Starting phenix.real_space_refine on Thu Oct 29 10:27:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9waf_65816/10_2026/9waf_65816.cif Found real_map, /net/cci-nas-00/data/ceres_data/9waf_65816/10_2026/9waf_65816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9waf_65816/10_2026/9waf_65816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9waf_65816/10_2026/9waf_65816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9waf_65816/10_2026/9waf_65816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9waf_65816/10_2026/9waf_65816.map" } resolution = 3.29 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= 0.004 sd= 0.511 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 41 5.49 5 Mg 2 5.21 5 S 119 5.16 5 C 19428 2.51 5 N 5557 2.21 5 O 5905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 31060 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1900, 15038 Classifications: {'peptide': 1900} Link IDs: {'PCIS': 2, 'PTRANS': 105, 'TRANS': 1792} Chain breaks: 6 Chain: "B" Number of atoms: 15198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1920, 15198 Classifications: {'peptide': 1920} Link IDs: {'PCIS': 1, 'PTRANS': 107, 'TRANS': 1811} Chain breaks: 5 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 760 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' MG': 1, ' ZN': 4, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' MG': 1, ' ZN': 4, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8447 SG CYS A1110 59.576 110.518 61.644 1.00 67.38 S ATOM 8467 SG CYS A1113 60.751 107.043 62.165 1.00 76.68 S ATOM 8562 SG CYS A1125 58.901 108.305 64.721 1.00 83.21 S ATOM 8586 SG CYS A1128 61.630 110.700 63.974 1.00 87.10 S ATOM 5015 SG CYS A 646 67.244 98.937 60.181 1.00 67.19 S ATOM 5035 SG CYS A 649 66.586 101.958 58.742 1.00 73.12 S ATOM 5786 SG CYS A 770 69.450 101.413 61.109 1.00 75.81 S ATOM 5808 SG CYS A 773 66.374 101.579 62.895 1.00 72.53 S ATOM 13901 SG CYS A1799 85.429 75.844 29.001 1.00 90.76 S ATOM 13929 SG CYS A1803 82.530 74.606 28.349 1.00 75.71 S ATOM 13958 SG CYS A1806 84.856 72.045 28.917 1.00 72.01 S ATOM 11654 SG CYS A1509 105.680 50.406 52.485 1.00110.79 S ATOM 11672 SG CYS A1512 105.540 49.959 47.827 1.00117.37 S ATOM 11777 SG CYS A1528 104.460 47.046 51.168 1.00118.02 S ATOM 11799 SG CYS A1531 107.527 47.937 49.711 1.00152.03 S ATOM 23572 SG CYS B1110 23.055 45.428 108.422 1.00 57.45 S ATOM 23592 SG CYS B1113 27.026 45.565 107.967 1.00 58.24 S ATOM 23687 SG CYS B1125 25.479 47.034 105.364 1.00 78.08 S ATOM 23711 SG CYS B1128 25.320 43.518 106.884 1.00 59.66 S ATOM 20031 SG CYS B 646 33.328 42.235 114.594 1.00 61.21 S ATOM 20051 SG CYS B 649 29.760 42.117 115.200 1.00 60.60 S ATOM 20933 SG CYS B 770 31.709 38.818 114.222 1.00 59.32 S ATOM 20955 SG CYS B 773 30.420 41.049 112.085 1.00 58.31 S ATOM 29026 SG CYS B1799 57.037 44.327 150.301 1.00 61.40 S ATOM 29054 SG CYS B1803 57.720 47.984 149.758 1.00 59.74 S ATOM 29083 SG CYS B1806 60.668 46.104 149.648 1.00 57.06 S ATOM 26779 SG CYS B1509 77.313 23.899 128.762 1.00 68.85 S ATOM 26797 SG CYS B1512 76.702 25.385 131.752 1.00 62.80 S ATOM 26902 SG CYS B1528 80.320 25.962 130.644 1.00 78.00 S ATOM 26924 SG CYS B1531 78.524 22.826 131.948 1.00 71.69 S Time building chain proxies: 6.56, per 1000 atoms: 0.21 Number of scatterers: 31060 At special positions: 0 Unit cell: (128.64, 127.68, 177.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 119 16.00 P 41 15.00 Mg 2 11.99 O 5905 8.00 N 5557 7.00 C 19428 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1128 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1113 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1125 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1110 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 770 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 649 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 773 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 646 " pdb=" ZN A2005 " pdb="ZN ZN A2005 " - pdb=" NE2 HIS A1795 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1803 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1799 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1806 " pdb=" ZN A2006 " pdb="ZN ZN A2006 " - pdb=" SG CYS A1531 " pdb="ZN ZN A2006 " - pdb=" SG CYS A1528 " pdb="ZN ZN A2006 " - pdb=" SG CYS A1509 " pdb="ZN ZN A2006 " - pdb=" SG CYS A1512 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1125 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1128 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1113 " pdb=" ZN B2004 " pdb="ZN ZN B2004 " - pdb=" SG CYS B 773 " pdb="ZN ZN B2004 " - pdb=" SG CYS B 646 " pdb="ZN ZN B2004 " - pdb=" SG CYS B 770 " pdb="ZN ZN B2004 " - pdb=" SG CYS B 649 " pdb=" ZN B2005 " pdb="ZN ZN B2005 " - pdb=" NE2 HIS B1795 " pdb="ZN ZN B2005 " - pdb=" SG CYS B1803 " pdb="ZN ZN B2005 " - pdb=" SG CYS B1806 " pdb="ZN ZN B2005 " - pdb=" SG CYS B1799 " pdb=" ZN B2006 " pdb="ZN ZN B2006 " - pdb=" SG CYS B1528 " pdb="ZN ZN B2006 " - pdb=" SG CYS B1509 " pdb="ZN ZN B2006 " - pdb=" SG CYS B1531 " pdb="ZN ZN B2006 " - pdb=" SG CYS B1512 " Number of angles added : 42 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 21 sheets defined 44.6% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 4 through 24 Processing helix chain 'A' and resid 28 through 41 Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.580A pdb=" N GLU A 69 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 94 removed outlier: 3.654A pdb=" N GLY A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.648A pdb=" N ARG A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 157 Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.620A pdb=" N VAL A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 256 through 294 removed outlier: 3.624A pdb=" N ASP A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.759A 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 Processing helix chain 'A' and resid 344 through 358 removed outlier: 3.757A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 358 " --> pdb=" O TRP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 375 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 415 through 431 Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.861A 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 removed outlier: 3.698A pdb=" N ASP A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 535 removed outlier: 3.723A 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: 3.540A pdb=" N ARG A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.529A pdb=" N MET A 692 " --> pdb=" O TYR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 816 Processing helix chain 'A' and resid 827 through 863 removed outlier: 3.902A pdb=" N ARG A 848 " --> pdb=" O ARG A 844 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 863 " --> pdb=" O VAL A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 883 Processing helix chain 'A' and resid 884 through 900 removed outlier: 4.393A pdb=" N VAL A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 890 " --> pdb=" O ASP A 886 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) 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: 4.739A pdb=" N GLU A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.741A 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 1029 removed outlier: 4.090A pdb=" N ASP A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A1029 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1043 removed outlier: 3.540A pdb=" N VAL A1043 " --> pdb=" O LYS A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1054 through 1065 Processing helix chain 'A' and resid 1069 through 1085 Processing helix chain 'A' and resid 1092 through 1095 removed outlier: 3.670A pdb=" N LYS A1095 " --> pdb=" O ASN A1092 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1092 through 1095' Processing helix chain 'A' and resid 1138 through 1146 removed outlier: 3.875A pdb=" N LEU A1142 " --> pdb=" O LYS A1138 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A1146 " --> pdb=" O LEU A1142 " (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: 3.814A pdb=" N VAL A1213 " --> pdb=" O THR A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1240 Processing helix chain 'A' and resid 1259 through 1268 removed outlier: 3.629A pdb=" N TYR A1265 " --> pdb=" O HIS A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1275 removed outlier: 4.356A pdb=" N ILE A1272 " --> pdb=" O HIS A1268 " (cutoff:3.500A) removed outlier: 3.654A 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 1322 Processing helix chain 'A' and resid 1333 through 1339 Processing helix chain 'A' and resid 1344 through 1356 removed outlier: 3.614A pdb=" N ARG A1348 " --> pdb=" O ASP A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1368 removed outlier: 4.254A pdb=" N ARG A1360 " --> pdb=" O THR A1356 " (cutoff:3.500A) removed outlier: 4.119A 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 1392 Processing helix chain 'A' and resid 1403 through 1412 Processing helix chain 'A' and resid 1419 through 1421 No H-bonds generated for 'chain 'A' and resid 1419 through 1421' Processing helix chain 'A' and resid 1451 through 1458 removed outlier: 4.238A pdb=" N PHE A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1647 Processing helix chain 'A' and resid 1696 through 1718 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 1757 Processing helix chain 'A' and resid 1765 through 1777 removed outlier: 3.545A pdb=" N ASP A1769 " --> pdb=" O PRO A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1788 Processing helix chain 'A' and resid 1789 through 1793 removed outlier: 3.527A pdb=" N GLU A1792 " --> pdb=" O THR A1789 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A1793 " --> pdb=" O GLY A1790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1789 through 1793' Processing helix chain 'A' and resid 1794 through 1799 Processing helix chain 'A' and resid 1812 through 1816 removed outlier: 3.746A pdb=" N HIS A1816 " --> pdb=" O ARG A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1833 removed outlier: 3.571A pdb=" N GLY A1824 " --> pdb=" O ASP A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1868 Processing helix chain 'A' and resid 1908 through 1917 removed outlier: 3.813A 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 Processing helix chain 'A' and resid 1935 through 1944 removed outlier: 3.601A pdb=" N ARG A1939 " --> pdb=" O ARG A1935 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS A1944 " --> pdb=" O LEU A1940 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 139 through 157 Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 200 through 216 removed outlier: 3.768A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 removed outlier: 3.525A pdb=" N THR B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 291 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.680A pdb=" N PHE B 306 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 332 through 341 Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.639A pdb=" N PHE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 374 through 393 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.675A pdb=" N LYS B 452 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 482 Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 515 through 535 removed outlier: 3.563A pdb=" N CYS B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'B' and resid 560 through 578 Proline residue: B 575 - end of helix removed outlier: 3.916A pdb=" N ASN B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 680 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 816 Processing helix chain 'B' and resid 827 through 862 Processing helix chain 'B' and resid 868 through 883 Processing helix chain 'B' and resid 884 through 900 Processing helix chain 'B' and resid 911 through 916 Processing helix chain 'B' and resid 924 through 934 removed outlier: 3.765A pdb=" N LEU B 933 " --> pdb=" O GLU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 953 removed outlier: 3.515A pdb=" N ARG B 953 " --> pdb=" O PRO B 950 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 950 through 953' Processing helix chain 'B' and resid 969 through 993 removed outlier: 3.798A pdb=" N GLU B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 Processing helix chain 'B' and resid 1016 through 1029 removed outlier: 3.551A 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 1065 Processing helix chain 'B' and resid 1069 through 1085 Processing helix chain 'B' and resid 1092 through 1095 Processing helix chain 'B' and resid 1139 through 1146 removed outlier: 3.640A pdb=" N GLU B1144 " --> pdb=" O GLU B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1159 removed outlier: 3.623A pdb=" N ARG B1151 " --> pdb=" O PHE B1147 " (cutoff:3.500A) removed outlier: 3.898A 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 1209 through 1213 removed outlier: 3.619A pdb=" N VAL B1213 " --> pdb=" O THR B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1231 through 1240 Processing helix chain 'B' and resid 1259 through 1268 removed outlier: 3.503A pdb=" N TYR B1265 " --> pdb=" O HIS B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1268 through 1275 removed outlier: 4.135A pdb=" N ILE B1272 " --> pdb=" O HIS B1268 " (cutoff:3.500A) Processing helix chain 'B' and resid 1287 through 1314 removed outlier: 3.768A pdb=" N LEU B1293 " --> pdb=" O ILE B1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1322 removed outlier: 4.368A pdb=" N LEU B1321 " --> pdb=" O PHE B1317 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B1322 " --> pdb=" O PRO B1318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1317 through 1322' Processing helix chain 'B' and resid 1333 through 1339 Processing helix chain 'B' and resid 1344 through 1355 removed outlier: 3.681A pdb=" N ARG B1348 " --> pdb=" O ASP B1344 " (cutoff:3.500A) Processing helix chain 'B' and resid 1357 through 1368 removed outlier: 3.561A pdb=" N ASP B1361 " --> pdb=" O GLN B1357 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B1368 " --> pdb=" O ILE B1364 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1381 Processing helix chain 'B' and resid 1382 through 1392 Processing helix chain 'B' and resid 1393 through 1397 Processing helix chain 'B' and resid 1403 through 1411 Processing helix chain 'B' and resid 1451 through 1458 removed outlier: 4.046A pdb=" N PHE B1456 " --> pdb=" O ASP B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1536 through 1540 Processing helix chain 'B' and resid 1641 through 1647 Processing helix chain 'B' and resid 1696 through 