Starting phenix.real_space_refine on Wed Oct 28 22:48:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wds_65901/10_2026/9wds_65901.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wds_65901/10_2026/9wds_65901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wds_65901/10_2026/9wds_65901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wds_65901/10_2026/9wds_65901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wds_65901/10_2026/9wds_65901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wds_65901/10_2026/9wds_65901.map" } resolution = 3.45 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= -0.008 sd= 0.475 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: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 40 5.49 5 S 112 5.16 5 C 18222 2.51 5 N 5209 2.21 5 O 5523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29113 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1895, 15001 Classifications: {'peptide': 1895} Link IDs: {'PCIS': 1, 'PTRANS': 105, 'TRANS': 1788} Chain breaks: 7 Chain: "B" Number of atoms: 13318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1682, 13318 Classifications: {'peptide': 1682} Link IDs: {'PCIS': 1, 'PTRANS': 91, 'TRANS': 1589} Chain breaks: 7 Chain: "C" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 756 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' ZN': 4, 'ANP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8355 SG CYS A1110 28.342 62.684 86.414 1.00 79.54 S ATOM 8375 SG CYS A1113 29.933 63.542 83.125 1.00 69.73 S ATOM 8470 SG CYS A1125 30.709 65.927 85.484 1.00 78.55 S ATOM 8494 SG CYS A1128 27.367 65.070 84.485 1.00 71.53 S ATOM 5007 SG CYS A 646 33.406 61.282 72.961 1.00 73.64 S ATOM 5027 SG CYS A 649 31.685 60.486 75.339 1.00 66.86 S ATOM 5749 SG CYS A 770 29.739 61.822 72.762 1.00 95.37 S ATOM 5771 SG CYS A 773 31.352 63.597 75.640 1.00 71.64 S ATOM 13809 SG CYS A1799 43.206 29.858 45.159 1.00 92.47 S ATOM 13837 SG CYS A1803 45.808 29.172 46.658 1.00 72.59 S ATOM 13866 SG CYS A1806 46.907 29.443 43.714 1.00 71.52 S ATOM 11562 SG CYS A1509 53.360 52.457 13.969 1.00 96.40 S ATOM 11580 SG CYS A1512 53.994 47.824 14.214 1.00 89.73 S ATOM 11685 SG CYS A1528 56.394 50.723 13.534 1.00 98.92 S ATOM 11707 SG CYS A1531 53.781 50.362 11.361 1.00100.01 S ATOM 23520 SG CYS B1110 99.683 110.989 76.487 1.00 90.90 S ATOM 23540 SG CYS B1113 99.583 110.140 73.912 1.00 69.74 S ATOM 23635 SG CYS B1125 99.122 107.821 75.841 1.00 81.97 S ATOM 23659 SG CYS B1128 102.126 108.564 73.807 1.00 70.95 S ATOM 20016 SG CYS B 646 98.163 115.908 66.240 1.00 80.72 S ATOM 20036 SG CYS B 649 100.105 116.866 68.984 1.00 73.28 S ATOM 20890 SG CYS B 770 101.280 116.123 65.030 1.00 75.75 S ATOM 20912 SG CYS B 773 100.705 113.729 67.930 1.00 68.94 S ATOM 27118 SG CYS B1799 92.138 144.045 52.809 1.00109.25 S ATOM 27146 SG CYS B1803 88.760 143.108 54.332 1.00 78.64 S ATOM 27175 SG CYS B1806 87.777 144.065 51.697 1.00102.16 S Time building chain proxies: 6.58, per 1000 atoms: 0.23 Number of scatterers: 29113 At special positions: 0 Unit cell: (138.24, 174.72, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 112 16.00 P 40 15.00 O 5523 8.00 N 5209 7.00 C 18222 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: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1110 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1125 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1113 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1128 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 770 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 773 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 649 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" NE2 HIS A1795 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1806 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1803 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1799 " pdb=" ZN A2005 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1531 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1528 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1509 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1512 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1113 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1128 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1125 " pdb=" ZN B2002 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 773 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 770 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 646 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 649 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" NE2 HIS B1795 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1803 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1806 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1799 " Number of angles added : 36 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6644 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 28 sheets defined 46.3% alpha, 13.8% beta 6 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 4 through 24 Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.522A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 157 removed outlier: 3.654A pdb=" N PHE A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.592A pdb=" N VAL A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.525A pdb=" N VAL A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 256 through 293 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.850A pdb=" N TYR A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.601A pdb=" N SER A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 344 through 358 removed outlier: 3.724A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 373 Processing helix chain 'A' and resid 374 through 393 Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.980A pdb=" N LYS A 452 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 482 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'A' and resid 515 through 535 removed outlier: 3.565A pdb=" N CYS A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'A' and resid 560 through 574 removed outlier: 3.755A pdb=" N ARG A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 796 through 816 Processing helix chain 'A' and resid 827 through 862 removed outlier: 3.956A pdb=" N ARG A 848 " --> pdb=" O ARG A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 883 Processing helix chain 'A' and resid 884 through 899 Processing helix chain 'A' and resid 903 through 906 Processing helix chain 'A' and resid 911 through 915 Processing helix chain 'A' and resid 924 through 934 Processing helix chain 'A' and resid 950 through 953 Processing helix chain 'A' and resid 969 through 992 removed outlier: 4.768A pdb=" N GLU A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 Processing helix chain 'A' and resid 1016 through 1028 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.516A pdb=" N GLU A1073 " --> pdb=" O ARG A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1095 Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 3.546A pdb=" N GLU A1144 " --> pdb=" O GLU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1159 Processing helix chain 'A' and resid 1176 through 1186 Processing helix chain 'A' and resid 1193 through 1201 Processing helix chain 'A' and resid 1208 through 1213 removed outlier: 3.639A pdb=" N GLU A1212 " --> pdb=" O THR A1209 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A1213 " --> pdb=" O THR A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1240 removed outlier: 3.505A pdb=" N GLY A1240 " --> pdb=" O GLN A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1268 removed outlier: 3.668A pdb=" N TYR A1264 " --> pdb=" O SER A1260 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR A1265 " --> pdb=" O HIS A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1275 removed outlier: 4.224A pdb=" N ILE A1272 " --> pdb=" O HIS A1268 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1273 " --> pdb=" O PRO A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1314 Processing helix chain 'A' and resid 1317 through 1321 Processing helix chain 'A' and resid 1333 through 1339 Processing helix chain 'A' and resid 1344 through 1356 removed outlier: 3.601A pdb=" N ARG A1348 " --> pdb=" O ASP A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1368 removed outlier: 4.274A pdb=" N ARG A1360 " --> pdb=" O THR A1356 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A1368 " --> pdb=" O ILE A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1381 Processing helix chain 'A' and resid 1382 through 1393 removed outlier: 3.903A pdb=" N GLN A1393 " --> pdb=" O GLU A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1397 Processing helix chain 'A' and resid 1403 through 1412 Processing helix chain 'A' and resid 1451 through 1458 removed outlier: 3.997A pdb=" N PHE A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1647 removed outlier: 3.639A pdb=" N SER A1646 " --> pdb=" O SER A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1695 removed outlier: 3.687A pdb=" N PHE A1694 " --> pdb=" O LYS A1691 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A1695 " --> pdb=" O GLY A1692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1691 through 1695' Processing helix chain 'A' and resid 1696 through 1719 Processing helix chain 'A' and resid 1721 through 1723 No