tmm) cc_final: 0.8759 (tmm) REVERT: A 2008 MET cc_start: 0.8040 (mmm) cc_final: 0.7515 (tpp) REVERT: A 2017 MET cc_start: 0.9193 (tpp) cc_final: 0.8669 (tpt) REVERT: D 257 LEU cc_start: 0.9305 (mm) cc_final: 0.9031 (tp) REVERT: D 279 TRP cc_start: 0.9127 (p90) cc_final: 0.8804 (p90) REVERT: D 390 MET cc_start: 0.9325 (tpp) cc_final: 0.9043 (tpp) REVERT: E 60 LEU cc_start: 0.9546 (mt) cc_final: 0.9094 (mm) REVERT: E 64 TYR cc_start: 0.8575 (m-80) cc_final: 0.8139 (m-80) REVERT: E 262 ASP cc_start: 0.9329 (m-30) cc_final: 0.8980 (m-30) outliers start: 83 outliers final: 61 residues processed: 361 average time/residue: 0.2404 time to fit residues: 149.0935 Evaluate side-chains 352 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 282 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1136 TYR Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1260 VAL Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1308 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1611 CYS Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1671 GLU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1761 CYS Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain F residue 186 TYR Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 775 HIS Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 731 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 913 PHE Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1336 LYS Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1663 TYR Chi-restraints excluded: chain A residue 1691 MET Chi-restraints excluded: chain A residue 1768 VAL Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 514 ASP Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 292 optimal weight: 0.9990 chunk 496 optimal weight: 5.9990 chunk 431 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 348 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 400 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 378 optimal weight: 2.9990 chunk 477 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** B1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.070497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.048418 restraints weight = 243985.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.050193 restraints weight = 126377.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.050562 restraints weight = 73336.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051236 restraints weight = 60003.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.051224 restraints weight = 59217.323| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42990 Z= 0.138 Angle : 0.639 14.350 58160 Z= 0.307 Chirality : 0.038 0.226 6584 Planarity : 0.004 0.057 7338 Dihedral : 4.317 63.192 5677 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.80 % Allowed : 14.19 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.67 (0.12), residues: 5120 helix: 2.25 (0.09), residues: 3484 sheet: 2.26 (0.79), residues: 42 loop : -1.65 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 777 TYR 0.026 0.001 TYR A 111 PHE 0.028 0.001 PHE B 131 TRP 0.038 0.001 TRP B1990 HIS 0.008 0.001 HIS H 775 Details of bonding type rmsd covalent geometry : bond 0.00311 (42990) covalent geometry : angle 0.63866 (58160) hydrogen bonds : bond 0.04033 ( 2479) hydrogen bonds : angle 3.59806 ( 7341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 293 time to evaluate : 1.793 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.9252 (ttp80) cc_final: 0.8965 (ttp80) REVERT: B 83 ILE cc_start: 0.9386 (tp) cc_final: 0.9171 (mt) REVERT: B 197 TYR cc_start: 0.7577 (p90) cc_final: 0.7250 (p90) REVERT: B 200 MET cc_start: 0.8046 (mmm) cc_final: 0.7687 (tpp) REVERT: B 334 ASN cc_start: 0.9484 (t0) cc_final: 0.9248 (m-40) REVERT: B 385 LEU cc_start: 0.9460 (mp) cc_final: 0.8961 (tp) REVERT: B 627 LEU cc_start: 0.9119 (mt) cc_final: 0.8889 (pp) REVERT: B 676 TRP cc_start: 0.9282 (t60) cc_final: 0.8725 (t60) REVERT: B 916 MET cc_start: 0.8873 (tpp) cc_final: 0.8607 (tpp) REVERT: B 1063 MET cc_start: 0.8586 (tmm) cc_final: 0.8343 (tmm) REVERT: B 1575 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9239 (tt) REVERT: B 1979 MET cc_start: 0.9101 (ppp) cc_final: 0.8685 (ppp) REVERT: F 259 MET cc_start: 0.9380 (mmt) cc_final: 0.8862 (mmm) REVERT: F 269 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9140 (mt) REVERT: F 390 MET cc_start: 0.9404 (tpt) cc_final: 0.9117 (tpp) REVERT: F 396 GLU cc_start: 0.7794 (mp0) cc_final: 0.7533 (mp0) REVERT: G 184 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8084 (pp) REVERT: A 56 LEU cc_start: 0.9711 (tt) cc_final: 0.9497 (pp) REVERT: A 380 MET cc_start: 0.9478 (ppp) cc_final: 0.9189 (ppp) REVERT: A 807 PHE cc_start: 0.9042 (m-10) cc_final: 0.8723 (m-10) REVERT: A 1010 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8258 (ppp) REVERT: A 1063 MET cc_start: 0.8428 (tmm) cc_final: 0.8177 (tmm) REVERT: A 1199 MET cc_start: 0.9358 (tpp) cc_final: 0.9117 (tmm) REVERT: A 1258 MET cc_start: 0.9341 (tmm) cc_final: 0.9022 (tmm) REVERT: A 1920 PHE cc_start: 0.9613 (OUTLIER) cc_final: 0.9332 (t80) REVERT: A 1964 MET cc_start: 0.7397 (tpp) cc_final: 0.7096 (tpp) REVERT: A 1965 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 2002 MET cc_start: 0.9049 (tmm) cc_final: 0.8760 (tmm) REVERT: A 2008 MET cc_start: 0.8152 (mmm) cc_final: 0.7644 (tpp) REVERT: A 2017 MET cc_start: 0.9169 (tpp) cc_final: 0.8646 (tpt) REVERT: D 257 LEU cc_start: 0.9290 (mm) cc_final: 0.9007 (tp) REVERT: D 279 TRP cc_start: 0.9122 (p90) cc_final: 0.8831 (p90) REVERT: D 390 MET cc_start: 0.9375 (tpp) cc_final: 0.9095 (tpp) REVERT: D 548 ASP cc_start: 0.8901 (t0) cc_final: 0.8664 (t0) REVERT: E 60 LEU cc_start: 0.9576 (mt) cc_final: 0.9139 (mm) REVERT: E 64 TYR cc_start: 0.8663 (m-80) cc_final: 0.8325 (m-80) REVERT: E 262 ASP cc_start: 0.9343 (m-30) cc_final: 0.8982 (m-30) outliers start: 83 outliers final: 56 residues processed: 367 average time/residue: 0.2375 time to fit residues: 149.9359 Evaluate side-chains 351 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1136 TYR Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1308 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1611 CYS Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1761 CYS Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain F residue 186 TYR Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 775 HIS Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 731 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 913 PHE Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1336 LYS Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1663 TYR Chi-restraints excluded: chain A residue 1768 VAL Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1965 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 353 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 391 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 428 optimal weight: 5.9990 chunk 416 optimal weight: 6.9990 chunk 366 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** B1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.075985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.051490 restraints weight = 208177.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.052437 restraints weight = 120315.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053061 restraints weight = 87796.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053481 restraints weight = 73648.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.053663 restraints weight = 66338.715| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 42990 Z= 0.229 Angle : 0.726 15.315 58160 Z= 0.357 Chirality : 0.041 0.307 6584 Planarity : 0.004 0.062 7338 Dihedral : 4.456 54.315 5674 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.78 % Favored : 94.20 % Rotamer: Outliers : 1.71 % Allowed : 14.69 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.31 (0.12), residues: 5120 helix: 1.95 (0.09), residues: 3498 sheet: 0.46 (0.70), residues: 56 loop : -1.72 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 777 TYR 0.028 0.002 TYR A 111 PHE 0.029 0.002 PHE B 131 TRP 0.040 0.002 TRP B1990 HIS 0.007 0.001 HIS B1109 Details of bonding type rmsd covalent geometry : bond 0.00511 (42990) covalent geometry : angle 0.72585 (58160) hydrogen bonds : bond 0.04996 ( 2479) hydrogen bonds : angle 4.00824 ( 7341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9941.59 seconds wall clock time: 171 minutes 19.77 seconds (10279.77 seconds total)