1719 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 removed outlier: 3.550A pdb=" N GLY B1756 " --> pdb=" O SER B1752 " (cutoff:3.500A) Processing helix chain 'B' and resid 1765 through 1777 removed outlier: 3.582A pdb=" N ASP B1769 " --> pdb=" O PRO B1765 " (cutoff:3.500A) Processing helix chain 'B' and resid 1780 through 1787 Processing helix chain 'B' and resid 1809 through 1813 Processing helix chain 'B' and resid 1820 through 1833 removed outlier: 3.530A pdb=" N VAL B1832 " --> pdb=" O LEU B1828 " (cutoff:3.500A) Processing helix chain 'B' and resid 1843 through 1847 removed outlier: 3.674A pdb=" N LYS B1846 " --> pdb=" O GLY B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1852 through 1868 removed outlier: 3.528A pdb=" N ARG B1856 " --> pdb=" O GLY B1852 " (cutoff:3.500A) Processing helix chain 'B' and resid 1908 through 1917 removed outlier: 3.858A pdb=" N MET B1912 " --> pdb=" O GLU B1908 " (cutoff:3.500A) Processing helix chain 'B' and resid 1918 through 1920 No H-bonds generated for 'chain 'B' and resid 1918 through 1920' Processing helix chain 'B' and resid 1929 through 1935 Processing helix chain 'B' and resid 1935 through 1946 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.962A pdb=" N PHE A 591 " --> pdb=" O SER A1250 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A1252 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 593 " --> pdb=" O VAL A1252 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR A1254 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 595 " --> pdb=" O THR A1254 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS A1256 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 597 " --> pdb=" O CYS A1256 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A1223 " --> pdb=" O VAL A1253 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N PHE A1255 " --> pdb=" O VAL A1223 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN A1225 " --> pdb=" O PHE A1255 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 822 " --> pdb=" O THR A1222 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY A 821 " --> pdb=" O LEU A1205 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A1207 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 823 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU A1168 " --> pdb=" O SER A1206 " (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: 6.872A pdb=" N PHE A 235 " --> pdb=" O MET A 314 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A 236 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ASN A 331 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 195 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE A 363 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 406 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU A 365 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N SER A 408 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE A 367 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLY A 130 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N SER A 409 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL A 132 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 604 through 608 removed outlier: 6.769A pdb=" N PHE A 604 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE A 619 " --> pdb=" O PHE A 604 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 615 through 620 current: chain 'A' and resid 652 through 657 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 652 through 657 current: chain 'A' and resid 728 through 731 Processing sheet with id=AA5, first strand: chain 'A' and resid 908 through 910 Processing sheet with id=AA6, first strand: chain 'A' and resid 955 through 958 Processing sheet with id=AA7, first strand: chain 'A' and resid 1108 through 1109 Processing sheet with id=AA8, first strand: chain 'A' and resid 1442 through 1450 removed outlier: 6.436A pdb=" N GLU A1443 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A1430 " --> pdb=" O GLU A1443 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER A1445 " --> pdb=" O VAL A1428 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY A1429 " --> pdb=" O THR A1551 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA A1548 " --> pdb=" O PHE A1476 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A1476 " --> pdb=" O ALA A1548 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG A1550 " --> pdb=" O ILE A1474 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1500 through 1508 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1515 through 1518 current: chain 'A' and resid 1585 through 1589 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1585 through 1589 current: chain 'A' and resid 1637 through 1640 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1637 through 1640 current: chain 'A' and resid 1736 through 1743 Processing sheet with id=AB1, first