H-bonds generated for 'chain 'A' and resid 1721 through 1723' Processing helix chain 'A' and resid 1750 through 1756 removed outlier: 3.604A pdb=" N GLY A1756 " --> pdb=" O SER A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1765 through 1777 Processing helix chain 'A' and resid 1780 through 1787 Processing helix chain 'A' and resid 1795 through 1799 Processing helix chain 'A' and resid 1812 through 1816 removed outlier: 3.577A pdb=" N HIS A1816 " --> pdb=" O ARG A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1833 removed outlier: 3.767A pdb=" N LEU A1831 " --> pdb=" O TYR A1827 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A1832 " --> pdb=" O LEU A1828 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1847 Processing helix chain 'A' and resid 1852 through 1868 Processing helix chain 'A' and resid 1908 through 1917 removed outlier: 3.558A pdb=" N MET A1912 " --> pdb=" O GLU A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1918 through 1920 No H-bonds generated for 'chain 'A' and resid 1918 through 1920' Processing helix chain 'A' and resid 1929 through 1935 removed outlier: 3.627A pdb=" N ARG A1934 " --> pdb=" O PHE A1930 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1943 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.759A pdb=" N GLU B 69 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 70 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 113 through 125 removed outlier: 4.163A pdb=" N ARG B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 157 removed outlier: 3.896A pdb=" N MET B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) Proline residue: B 147 - end of helix removed outlier: 3.592A pdb=" N VAL B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 216 removed outlier: 3.923A pdb=" N ARG B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 removed outlier: 3.551A pdb=" N THR B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 294 removed outlier: 3.594A pdb=" N ASP B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.707A pdb=" N SER B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 358 removed outlier: 4.162A pdb=" N PHE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 373 Processing helix chain 'B' and resid 374 through 393 removed outlier: 3.582A pdb=" N GLY B 378 " --> pdb=" O ARG B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 5.495A pdb=" N TYR B 401 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 446 through 452 Processing helix chain 'B' and resid 471 through 483 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.711A pdb=" N LYS B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 535 Processing helix chain 'B' and resid 545 through 554 removed outlier: 3.959A pdb=" N ARG B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 578 Proline residue: B 575 - end of helix removed outlier: 3.935A pdb=" N ASN B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 683 Processing helix chain 'B' and resid 688 through 692 removed outlier: 3.533A pdb=" N MET B 692 " --> pdb=" O TYR B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 752 Processing helix chain 'B' and resid 796 through 815 Processing helix chain 'B' and resid 827 through 865 removed outlier: 3.753A pdb=" N MET B 836 " --> pdb=" O ALA B 832 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 883 removed outlier: 3.737A pdb=" N GLU B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 Processing helix chain 'B' and resid 893 through 900 removed outlier: 3.608A pdb=" N LYS B 897 " --> pdb=" O GLU B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.614A pdb=" N LEU B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 934 removed outlier: 3.716A pdb=" N LEU B 933 " --> pdb=" O GLU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 953 Processing helix chain 'B' and resid 969 through 993 removed outlier: 3.675A pdb=" N GLU B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 removed outlier: 3.503A pdb=" N THR B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1029 removed outlier: 3.660A pdb=" N ASP B1020 " --> pdb=" O ASP B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1052 Processing helix chain 'B' and resid 1054 through 1066 Processing helix chain 'B' and resid 1069 through 1085 Processing helix chain 'B' and resid 1092 through 1095 Processing helix chain 'B' and resid 1138 through 1146 removed outlier: 3.660A pdb=" N LEU B1142 " --> pdb=" O LYS B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1159 removed outlier: 3.539A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1186 Processing helix chain 'B' and resid 1193 through 1201 Processing helix chain 'B' and resid 1210 through 1212 No H-bonds generated for 'chain 'B' and resid 1210 through 1212' Processing helix chain 'B' and resid 1231 through 1241 removed outlier: 3.550A pdb=" N TYR B1235 " --> pdb=" O GLN B1231 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B1241 " --> pdb=" O GLN B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1268 Processing helix chain 'B' and resid 1268 through 1273 removed outlier: 4.065A pdb=" N ILE B1272 " --> pdb=" O HIS B1268 " (cutoff:3.500A) Processing helix chain 'B' and resid 1287 through 1314 removed outlier: 3.546A pdb=" N ALA B1301 " --> pdb=" O THR B1297 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1322 removed outlier: 3.620A pdb=" N LEU B1322 " --> pdb=" O GLY B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1333 through 1339 Processing helix chain 'B' and resid 1344 through 1354 removed outlier: 4.168A pdb=" N ARG B1348 " --> pdb=" O ASP B1344 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B1354 " --> pdb=" O SER B1350 " (cutoff:3.500A) Processing helix chain 'B' and resid 1356 through 1368 removed outlier: 4.130A pdb=" N ARG B1360 " --> pdb=" O THR B1356 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B1368 " --> pdb=" O ILE B1364 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1380 Processing helix chain 'B' and resid 1382 through 1392 Processing helix chain 'B' and resid 1393 through 1397 removed outlier: 3.521A pdb=" N HIS B1396 " --> pdb=" O GLN B1393 " (cutoff:3.500A) Processing helix chain 'B' and resid 1403 through 1411 Processing helix chain 'B' and resid 1691 through 1695 removed outlier: 3.776A pdb=" N PHE B1694 " --> pdb=" O LYS B1691 " (cutoff:3.500A) Processing helix chain 'B' and resid 1696 through 1718 Processing helix chain 'B' and resid 1721 through 1723 No H-bonds generated for 'chain 'B' and resid 1721 through 1723' Processing helix chain 'B' and resid 1750 through 1756 Processing helix chain 'B' and resid 1765 through 1777 Processing helix chain 'B' and resid 1780 through 1787 Processing helix chain 'B' and resid 1794 through 1799 Processing helix chain 'B' and resid 1820 through 1831 Processing helix chain 'B' and resid 1852 through 1868 removed outlier: 3.568A pdb=" N ARG B1856 " --> pdb=" O GLY B1852 " (cutoff:3.500A) Processing helix chain 'B' and resid 1908 through 1917 removed outlier: 3.656A pdb=" N MET B1912 " --> pdb=" O GLU B1908 " (cutoff:3.500A) Processing helix chain 'B' and resid 1929 through 1935 Processing helix chain 'B' and resid 1935 through 1944 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.973A pdb=" N PHE A 591 " --> pdb=" O SER A1250 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL A1252 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL A 593 " --> pdb=" O VAL A1252 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR A1254 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR A 595 " --> pdb=" O THR A1254 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N CYS A1256 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 597 " --> pdb=" O CYS A1256 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL A1223 " --> pdb=" O VAL A1253 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N PHE A1255 " --> pdb=" O VAL A1223 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN A1225 " --> pdb=" O PHE A1255 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE A 822 " --> pdb=" O THR A1222 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 821 " --> pdb=" O LEU A1205 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL A1207 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL A 823 " --> pdb=" O VAL A1207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.810A pdb=" N PHE A 235 " --> pdb=" O MET A 314 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY A 236 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N ASN A 331 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 195 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP A 368 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A 197 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE A 363 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A 406 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 365 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N SER A 408 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE A 367 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A 130 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 131 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 620 removed outlier: 4.257A pdb=" N PHE A 619 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE A 604 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 605 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 13.332A pdb=" N PHE A 697 " --> pdb=" O GLN A 747 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLN A 747 " --> pdb=" O PHE A 697 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 699 " --> pdb=" O TYR A 745 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR A 745 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 668 " --> pdb=" O VAL A 729 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 615 through 620 removed outlier: 4.257A pdb=" N PHE A 619 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE A 604 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 605 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 908 through 910 Processing sheet with id=AA7, first strand: chain 'A' and resid 955 through 958 Processing sheet with id=AA8, first strand: chain 'A' and resid 1116 through 1117 removed outlier: 3.665A pdb=" N GLY A1137 " --> pdb=" O PHE A1107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1441 through 1450 removed outlier: 7.450A pdb=" N GLU A1441 " --> pdb=" O GLU A1432 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU A1432 " --> pdb=" O GLU A1441 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU A1443 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A1430 " --> pdb=" O GLU A1443 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A1445 " --> pdb=" O VAL A1428 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N PHE A1549 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASN A1425 " --> pdb=" O PHE A1549 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N THR A1551 " --> pdb=" O ASN A1425 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR A1427 " --> pdb=" O THR A1551 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA A1548 " --> pdb=" O PHE A1476 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE A1476 " --> pdb=" O ALA A1548 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG A1550 " --> pdb=" O ILE A1474 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ILE A1474 " --> pdb=" O GLU A1640 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A1640 " --> pdb=" O ILE A1474 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N GLN A1666 " --> pdb=" O PRO A1546 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A1502 " --> pdb=" O THR A1545 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1463 through 1466 removed outlier: 8.230A pdb=" N ILE A1474 " --> pdb=" O GLU A1640 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A1640 " --> pdb=" O ILE A1474 " (cutoff:3.500A) removed outlier: 11.182A pdb=" N PHE A1661 " --> pdb=" O GLY A1601 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY A1601 " --> pdb=" O PHE A1661 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU A1567 " --> pdb=" O ASP A1600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1484 through 1486 removed outlier: 3.567A pdb=" N GLU A1491 " --> pdb=" O GLN A1484 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A1486 " --> pdb=" O SER A1489 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1526 through 1527 removed outlier: 3.751A pdb=" N LEU A1526 " --> pdb=" O ILE A1535 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1580 through 1581 Processing sheet with id=AB5, first strand: chain 'A' and resid 1580 through 1581 Processing sheet with id=AB6, first strand: chain 'A' and resid 1789 through 1790 removed outlier: 3.853A pdb=" N GLY A1790 " --> pdb=" O GLY A1793 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1872 through 1876 removed outlier: 3.619A pdb=" N VAL A1899 " --> pdb=" O PRO A1883 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG A1896 " --> pdb=" O ARG A1925 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU A1927 " --> pdb=" O ARG A1896 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A1898 " --> pdb=" O LEU A1927 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 54 removed outlier: 6.283A pdb=" N VAL B1223 " --> pdb=" O VAL B1253 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE B1255 " --> pdb=" O VAL B1223 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN B1225 " --> pdb=" O PHE B1255 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE B 822 " --> pdb=" O THR B1222 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B1224 " --> pdb=" O ILE B 822 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 824 " --> pdb=" O TYR B1224 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY B 821 " --> pdb=" O LEU B1205 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL B1207 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 823 " --> pdb=" O VAL B1207 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU B1168 " --> pdb=" O SER B1206 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N THR B1208 " --> pdb=" O GLU B1168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AC1, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.666A pdb=" N PHE B 235 " --> pdb=" O MET B 314 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY B 236 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N ASN B 331 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 195 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP B 368 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU B 197 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE B 363 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU B 406 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU B 365 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER B 408 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE B 367 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY B 130 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 131 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 536 through 537 Processing sheet with id=AC3, first strand: chain 'B' and resid 615 through 620 removed outlier: 4.314A pdb=" N PHE B 619 " --> pdb=" O PHE B 604 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 604 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 642 " --> pdb=" O GLY B 655 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 615 through 620 removed outlier: 4.314A pdb=" N PHE B 619 " --> pdb=" O PHE B 604 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 604 " --> pdb=" O PHE B 619 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 641 through 646 current: chain 'B' and resid 740 through 747 removed outlier: 4.135A pdb=" N GLU B 669 " --> pdb=" O GLY B 659 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 659 " --> pdb=" O GLU B 669 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 908 through 910 Processing sheet with id=AC6, first strand: chain 'B' and resid 955 through 958 Processing sheet with id=AC7, first strand: chain 'B' and resid 1108 through 1109 Processing sheet with id=AC8, first strand: chain 'B' and resid 1580 through 1582 removed outlier: 3.656A pdb=" N LEU B1676 " --> pdb=" O PRO B1737 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B1742 " --> pdb=" O GLU B1726 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1580 through 1582 removed outlier: 3.656A pdb=" N LEU B1676 " --> pdb=" O PRO B1737 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1872 through 1876 removed outlier: 3.782A pdb=" N TRP B1895 " --> pdb=" O GLU B1887 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS B1889 " --> pdb=" O GLU B1893 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU B1893 " --> pdb=" O LYS B1889 " (cutoff:3.500A) 1280 hydrogen bonds defined for protein. 3600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 8.60 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9152 1.33 - 1.45: 4160 1.45 - 1.57: 16240 1.57 - 1.69: 74 1.69 - 1.81: 174 Bond restraints: 29800 Sorted by residual: bond pdb=" C1' DC C 64 " pdb=" N1 DC C 64 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.01e+01 bond pdb=" C1' DT C 56 " pdb=" N1 DT C 56 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.27e+00 bond pdb=" C3' DT C 7 " pdb=" C2' DT C 7 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.02e+00 bond pdb=" C1' DT C 4 " pdb=" N1 DT C 4 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.96e+00 bond pdb=" C3' DA C 46 " pdb=" C2' DA C 46 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.06e+00 ... (remaining 29795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 39308 1.43 - 2.85: 942 2.85 - 4.28: 223 4.28 - 5.71: 21 5.71 - 7.14: 9 Bond angle restraints: 40503 Sorted by residual: angle pdb=" O4' DG C 45 " pdb=" C4' DG C 45 " pdb=" C3' DG C 45 " ideal model delta sigma weight residual 106.00 103.35 2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O5' DG C 63 " pdb=" C5' DG C 63 " pdb=" C4' DG C 63 " ideal model delta sigma weight residual 109.40 112.76 -3.36 8.00e-01 1.56e+00 1.76e+01 angle pdb=" N3 DT C 51 " pdb=" C4 DT C 51 " pdb=" O4 DT C 51 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT C 53 " pdb=" C4 DT C 53 " pdb=" O4 DT C 53 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT C 43 " pdb=" C4 DT C 43 " pdb=" O4 DT C 43 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 40498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 17262 35.23 - 70.45: 682 70.45 - 105.68: 32 105.68 - 140.91: 0 140.91 - 176.14: 2 Dihedral angle restraints: 17978 sinusoidal: 7671 harmonic: 10307 Sorted by residual: dihedral pdb=" O1A ANP A2001 " pdb=" O3A ANP A2001 " pdb=" PA ANP A2001 " pdb=" PB ANP A2001 " ideal model delta sinusoidal sigma weight residual 