strand: chain 'A' and resid 1526 through 1527 Processing sheet with id=AB2, first strand: chain 'A' and resid 1873 through 1876 removed outlier: 3.508A pdb=" N ALA A1897 " --> pdb=" O LEU A1885 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 50 through 54 removed outlier: 7.001A pdb=" N PHE B 591 " --> pdb=" O SER B1250 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL B1252 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL B 593 " --> pdb=" O VAL B1252 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR B1254 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR B 595 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N CYS B1256 " --> pdb=" O THR B 595 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 597 " --> pdb=" O CYS B1256 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B1223 " --> pdb=" O VAL B1253 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE B1255 " --> pdb=" O VAL B1223 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLN B1225 " --> pdb=" O PHE B1255 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE B 822 " --> pdb=" O THR B1222 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY B 821 " --> pdb=" O LEU B1205 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL B1207 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B 823 " --> pdb=" O VAL B1207 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU B1168 " --> pdb=" O SER B1206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB5, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.721A pdb=" N PHE B 235 " --> pdb=" O MET B 314 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY B 236 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ASN B 331 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 195 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 131 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 604 through 608 removed outlier: 6.593A pdb=" N PHE B 604 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 619 " --> pdb=" O PHE B 604 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 615 through 620 current: chain 'B' and resid 653 through 659 removed outlier: 3.705A pdb=" N GLU B 669 " --> pdb=" O GLY B 659 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 667 through 671 current: chain 'B' and resid 728 through 731 Processing sheet with id=AB7, first strand: chain 'B' and resid 908 through 910 Processing sheet with id=AB8, first strand: chain 'B' and resid 955 through 958 Processing sheet with id=AB9, first strand: chain 'B' and resid 1116 through 1117 removed outlier: 3.699A pdb=" N GLY B1137 " --> pdb=" O PHE B1107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1423 through 1432 removed outlier: 6.609A pdb=" N SER B1445 " --> pdb=" O VAL B1428 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU B1430 " --> pdb=" O GLU B1443 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU B1443 " --> pdb=" O LEU B1430 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1442 through 1450 current: chain 'B' and resid 1469 through 1476 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1469 through 1476 current: chain 'B' and resid 1515 through 1518 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1515 through 1518 current: chain 'B' and resid 1585 through 1602 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1585 through 1602 current: chain 'B' and resid 1637 through 1640 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1637 through 1640 current: chain 'B' and resid 1736 through 1743 Processing sheet with id=AC2, first strand: chain 'B' and resid 1526 through 1527 removed outlier: 3.574A pdb=" N LEU B1526 " --> pdb=" O ILE B1535 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1872 through 1876 removed outlier: 3.879A pdb=" N TRP B1895 " --> pdb=" O GLU B1887 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS B1889 " --> pdb=" O GLU B1893 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU B1893 " --> pdb=" O LYS B1889 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ARG B1925 " --> pdb=" O LEU B1894 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG B1896 " --> pdb=" O ARG B1925 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B1927 " --> pdb=" O ARG B1896 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL B1898 " --> pdb=" O LEU B1927 " (cutoff:3.500A) 1184 hydrogen bonds defined for protein. 