83.11 -86.92 170.03 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C4' DG C 48 " pdb=" C3' DG C 48 " pdb=" O3' DG C 48 " pdb=" P DA C 49 " ideal model delta sinusoidal sigma weight residual 220.00 43.86 176.14 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA HIS A1286 " pdb=" C HIS A1286 " pdb=" N ASP A1287 " pdb=" CA ASP A1287 " ideal model delta harmonic sigma weight residual -180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 17975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3158 0.037 - 0.073: 906 0.073 - 0.110: 240 0.110 - 0.146: 106 0.146 - 0.183: 10 Chirality restraints: 4420 Sorted by residual: chirality pdb=" C3' DG C 12 " pdb=" C4' DG C 12 " pdb=" O3' DG C 12 " pdb=" C2' DG C 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" C3' DC C 8 " pdb=" C4' DC C 8 " pdb=" O3' DC C 8 " pdb=" C2' DC C 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" C3' DC C 54 " pdb=" C4' DC C 54 " pdb=" O3' DC C 54 " pdb=" C2' DC C 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 4417 not shown) Planarity restraints: 5195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C 63 " 0.030 2.00e-02 2.50e+03 1.28e-02 4.92e+00 pdb=" N9 DG C 63 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DG C 63 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG C 63 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG C 63 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG C 63 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG C 63 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG C 63 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG C 63 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG C 63 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG C 63 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG C 63 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1342 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" CD GLU A1342 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU A1342 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A1342 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 875 " -0.157 9.50e-02 1.11e+02 7.05e-02 3.37e+00 pdb=" NE ARG B 875 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 875 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 875 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 875 " -0.002 2.00e-02 2.50e+03 ... (remaining 5192 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4406 2.76 - 3.29: 27175 3.29 - 3.83: 44520 3.83 - 4.36: 51781 4.36 - 4.90: 91187 Nonbonded interactions: 219069 Sorted by model distance: nonbonded pdb=" O ASP A1015 " pdb=" OD1 ASP A1015 " model vdw 2.225 3.040 nonbonded pdb=" O ASP B1190 " pdb=" OD1 ASP B1190 " model vdw 2.254 3.040 nonbonded pdb=" O ALA A1271 " pdb=" OD1 ASP A1275 " model vdw 2.286 3.040 nonbonded pdb=" OE2 GLU A 718 " pdb=" O PRO A 719 " model vdw 2.325 3.040 nonbonded pdb=" O GLN B1357 " pdb=" OD1 ASP B1361 " model vdw 2.345 3.040 ... (remaining 219064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 899 or resid 905 through 939 or resid 948 throug \ h 1418 or resid 1579 through 1592 or resid 1668 through 1944 or resid 2002 throu \ gh 2004)) selection = (chain 'B' and (resid 1 through 537 or resid 539 through 658 or resid 665 throug \ h 678 or resid 689 through 750 or resid 764 through 864 or resid 870 through 899 \ or resid 905 through 1944 or resid 2001 through 2003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 36.280 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 29828 Z= 0.192 Angle : 0.831 40.790 40539 Z= 0.357 Chirality : 0.041 0.183 4420 Planarity : 0.005 0.070 5195 Dihedral : 17.088 176.137 11334 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.53 % Allowed : 16.41 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3545 helix: 1.81 (0.14), residues: 1423 sheet: 0.53 (0.25), residues: 451 loop : -1.05 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 875 TYR 0.015 0.001 TYR A1007 PHE 0.016 0.001 PHE A 144 TRP 0.013 0.001 TRP B1821 HIS 0.005 0.001 HIS B1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 (29800) covalent geometry : angle 0.56755 / 0.34 (40503) hydrogen bonds : bond 0.14667 / 9.83 ( 1251) hydrogen bonds : angle 5.57364 / 4.11 ( 3630) metal coordination : bond 0.07058 / 4.35 ( 28) metal coordination : angle 20.37196 / 11.18 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 1.199 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: A 414 MET cc_start: 0.8251 (mmm) cc_final: 0.8025 (mmm) REVERT: A 636 ARG cc_start: 0.8551 (mtp85) cc_final: 0.7904 (mtp85) REVERT: A 714 TYR cc_start: 0.8936 (m-10) cc_final: 0.8507 (m-10) REVERT: A 870 LYS cc_start: 0.8320 (mmmt) cc_final: 0.7988 (tptp) REVERT: A 1291 MET cc_start: 0.8934 (mmm) cc_final: 0.8437 (mmm) REVERT: A 1307 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8652 (ttm170) REVERT: A 1596 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8534 (mt) REVERT: A 1724 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: A 1913 ARG cc_start: 0.8627 (ttm170) cc_final: 0.8425 (ttm-80) REVERT: B 250 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.7721 (t-90) REVERT: B 258 GLN cc_start: 0.8760 (mp10) cc_final: 0.8532 (mp10) REVERT: B 485 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9127 (mmmm) REVERT: B 583 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8620 (mmtt) REVERT: B 880 GLU cc_start: 0.9278 (tm-30) cc_final: 0.8858 (tm-30) REVERT: B 1082 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 1093 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8988 (tt) REVERT: B 1173 GLN cc_start: 0.7912 (pm20) cc_final: 0.7654 (pm20) REVERT: B 1338 TYR cc_start: 0.8466 (m-80) cc_final: 0.8215 (m-80) REVERT: B 1380 LYS cc_start: 0.9025 (mtpp) cc_final: 0.8739 (tptp) REVERT: B 1687 MET cc_start: 0.8292 (mtm) cc_final: 0.7582 (mtm) REVERT: B 1695 MET cc_start: 0.9013 (mmm) cc_final: 0.8738 (tpp) outliers start: 46 outliers final: 35 residues processed: 316 average time/residue: 0.2395 time to fit residues: 110.9668 Evaluate side-chains 315 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1375 GLN Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1864 VAL Chi-restraints excluded: chain A residue 1919 ASP Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1416 MET Chi-restraints excluded: chain B residue 1726 GLU Chi-restraints excluded: chain B residue 1774 ILE Chi-restraints excluded: chain B residue 1799 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1305 GLN A1486 GLN A1654 GLN B1117 HIS B1261 HIS B1772 HIS B1859 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.050372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.039992 restraints weight = 88901.896| |-----------------------------------------------------------------------------| r_work (start): 0.2375 rms_B_bonded: 2.16 r_work: 0.2277 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2166 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29828 Z= 0.157 Angle : 0.637 19.327 40539 Z= 0.320 Chirality : 0.042 0.219 4420 Planarity : 0.005 0.053 5195 Dihedral : 12.047 177.329 4475 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.13 % Allowed : 15.87 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3545 helix: 1.91 (0.14), residues: 1458 sheet: 0.78 (0.25), residues: 452 loop : -0.93 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 875 TYR 0.014 0.001 TYR A1007 PHE 0.018 0.001 PHE A 144 TRP 0.011 0.001 TRP B1821 HIS 0.009 0.001 HIS B1339 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (29800) covalent geometry : angle 0.58788 / 0.32 (40503) hydrogen bonds : bond 0.06260 / 4.29 ( 1251) hydrogen bonds : angle 4.53058 / 3.31 ( 3630) metal coordination : bond 0.01791 / 1.24 ( 28) metal coordination : angle 8.22446 / 4.42 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 285 time to evaluate : 1.301 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: A 94 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8593 (pp) REVERT: A 414 MET cc_start: 0.8392 (mmm) cc_final: 0.8138 (mmm) REVERT: A 617 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8687 (m-30) REVERT: A 636 ARG cc_start: 0.8684 (mtp85) cc_final: 0.8116 (mtp85) REVERT: A 714 TYR cc_start: 0.8959 (m-10) cc_final: 0.8492 (m-10) REVERT: A 874 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8844 (mp0) REVERT: A 1291 MET cc_start: 0.8973 (mmm) cc_final: 0.8461 (mmm) REVERT: A 1307 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8667 (ttm170) REVERT: A 1596 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8538 (mt) REVERT: A 1913 ARG cc_start: 0.8708 (ttm170) cc_final: 0.8427 (ttm-80) REVERT: B 250 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.7940 (m-70) REVERT: B 258 GLN cc_start: 0.8799 (mp10) cc_final: 0.8583 (mp10) REVERT: B 446 ASP cc_start: 0.8085 (t0) cc_final: 0.7843 (t0) REVERT: B 485 LYS cc_start: 0.9317 (mmmm) cc_final: 0.9078 (mmmm) REVERT: B 583 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8882 (mmtt) REVERT: B 880 GLU cc_start: 0.9361 (tm-30) cc_final: 0.8953 (tm-30) REVERT: B 1162 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8948 (mtt-85) REVERT: B 1380 LYS cc_start: 0.9079 (mtpp) cc_final: 0.8726 (tptp) REVERT: B 1687 MET cc_start: 0.8495 (mtm) cc_final: 0.7850 (mtm) REVERT: B 1888 GLN cc_start: 0.8447 (pp30) cc_final: 0.8030 (pp30) outliers start: 64 outliers final: 35 residues processed: 333 average