3369 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.11 Time building geometry restraints manager: 3.69 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: 9830 1.33 - 1.45: 4345 1.45 - 1.57: 17362 1.57 - 1.69: 78 1.69 - 1.81: 181 Bond restraints: 31796 Sorted by residual: bond pdb=" C3' DT C 10 " pdb=" C2' DT C 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.51e+00 bond pdb=" C1' DT C 1 " pdb=" N1 DT C 1 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.39e+00 bond pdb=" C1' DT C 56 " pdb=" N1 DT C 56 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.35e+00 bond pdb=" C3' DG C 65 " pdb=" C2' DG C 65 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.89e+00 bond pdb=" C3' DT C 52 " pdb=" C2' DT C 52 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.62e+00 ... (remaining 31791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 41681 1.27 - 2.53: 1161 2.53 - 3.80: 328 3.80 - 5.07: 44 5.07 - 6.33: 14 Bond angle restraints: 43228 Sorted by residual: angle pdb=" N3 DT C 1 " pdb=" C4 DT C 1 " pdb=" O4 DT C 1 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C 51 " pdb=" C4 DT C 51 " pdb=" O4 DT C 51 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+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 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT C 60 " pdb=" C4 DT C 60 " pdb=" O4 DT C 60 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 43223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 16660 17.84 - 35.69: 1849 35.69 - 53.53: 522 53.53 - 71.37: 112 71.37 - 89.22: 28 Dihedral angle restraints: 19171 sinusoidal: 8152 harmonic: 11019 Sorted by residual: dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 10.97 -70.97 1 2.00e+01 2.50e-03 1.62e+01 dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 -130.61 70.61 1 2.00e+01 2.50e-03 1.60e+01 dihedral pdb=" CA THR B 242 " pdb=" C THR B 242 " pdb=" N PRO B 243 " pdb=" CA PRO B 243 " ideal model delta harmonic sigma weight residual -180.00 -160.04 -19.96 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 19168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3393 0.037 - 0.073: 951 0.073 - 0.110: 249 0.110 - 0.146: 107 0.146 - 0.183: 15 Chirality restraints: 4715 Sorted by residual: chirality pdb=" C3' DG C 61 " pdb=" C4' DG C 61 " pdb=" O3' DG C 61 " pdb=" C2' DG C 61 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" C3' DT C 60 " pdb=" C4' DT C 60 " pdb=" O3' DT C 60 " pdb=" C2' DT C 60 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" C3' DA C 59 " pdb=" C4' DA C 59 " pdb=" O3' DA C 59 " pdb=" C2' DA C 59 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 4712 not shown) Planarity restraints: 5552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 71 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" CD GLU B 71 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU B 71 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 71 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1777 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO A1778 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1778 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1778 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 431 " 0.028 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 432 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " 0.021 5.00e-02 4.00e+02 ... (remaining 5549 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 53 2.53 - 3.12: 22699 3.12 - 3.72: 44284 3.72 - 4.31: 60976 4.31 - 4.90: 107312 Nonbonded interactions: 235324 Sorted by model distance: nonbonded pdb=" O3B ADP B2001 " pdb="MG MG B2002 " model vdw 1.940 2.170 nonbonded pdb=" OD2 ASP A 368 " pdb="MG MG A2002 " model vdw 2.048 2.170 nonbonded pdb=" OD1 ASP A 368 " pdb="MG MG A2002 " model vdw 2.110 2.170 nonbonded pdb=" O2B ADP B2001 " pdb="MG MG B2002 " model vdw 2.239 2.170 nonbonded pdb=" CG ASP A 368 " pdb="MG MG A2002 " model vdw 2.365 2.400 ... (remaining 235319 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 3 through 294 or resid 300 through 900 or resid 905 throug \ h 2006)) selection = (chain 'B' and (resid 3 through 658 or resid 666 through 680 or resid 688 throug \ h 750 or resid 763 through 1886 or resid 1894 through 1944 or resid 2001 through \ 2006)) } 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: 6.370 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: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 32.050 Find NCS groups from input model: 0.710 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 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 0.245 31828 Z= 0.196 Angle : 0.729 31.453 43270 Z= 0.339 Chirality : 0.040 0.183 4715 Planarity : 0.004 0.043 5552 Dihedral : 16.552 89.215 12067 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.71 % Allowed : 15.16 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.41 (0.14), residues: 3794 helix: 1.59 (0.14), residues: 1504 sheet: 0.44 (0.22), residues: 569 loop : -0.99 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 683 TYR 0.015 0.001 TYR B1007 PHE 0.018 0.001 PHE B 144 TRP 0.012 0.001 TRP B1821 HIS 0.005 0.001 HIS B1339 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.17 (31796) covalent geometry : angle 0.55819 / 0.33 (43228) hydrogen bonds : bond 0.14719 / 9.82 ( 1184) hydrogen bonds : angle 5.42415 / 3.85 ( 3369) metal coordination : bond 0.08515 / 6.36 ( 