time/residue: 0.2430 time to fit residues: 117.9012 Evaluate side-chains 315 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1305 GLN Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1375 GLN Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1530 ASP Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1729 GLU Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1864 VAL Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1774 ILE Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1885 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: [141, 172, 198, 154, 260, 213, 232, 79, 329, 17, 294] chunk 141 optimal weight: 0.0060 chunk 172 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 260 optimal weight: 0.8980 chunk 213 optimal weight: 0.0170 chunk 232 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 329 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1305 GLN A1471 HIS A1879 HIS B 292 GLN B1017 GLN B1859 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.051902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.041439 restraints weight = 88475.209| |-----------------------------------------------------------------------------| r_work (start): 0.2418 rms_B_bonded: 2.17 r_work: 0.2321 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2209 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29828 Z= 0.120 Angle : 0.570 15.172 40539 Z= 0.296 Chirality : 0.040 0.217 4420 Planarity : 0.004 0.050 5195 Dihedral : 11.741 179.738 4433 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.40 % Allowed : 15.87 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3545 helix: 2.04 (0.14), residues: 1456 sheet: 0.95 (0.25), residues: 444 loop : -0.86 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1731 TYR 0.019 0.001 TYR A1442 PHE 0.014 0.001 PHE A 144 TRP 0.011 0.001 TRP A1781 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (29800) covalent geometry : angle 0.55112 / 0.29 (40503) hydrogen bonds : bond 0.05022 / 3.45 ( 1251) hydrogen bonds : angle 4.28532 / 3.12 ( 3630) metal coordination : bond 0.01027 / 0.79 ( 28) metal coordination : angle 4.91653 / 2.65 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 288 time to evaluate : 0.934 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: A 94 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8577 (pp) REVERT: A 414 MET cc_start: 0.8353 (mmm) cc_final: 0.8071 (mmm) REVERT: A 636 ARG cc_start: 0.8561 (mtp85) cc_final: 0.7850 (mtp85) REVERT: A 714 TYR cc_start: 0.8920 (m-10) cc_final: 0.8526 (m-10) REVERT: A 874 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8861 (mp0) REVERT: A 884 ASP cc_start: 0.8796 (p0) cc_final: 0.8559 (p0) REVERT: A 1291 MET cc_start: 0.8890 (mmm) cc_final: 0.8500 (mmm) REVERT: A 1596 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8555 (mt) REVERT: A 1724 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: A 1913 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8446 (ttm-80) REVERT: B 250 HIS cc_start: 0.8701 (OUTLIER) cc_final: 0.7932 (m-70) REVERT: B 258 GLN cc_start: 0.8742 (mp10) cc_final: 0.8453 (mp10) REVERT: B 446 ASP cc_start: 0.8006 (t0) cc_final: 0.7751 (t0) REVERT: B 583 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8771 (mmtt) REVERT: B 613 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8833 (m-30) REVERT: B 1093 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8981 (tp) REVERT: B 1162 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8897 (mtt-85) REVERT: B 1380 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8698 (tptp) REVERT: B 1406 ARG cc_start: 0.9233 (tpp80) cc_final: 0.8975 (mmm-85) REVERT: B 1582 TYR cc_start: 0.8557 (t80) cc_final: 0.8356 (t80) REVERT: B 1687 MET cc_start: 0.8458 (mtm) cc_final: 0.7810 (mtm) REVERT: B 1888 GLN cc_start: 0.8437 (pp30) cc_final: 0.8011 (pp30) outliers start: 72 outliers final: 40 residues processed: 344 average time/residue: 0.2344 time to fit residues: 118.3845 Evaluate side-chains 330 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1305 GLN Chi-restraints excluded: chain A residue 1375 GLN Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1530 ASP Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1729 GLU Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1416 MET Chi-restraints excluded: chain B residue 1695 MET Chi-restraints excluded: chain B residue 1774 ILE Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1885 LEU Chi-restraints excluded: chain B residue 1927 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: [192, 229, 204, 78, 131, 74, 120, 338, 95, 12, 57] chunk 192 optimal weight: 0.5980 chunk 229 optimal weight: 0.1980 chunk 204 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 338 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1305 GLN A1654 GLN B 292 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.052141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.041818 restraints weight = 87689.165| |-----------------------------------------------------------------------------| r_work (start): 0.2429 rms_B_bonded: 2.09 r_work: 0.2335 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2226 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29828 Z= 0.121 Angle : 0.558 14.437 40539 Z= 0.288 Chirality : 0.040 0.220 4420 Planarity : 0.004 0.050 5195 Dihedral : 11.643 178.998 4426 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.10 % Allowed : 16.74 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.00 (0.14), residues: 3545 helix: 2.15 (0.14), residues: 1446 sheet: 0.94 (0.25), residues: 446 loop : -0.79 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1731 TYR 0.013 0.001 TYR A1007 PHE 0.015 0.001 PHE A 144 TRP 0.009 0.001 TRP B1821 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (29800) covalent geometry : angle 0.54165 / 0.29 (40503) hydrogen bonds : bond 0.04799 / 3.30 ( 1251) hydrogen bonds : angle 4.16035 / 3.03 ( 3630) metal coordination : bond 0.00910 / 0.70 ( 28) metal coordination : angle 4.49991 / 2.40 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 290 time to evaluate : 1.729 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: A 62 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.9098 (mttm) REVERT: A 94 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8542 (pp) REVERT: A 414 MET cc_start: 0.8343 (mmm) cc_final: 0.8043 (mmm) REVERT: A 617 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8668 (m-30) REVERT: A 636 ARG cc_start: 0.8523 (mtp85) cc_final: 0.7971 (mtp85) REVERT: A 695 ASP cc_start: 0.5892 (t0) cc_final: 0.5081 (t0) REVERT: A 1291 MET cc_start: 0.8870 (mmm) cc_final: 0.8461 (mmm) REVERT: A 1335 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8808 (ttpp) REVERT: A 1596 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8523 (mt) REVERT: A 1681 LYS cc_start: 0.8887 (tppt) cc_final: 0.8480 (tppt) REVERT: A 1724 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: A 1913 ARG cc_start: 0.8672 (ttm170) cc_final: 0.8374 (ttm-80) REVERT: B 250 HIS cc_start: 0.8649 (OUTLIER) cc_final: 0.7880 (m-70) REVERT: B 258 GLN cc_start: 0.8737 (mp10) cc_final: 0.8436 (mp10) REVERT: B 446 ASP cc_start: 0.7960 (t0) cc_final: 0.7705 (t0) REVERT: B 485 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8832 (mttt) REVERT: B 491 GLN cc_start: 0.9121 (tt0) cc_final: 0.8595 (tm-30) REVERT: B 494 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7169 (ttp80) REVERT: B 499 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: B 583 LYS cc_start: 0.9135 (mmtt) cc_final: 0.8747 (mmtt) REVERT: B 613 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8830 (m-30) REVERT: B 880 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9202 (tm-30) REVERT: B 1093 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8931 (tp) REVERT: B 1162 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8569 (mtt-85) REVERT: B 1380 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8673 (tptp) REVERT: B 1687 MET cc_start: 0.8488 (mtm) cc_final: 0.7891 (mtm) REVERT: B 1888 GLN cc_start: 0.8449 (pp30) cc_final: 0.7976 (pp30) outliers start: 63 outliers final: 37 residues processed: 336 average time/residue: 0.2473 time to fit residues: 122.5399 Evaluate side-chains 328 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 279 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1335 LYS Chi-restraints excluded: chain A residue 1375 GLN Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1530 ASP Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1729 GLU Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1416 MET Chi-restraints excluded: chain B residue 1885 LEU Chi-restraints excluded: chain B residue 1927 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: [337, 345, 321, 294, 41, 281, 211, 94, 62, 72, 24] chunk 337 optimal weight: 5.9990 chunk 345 optimal weight: 0.7980 chunk 321 optimal weight: 5.9990 chunk 294 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 281 optimal weight: 0.6980 chunk 211 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.0060 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1654 GLN B1270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.051997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.041437 restraints weight = 88546.855| |-----------------------------------------------------------------------------| r_work (start): 0.2419 rms_B_bonded: 2.23 r_work: 0.2321 