32) metal coordination : angle 15.04117 / 10.31 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 340 time to evaluate : 1.124 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: A 36 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8066 (ttm110) REVERT: A 187 LYS cc_start: 0.8420 (mptt) cc_final: 0.8192 (mmtm) REVERT: A 248 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: A 504 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7961 (tm-30) REVERT: A 696 GLU cc_start: 0.8832 (mp0) cc_final: 0.8354 (mp0) REVERT: A 787 ARG cc_start: 0.8648 (mmt180) cc_final: 0.8303 (mmm-85) REVERT: A 871 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8802 (tm-30) REVERT: A 874 GLU cc_start: 0.9015 (pp20) cc_final: 0.8726 (pp20) REVERT: A 896 LYS cc_start: 0.9315 (mtpp) cc_final: 0.9069 (ttmm) REVERT: A 897 LYS cc_start: 0.9551 (mttt) cc_final: 0.9224 (mtmm) REVERT: A 1015 ASP cc_start: 0.7962 (p0) cc_final: 0.7716 (p0) REVERT: A 1251 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: A 1446 MET cc_start: 0.9137 (ptt) cc_final: 0.8881 (ptm) REVERT: A 1565 MET cc_start: 0.8794 (ppp) cc_final: 0.8464 (ppp) REVERT: A 1597 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: A 1646 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8986 (m) REVERT: A 1687 MET cc_start: 0.9206 (mtm) cc_final: 0.8721 (mtm) REVERT: A 1884 CYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7386 (p) REVERT: B 66 ASP cc_start: 0.8001 (t0) cc_final: 0.7307 (t0) REVERT: B 69 GLU cc_start: 0.8324 (mp0) cc_final: 0.7523 (mp0) REVERT: B 70 GLU cc_start: 0.7998 (pm20) cc_final: 0.7747 (pm20) REVERT: B 290 ASP cc_start: 0.8898 (t0) cc_final: 0.8388 (t0) REVERT: B 452 LYS cc_start: 0.6416 (pttp) cc_final: 0.5672 (pttm) REVERT: B 478 MET cc_start: 0.9232 (tpt) cc_final: 0.8685 (tpt) REVERT: B 513 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8381 (mp0) REVERT: B 761 GLN cc_start: 0.7843 (mt0) cc_final: 0.7266 (mm-40) REVERT: B 1051 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8704 (m-30) REVERT: B 1869 LYS cc_start: 0.9087 (tppp) cc_final: 0.8799 (ttpt) outliers start: 55 outliers final: 43 residues processed: 381 average time/residue: 0.2319 time to fit residues: 133.7222 Evaluate side-chains 384 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 334 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1284 THR Chi-restraints excluded: chain A residue 1437 SER Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1675 GLU Chi-restraints excluded: chain A residue 1884 CYS Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1928 ASP Chi-restraints excluded: chain A residue 1932 LEU Chi-restraints excluded: chain A residue 1934 ARG Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1589 SER Chi-restraints excluded: chain B residue 1649 SER Chi-restraints excluded: chain B residue 1657 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.0010 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 1.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 HIS A 784 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.051776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2320 r_free = 0.2320 target = 0.040170 restraints weight = 82219.119| |-----------------------------------------------------------------------------| r_work (start): 0.2318 rms_B_bonded: 2.03 r_work: 0.2226 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2122 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31828 Z= 0.126 Angle : 0.595 23.326 43270 Z= 0.298 Chirality : 0.041 0.237 4715 Planarity : 0.004 0.050 5552 Dihedral : 10.228 68.372 4735 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.77 % Allowed : 15.22 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3794 helix: 1.90 (0.14), residues: 1512 sheet: 0.52 (0.21), residues: 606 loop : -0.86 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 780 TYR 0.013 0.001 TYR B 113 PHE 0.022 0.001 PHE B 144 TRP 0.014 0.001 TRP A1781 HIS 0.004 0.001 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (31796) covalent geometry : angle 0.55026 / 0.30 (43228) hydrogen bonds : bond 0.05624 / 3.86 ( 1184) hydrogen bonds : angle 4.32741 / 3.07 ( 3369) metal coordination : bond 0.00637 / 0.39 ( 32) metal coordination : angle 7.29457 / 6.01 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 342 time to evaluate : 1.220 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 187 LYS cc_start: 0.8451 (mptt) cc_final: 0.8249 (mmtm) REVERT: A 504 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8008 (tm-30) REVERT: A 696 GLU cc_start: 0.8887 (mp0) cc_final: 0.8341 (mp0) REVERT: A 787 ARG cc_start: 0.8647 (mmt180) cc_final: 0.8244 (mmm-85) REVERT: A 874 GLU cc_start: 0.9132 (pp20) cc_final: 0.8850 (pp20) REVERT: A 897 LYS cc_start: 0.9569 (mttt) cc_final: 0.9278 (mtmm) REVERT: A 1015 ASP cc_start: 0.8100 (p0) cc_final: 0.7856 (p0) REVERT: A 1047 