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2209 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29828 Z= 0.122 Angle : 0.556 13.342 40539 Z= 0.288 Chirality : 0.040 0.227 4420 Planarity : 0.004 0.050 5195 Dihedral : 11.544 178.353 4417 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.76 % Allowed : 16.61 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.04 (0.14), residues: 3545 helix: 2.15 (0.14), residues: 1448 sheet: 0.94 (0.25), residues: 456 loop : -0.75 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1731 TYR 0.029 0.001 TYR A 714 PHE 0.016 0.001 PHE A 144 TRP 0.009 0.001 TRP B1821 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (29800) covalent geometry : angle 0.54234 / 0.29 (40503) hydrogen bonds : bond 0.04709 / 3.25 ( 1251) hydrogen bonds : angle 4.10664 / 2.98 ( 3630) metal coordination : bond 0.00861 / 0.67 ( 28) metal coordination : angle 4.07575 / 2.18 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 292 time to evaluate : 1.389 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: A 62 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9085 (mttm) REVERT: A 94 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8619 (pp) REVERT: A 414 MET cc_start: 0.8361 (mmm) cc_final: 0.8056 (mmm) REVERT: A 617 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8662 (m-30) REVERT: A 695 ASP cc_start: 0.5995 (t0) cc_final: 0.5253 (t0) REVERT: A 1291 MET cc_start: 0.8880 (mmm) cc_final: 0.8458 (mmm) REVERT: A 1335 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8841 (ttpp) REVERT: A 1362 ARG cc_start: 0.8456 (tpt90) cc_final: 0.8137 (tpt170) REVERT: A 1596 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8629 (mt) REVERT: A 1724 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: B 250 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.7767 (m-70) REVERT: B 258 GLN cc_start: 0.8737 (mp10) cc_final: 0.8482 (mp10) REVERT: B 446 ASP cc_start: 0.7977 (t0) cc_final: 0.7733 (t0) REVERT: B 485 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8829 (mttt) REVERT: B 491 GLN cc_start: 0.9149 (tt0) cc_final: 0.8492 (tm-30) REVERT: B 494 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7166 (ttp80) REVERT: B 499 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8299 (m-30) REVERT: B 583 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8777 (mmtt) REVERT: B 613 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8803 (m-30) REVERT: B 880 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9205 (tm-30) REVERT: B 1093 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8964 (tp) REVERT: B 1162 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8941 (mtt-85) REVERT: B 1275 ASP cc_start: 0.9102 (t0) cc_final: 0.8867 (t0) REVERT: B 1380 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8676 (tptp) REVERT: B 1687 MET cc_start: 0.8439 (mtm) cc_final: 0.7895 (mtm) REVERT: B 1888 GLN cc_start: 0.8441 (pp30) cc_final: 0.7959 (pp30) outliers start: 83 outliers final: 55 residues processed: 355 average time/residue: 0.2355 time to fit residues: 123.4054 Evaluate side-chains 355 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 288 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1335 LYS Chi-restraints excluded: chain A residue 1375 GLN Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1530 ASP Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1729 GLU Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1851 GLN Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1389 GLU Chi-restraints excluded: chain B residue 1416 MET Chi-restraints excluded: chain B residue 1582 TYR Chi-restraints excluded: chain B residue 1869 LYS Chi-restraints excluded: chain B residue 1885 LEU Chi-restraints excluded: chain B residue 1927 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: [64, 259, 214, 142, 93, 97, 26, 343, 176, 182, 75] chunk 64 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 chunk 214 optimal weight: 0.0030 chunk 142 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 343 optimal weight: 0.0050 chunk 176 optimal weight: 0.9980 chunk 182 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 overall best weight: 0.2404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 627 HIS A1654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.053324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.042749 restraints weight = 87981.060| |-----------------------------------------------------------------------------| r_work (start): 0.2457 rms_B_bonded: 2.22 r_work: 0.2361 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2249 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29828 Z= 0.107 Angle : 0.546 12.250 40539 Z= 0.282 Chirality : 0.039 0.222 4420 Planarity : 0.004 0.050 5195 Dihedral : 11.494 177.629 4417 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.33 % Allowed : 17.27 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.16 (0.14), residues: 3545 helix: 2.27 (0.14), residues: 1444 sheet: 0.94 (0.24), residues: 466 loop : -0.69 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.000 ARG B 875 TYR 0.018 0.001 TYR A 714 PHE 0.011 0.001 PHE A 144 TRP 0.009 0.001 TRP A1781 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (29800) covalent geometry : angle 0.53512 / 0.28 (40503) hydrogen bonds : bond 0.04055 / 2.81 ( 1251) hydrogen bonds : angle 3.98549 / 2.89 ( 3630) metal coordination : bond 0.00650 / 0.51 ( 28) metal coordination : angle 3.60087 / 1.91 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 299 time to evaluate : 0.993 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: A 62 LYS cc_start: 0.9472 (OUTLIER) cc_final: 0.9085 (mttm) REVERT: A 94 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8648 (pp) REVERT: A 414 MET cc_start: 0.8317 (mmm) cc_final: 0.8020 (mmm) REVERT: A 617 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8641 (m-30) REVERT: A 636 ARG cc_start: 0.8477 (mtp85) cc_final: 0.7984 (mtp85) REVERT: A 695 ASP cc_start: 0.5846 (t0) cc_final: 0.5226 (t0) REVERT: A 1251 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8406 (m-80) REVERT: A 1291 MET cc_start: 0.8828 (mmm) cc_final: 0.8406 (mmm) REVERT: A 1335 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8829 (ttpp) REVERT: A 1362 ARG cc_start: 0.8486 (tpt90) cc_final: 0.8135 (tpt170) REVERT: A 1637 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7843 (mm-40) REVERT: A 1689 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8064 (p) REVERT: A 1690 ARG cc_start: 0.9130 (mmm-85) cc_final: 0.8883 (tpp80) REVERT: A 1913 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8379 (ttm-80) REVERT: B 250 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.7684 (m-70) REVERT: B 258 GLN cc_start: 0.8646 (mp10) cc_final: 0.8434 (mp10) REVERT: B 446 ASP cc_start: 0.8057 (t0) cc_final: 0.7774 (t0) REVERT: B 485 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8825 (mttt) REVERT: B 491 GLN cc_start: 0.9116 (tt0) cc_final: 0.8530 (tm-30) REVERT: B 494 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7072 (ttp80) REVERT: B 499 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: B 583 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8751 (mmtt) REVERT: B 613 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8854 (m-30) REVERT: B 1093 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8953 (tp) REVERT: B 1162 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8891 (mtt-85) REVERT: B 1307 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.8035 (ttp-170) REVERT: B 1380 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8678 (tptp) REVERT: B 1687 MET cc_start: 0.8457 (mtm) cc_final: 0.7941 (mtm) REVERT: B 1888 GLN cc_start: 0.8403 (pp30) cc_final: 0.7944 (pp30) outliers start: 70 outliers final: 45 residues processed: 353 average time/residue: 0.2368 time to fit residues: 123.6093 Evaluate side-chains 341 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 283 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1335 LYS Chi-restraints excluded: chain A residue 1375 GLN Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1530 ASP Chi-restraints excluded: chain A residue 1637 GLN Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1729 GLU Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1771 LEU Chi-restraints excluded: chain A residue 1851 GLN Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1389 GLU Chi-restraints excluded: chain B residue 1416 MET Chi-restraints excluded: chain B residue 1582 TYR Chi-restraints excluded: chain B residue 1587 VAL Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1885 LEU Chi-restraints excluded: chain B residue 1903 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: [326, 328, 265, 63, 75, 7, 351, 270, 309, 299, 106] chunk 326 optimal weight: 0.2980 chunk 328 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 351 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 299 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1520 GLN A1654 GLN B 292 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.051013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.040468 restraints weight = 88538.390| |-----------------------------------------------------------------------------| r_work (start): 0.2389 rms_B_bonded: 2.21 r_work: 0.2290 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2178 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 29828 Z= 0.174 Angle : 0.598 13.325 40539 Z= 0.310 Chirality : 0.042 0.222 4420 Planarity : 0.004 0.049 5195 Dihedral : 11.541 178.396 4413 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 2.60 % Allowed : 17.40 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.06 (0.14), residues: 3545 helix: 2.08 (0.14), residues: 1458 sheet: 1.02 (0.25), residues: 455 loop : -0.68 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 890 TYR 0.016 0.002 TYR A 714 PHE 0.024 0.002 PHE A 144 TRP 0.009 0.001 TRP B1821 HIS 0.008 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (29800) covalent geometry : angle 0.58629 / 0.31 (40503) hydrogen bonds : bond 0.05451 / 3.76 ( 1251) hydrogen bonds : angle 4.14184 / 3.01 ( 3630) metal coordination : bond 0.00928 / 0.66 ( 28) metal coordination : angle 4.03952 / 2.15 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 293 time to evaluate : 1.394 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: A 62 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9080 (mttm) REVERT: A 94 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8659 (pp) REVERT: A 356 MET cc_start: 0.9225 (mmp) cc_final: 0.8995 (mmm) REVERT: A 414 MET cc_start: 0.8411 (mmm) cc_final: 0.8092 (mmm) REVERT: A 617 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8655 (m-30) REVERT: A 636 ARG cc_start: 0.8400 (mtp85) cc_final: 0.7821 (mtp85) REVERT: A 714 TYR cc_start: 0.8458 (m-80) cc_final: 0.8235 (m-80) REVERT: A 1291 MET cc_start: 0.8921 (mmm) cc_final: 0.8511 (mmm) REVERT: A 1335 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8858 (ttpp) REVERT: A 1596 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8618 (mt) REVERT: A 1690 ARG cc_start: 0.9120 (mmm-85) cc_final: 0.8864 (tpp80) REVERT: A 1913 ARG cc_start: 0.8703 (ttm170) cc_final: 0.8223 (ttm-80) REVERT: B 250 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.7718 (m-70) REVERT: B 446 ASP cc_start: 0.8011 (t0) cc_final: 0.7758 (t0) REVERT: B 485 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8829 (mttt) REVERT: B 491 GLN cc_start: 0.9127 (tt0) cc_final: 0.8669 (tm-30) REVERT: B 583 LYS cc_start: 0.9169 (mmtt) cc_final: 0.8848 (mmtt) REVERT: B 613 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8806 (m-30) REVERT: B 1093 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8980 (tp) REVERT: B 1162 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8953 (mtt-85) REVERT: B 1190 ASP cc_start: 0.7715 (p0) cc_final: 0.7472 (p0) REVERT: B 1380 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8666 (tptp) REVERT: B 1687 MET cc_start: 0.8561 (mtm) cc_final: 0.7994 (mtm) REVERT: B 1888 GLN cc_start: 0.8473 (pp30) cc_final: 0.7992 (pp30) outliers start: 78 outliers final: 54 residues processed: 354 average time/residue: 0.2355 time to fit residues: 123.6202 Evaluate side-chains 344 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1335 LYS Chi-restraints excluded: chain A residue 1375 GLN Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1530 ASP Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1729 GLU Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1851 GLN Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1416 MET Chi-restraints excluded: chain B residue 1582 TYR Chi-restraints excluded: chain B residue 1587 VAL Chi-restraints excluded: chain B residue 1705 SER Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1885 LEU Chi-restraints excluded: chain B residue 1927 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: [149, 136, 230, 71, 92, 176, 308, 212, 73, 36, 171] chunk 149 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 308 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 171 optimal weight: 0.0270 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1520 GLN A1654 GLN B1270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.051464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.040920 restraints weight = 88332.347| |-----------------------------------------------------------------------------| r_work (start): 0.2403 rms_B_bonded: 2.22 r_work: 0.2305 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2193 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 29828 Z= 0.139 Angle : 0.591 14.572 40539 Z= 0.307 Chirality : 0.041 0.225 4420 Planarity : 0.004 0.052 5195 Dihedral : 11.547 178.236 4413 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 2.63 % Allowed : 17.57 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.06 (0.14), residues: 3545 helix: 2.11 (0.14), residues: 1444 sheet: 1.00 (0.25), residues: 457 loop : -0.69 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1731 TYR 0.014 0.001 TYR B1007 PHE 0.018 0.001 PHE A 144 TRP 0.010 0.001 TRP B1821 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (29800) covalent geometry : angle 0.58079 / 0.31 (40503) hydrogen bonds : bond 0.05039 / 3.48 ( 1251) hydrogen bonds : angle 4.12297 / 2.99 ( 3630) metal coordination : bond 0.00799 / 0.58 ( 28) metal coordination : angle 3.76704 / 2.00 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 288 time to evaluate : 1.139 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: A 62 LYS cc_start: 0.9481 (OUTLIER) cc_final: 0.9108 (mttm) REVERT: A 94 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8636 (pp) REVERT: A 356 MET cc_start: 0.9209 (mmp) cc_final: 0.8976 (mmm) REVERT: A 414 MET cc_start: 0.8408 (mmm) cc_final: 0.8093 (mmm) REVERT: A 617 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8642 (m-30) REVERT: A 636 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7838 (mtp85) REVERT: A 695 ASP cc_start: 0.5999 (t0) cc_final: 0.5360 (t0) REVERT: A 714 TYR cc_start: 0.8513 (m-80) cc_final: 0.8285 (m-80) REVERT: A 1291 MET cc_start: 0.8912 (mmm) cc_final: 0.8510 (mmm) REVERT: A 1335 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8845 (ttpp) REVERT: A 1362 ARG cc_start: 0.8454 (tpt90) cc_final: 0.8151 (tpt170) REVERT: A 1596 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8623 (mt) REVERT: A 1637 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: B 250 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.7696 (m-70) REVERT: B 446 ASP cc_start: 0.8011 (t0) cc_final: 0.7767 (t0) REVERT: B 485 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8825 (mttt) REVERT: B 491 GLN cc_start: 0.9118 (tt0) cc_final: 0.8700 (tm-30) REVERT: B 583 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8845 (mmtt) REVERT: B 613 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8825 (m-30) REVERT: B 1093 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8952 (tt) REVERT: B 1162 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8943 (mtt-85) REVERT: B 1380 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8689 (tptp) REVERT: B 1687 MET cc_start: 0.8466 (mtm) cc_final: 0.7818 (mtm) REVERT: B 1888 GLN cc_start: 0.8464 (pp30) cc_final: 0.7986 (pp30) outliers start: 79 outliers final: 59 residues processed: 352 average time/residue: 0.2379 time to fit residues: 123.6119 Evaluate side-chains 351 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 282 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1335 LYS Chi-restraints excluded: chain A residue 1375 GLN Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain A residue 1530 ASP Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1637 GLN Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1729 GLU Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1851 GLN Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1213 VAL Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1416 MET Chi-restraints excluded: chain B residue 1582 TYR Chi-restraints excluded: chain B residue 1587 VAL Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1885 LEU Chi-restraints excluded: chain B residue 1927 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: [207, 231, 56, 305, 245, 147, 113, 52, 135, 304, 89] chunk 207 optimal weight: 0.0010 chunk 231 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.9562 > 50:) chunk 56 optimal weight: 2.9990 chunk 305 optimal weight: 0.7980 chunk 245 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.052093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.041510 restraints weight = 88269.938| |-----------------------------------------------------------------------------| r_work (start): 0.2421 rms_B_bonded: 2.22 r_work: 0.2322 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29828 Z= 0.125 Angle : 0.585 14.796 40539 Z= 0.306 Chirality : 0.041 0.225 4420 Planarity : 0.004 0.060 5195 Dihedral : 11.467 178.089 4410 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 2.46 % Allowed : 17.70 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.08 (0.14), residues: 3545 helix: 2.12 (0.14), residues: 1448 sheet: 1.04 (0.24), residues: 466 loop : -0.70 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1731 TYR 0.013 0.001 TYR A1007 PHE 0.016 0.001 PHE A 144 TRP 0.010 0.001 TRP B1821 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (29800) covalent geometry : angle 0.57587 / 0.31 (40503) hydrogen bonds : bond 0.04681 / 3.23 ( 1251) hydrogen bonds : angle 4.10314 / 2.97 ( 3630) metal coordination : bond 0.00714 / 0.53 ( 28) metal coordination : angle 3.55690 / 1.88 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 291 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.9481 (OUTLIER) cc_final: 0.9089 (mttm) REVERT: A 94 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8639 (pp) REVERT: A 356 MET cc_start: 0.9202 (mmp) cc_final: 0.8985 (mmm) REVERT: A 414 MET cc_start: 0.8360 (mmm) cc_final: 0.8058 (mmm) REVERT: A 617 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8642 (m-30) REVERT: A 636 ARG cc_start: 0.8377 (mtp85) cc_final: 0.7796 (mtp85) REVERT: A 695 ASP cc_start: 0.5927 (t0) cc_final: 0.5273 (t0) REVERT: A 714 TYR cc_start: 0.8526 (m-80) cc_final: 0.8274 (m-80) REVERT: A 874 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8521 (mp0) REVERT: A 1291 MET cc_start: 0.8882 (mmm) cc_final: 0.8478 (mmm) REVERT: A 1335 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8845 (ttpp) REVERT: A 1362 ARG cc_start: 0.8465 (tpt90) cc_final: 0.8148 (tpt170) REVERT: A 1557 ASP cc_start: 0.8648 (t0) cc_final: 0.8369 (t0) REVERT: A 1596 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8633 (mt) REVERT: A 1637 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7871 (mm-40) REVERT: A 1913 ARG cc_start: 0.8717 (ttm170) cc_final: 0.8251 (ttm-80) REVERT: B 446 ASP cc_start: 0.7988 (t0) cc_final: 0.7739 (t0) REVERT: B 485 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8830 (mttt) REVERT: B 491 GLN cc_start: 0.9098 (tt0) cc_final: 0.8696 (tm-30) REVERT: B 583 LYS cc_start: 0.9176 (mmtt) cc_final: 0.8849 (mmtt) REVERT: B 613 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8798 (m-30) REVERT: B 1093 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8936 (tt) REVERT: B 1162 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8616 (mtt-85) REVERT: B 1190 ASP cc_start: 0.7704 (p0) cc_final: 0.7465 (p0) REVERT: B 1380 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8674 (tptp) REVERT: B 1687 MET cc_start: 0.8482 (mtm) cc_final: 0.7907 (mtm) REVERT: B 1888 GLN cc_start: 0.8457 (pp30) cc_final: 0.7984 (pp30) outliers start: 74 outliers final: 56 residues processed: 350 average time/residue: 0.2285 time to fit residues: 118.4761 Evaluate side-chains 350 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 285 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1335 LYS Chi-restraints excluded: chain A residue 1375 GLN Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1530 ASP Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1637 GLN Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1729 GLU Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1851 GLN Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1213 VAL Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1310 CYS Chi-restraints excluded: chain B residue 1582 TYR Chi-restraints excluded: chain B residue 1587 VAL Chi-restraints excluded: chain B residue 1711 VAL Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1885 LEU Chi-restraints excluded: chain B residue 1903 LEU Chi-restraints excluded: chain B residue 1927 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: [151, 245, 199, 332, 105, 82, 211, 111, 32, 33, 76] chunk 151 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 199 optimal weight: 0.0570 chunk 332 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 211 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.0020 chunk 33 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.5508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1520 GLN A1654 GLN B1270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.052584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.041962 restraints weight = 87862.273| |-----------------------------------------------------------------------------| r_work (start): 0.2434 rms_B_bonded: 2.23 r_work: 0.2337 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2225 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29828 Z= 0.122 Angle : 0.598 14.554 40539 Z= 0.310 Chirality : 0.040 0.225 4420 Planarity : 0.004 0.064 5195 Dihedral : 11.450 178.074 4408 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 2.26 % Allowed : 17.97 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.12 (0.14), residues: 3545 helix: 2.15 (0.14), residues: 1449 sheet: 1.07 (0.24), residues: 465 loop : -0.68 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1731 TYR 0.014 0.001 TYR A1007 PHE 0.015 0.001 PHE A 144 TRP 0.011 0.001 TRP B1821 HIS 0.005 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (29800) covalent geometry : angle 0.58997 / 0.31 (40503) hydrogen bonds : bond 0.04451 / 3.07 ( 1251) hydrogen bonds : angle 4.07391 / 2.94 ( 3630) metal coordination : bond 0.00632 / 0.47 ( 28) metal coordination : angle 3.41330 / 1.80 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 290 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.9082 (mttm) REVERT: A 94 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8616 (pp) REVERT: A 356 MET cc_start: 0.9196 (mmp) cc_final: 0.8996 (mmm) REVERT: A 414 MET cc_start: 0.8356 (mmm) cc_final: 0.8050 (mmm) REVERT: A 617 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8631 (m-30) REVERT: A 636 ARG cc_start: 0.8367 (mtp85) cc_final: 0.7783 (mtp85) REVERT: A 695 ASP cc_start: 0.5841 (t0) cc_final: 0.5246 (t0) REVERT: A 714 TYR cc_start: 0.8574 (m-80) cc_final: 0.8273 (m-80) REVERT: A 874 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8547 (mp0) REVERT: A 1291 MET cc_start: 0.8857 (mmm) cc_final: 0.8442 (mmm) REVERT: A 1335 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8851 (ttpp) REVERT: A 1557 ASP cc_start: 0.8525 (t0) cc_final: 0.8201 (t0) REVERT: A 1596 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8647 (mt) REVERT: A 1637 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7858 (mm-40) REVERT: A 1913 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8225 (ttm-80) REVERT: B 301 LYS cc_start: 0.8101 (tppt) cc_final: 0.7842 (mmmt) REVERT: B 446 ASP cc_start: 0.7982 (t0) cc_final: 0.7725 (t0) REVERT: B 485 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8812 (mttt) REVERT: B 491 GLN cc_start: 0.9099 (tt0) cc_final: 0.8679 (tm-30) REVERT: B 583 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8849 (mmtt) REVERT: B 613 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8777 (m-30) REVERT: B 893 GLU cc_start: 0.8987 (tp30) cc_final: 0.8655 (mp0) REVERT: B 1093 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8925 (tt) REVERT: B 1162 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8594 (mtt-85) REVERT: B 1190 ASP cc_start: 0.7683 (p0) cc_final: 0.7460 (p0) REVERT: B 1211 MET cc_start: 0.8739 (ptt) cc_final: 0.8374 (ptt) REVERT: B 1307 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7939 (ttp-170) REVERT: B 1380 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8645 (tptp) REVERT: B 1687 MET cc_start: 0.8465 (mtm) cc_final: 0.7905 (mtm) REVERT: B 1731 ARG cc_start: 0.8598 (mmm160) cc_final: 0.8366 (mmm160) REVERT: B 1888 GLN cc_start: 0.8454 (pp30) cc_final: 0.7969 (pp30) outliers start: 68 outliers final: 55 residues processed: 346 average time/residue: 0.2359 time to fit residues: 121.2092 Evaluate side-chains 348 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 284 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1335 LYS Chi-restraints excluded: chain A residue 1375 GLN Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain A residue 1530 ASP Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1637 GLN Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1729 GLU Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1851 GLN Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1582 TYR Chi-restraints excluded: chain B residue 1587 VAL Chi-restraints excluded: chain B residue 1711 VAL Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1885 LEU Chi-restraints excluded: chain B residue 1903 LEU Chi-restraints excluded: chain B residue 1927 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: [342, 56, 50, 7, 354, 128, 6, 328, 252, 104, 207] chunk 342 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 354 optimal weight: 0.0970 chunk 128 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 328 optimal weight: 6.9990 chunk 252 optimal weight: 0.0060 chunk 104 optimal weight: 3.9990 chunk 207 optimal weight: 0.2980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.043083 restraints weight = 88320.348| |-----------------------------------------------------------------------------| r_work (start): 0.2467 rms_B_bonded: 2.25 r_work: 0.2371 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2259 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 29828 Z= 0.113 Angle : 0.587 13.898 40539 Z= 0.305 Chirality : 0.040 0.226 4420 Planarity : 0.004 0.065 5195 Dihedral : 11.441 178.150 4408 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 1.93 % Allowed : 18.47 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.24 (0.14), residues: 3545 helix: 2.27 (0.14), residues: 1443 sheet: 1.13 (0.25), residues: 465 loop : -0.62 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1731 TYR 0.012 0.001 TYR A1007 PHE 0.015 0.001 PHE B 144 TRP 0.011 0.001 TRP A1781 HIS 0.021 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (29800) covalent geometry : angle 0.58014 / 0.30 (40503) hydrogen bonds : bond 0.03919 / 2.71 ( 1251) hydrogen bonds : angle 3.99345 / 2.89 ( 3630) metal coordination : bond 0.00544 / 0.42 ( 28) metal coordination : angle 3.12672 / 1.66 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6390.32 seconds wall clock time: 109 minutes 57.44 seconds (6597.44 seconds total)