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.8855 (mt0) REVERT: A 1084 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 1251 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: A 1446 MET cc_start: 0.9094 (ptt) cc_final: 0.8820 (ptm) REVERT: A 1565 MET cc_start: 0.8746 (ppp) cc_final: 0.8375 (ppp) REVERT: A 1576 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7851 (tm-30) REVERT: A 1597 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: A 1687 MET cc_start: 0.9065 (mtm) cc_final: 0.8629 (mtm) REVERT: A 1884 CYS cc_start: 0.7739 (t) cc_final: 0.7409 (p) REVERT: B 70 GLU cc_start: 0.7928 (pm20) cc_final: 0.7657 (pm20) REVERT: B 114 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8609 (mmt-90) REVERT: B 256 ASP cc_start: 0.6884 (t0) cc_final: 0.6671 (t0) REVERT: B 452 LYS cc_start: 0.6424 (pttp) cc_final: 0.5657 (pttm) REVERT: B 485 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8571 (mttt) REVERT: B 513 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8558 (mp0) REVERT: B 635 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7562 (ptt-90) REVERT: B 761 GLN cc_start: 0.7862 (mt0) cc_final: 0.7287 (mm-40) REVERT: B 813 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7699 (t-90) REVERT: B 1047 GLN cc_start: 0.9519 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: B 1491 GLU cc_start: 0.8926 (tp30) cc_final: 0.8667 (tp30) REVERT: B 1637 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.6773 (mm-40) REVERT: B 1869 LYS cc_start: 0.9022 (tppp) cc_final: 0.8738 (ttpt) outliers start: 57 outliers final: 25 residues processed: 386 average time/residue: 0.2386 time to fit residues: 139.2558 Evaluate side-chains 364 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 330 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1396 HIS Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1600 ASP Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1934 ARG Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1372 GLU Chi-restraints excluded: chain B residue 1481 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1767 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [307, 38, 267, 122, 202, 350, 129, 91, 47, 291, 383] chunk 307 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 267 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 202 optimal weight: 0.0000 chunk 350 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 291 optimal weight: 0.9990 chunk 383 optimal weight: 9.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1901 HIS B1341 GLN B1355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.052122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.040484 restraints weight = 82512.343| |-----------------------------------------------------------------------------| r_work (start): 0.2326 rms_B_bonded: 2.05 r_work: 0.2235 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2130 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31828 Z= 0.118 Angle : 0.560 17.486 43270 Z= 0.284 Chirality : 0.040 0.247 4715 Planarity : 0.004 0.055 5552 Dihedral : 9.722 70.403 4669 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.08 % Allowed : 15.56 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.83 (0.14), residues: 3794 helix: 2.04 (0.14), residues: 1506 sheet: 0.53 (0.22), residues: 589 loop : -0.82 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1700 TYR 0.014 0.001 TYR A1007 PHE 0.022 0.001 PHE B 144 TRP 0.016 0.001 TRP A1920 HIS 0.007 0.001 HIS A1879 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (31796) covalent geometry : angle 0.52878 / 0.28 (43228) hydrogen bonds : bond 0.05145 / 3.54 ( 1184) hydrogen bonds : angle 4.14946 / 2.95 ( 3369) metal coordination : bond 0.00516 / 0.33 ( 32) metal coordination : angle 5.91583 / 4.75 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 346 time to evaluate : 1.063 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 187 LYS cc_start: 0.8429 (mptt) cc_final: 0.8204 (mmtm) REVERT: A 252 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8125 (mtm180) REVERT: A 504 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 696 GLU cc_start: 0.8885 (mp0) cc_final: 0.8356 (mp0) REVERT: A 787 ARG cc_start: 0.8631 (mmt180) cc_final: 0.8231 (mmm-85) REVERT: A 871 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8982 (tm-30) REVERT: A 874 GLU cc_start: 0.9177 (pp20) cc_final: 0.8866 (pp20) REVERT: A 897 LYS cc_start: 0.9578 (mttt) cc_final: 0.9312 (mtpp) REVERT: A 967 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8953 (p) REVERT: A 1012 MET cc_start: 0.8392 (ppp) cc_final: 0.7732 (ppp) REVERT: A 1015 ASP cc_start: 0.8106 (p0) cc_final: 0.7845 (p0) REVERT: A 1047 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.8864 (mt0) REVERT: A 1251 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: A 1561 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8141 (pp20) REVERT: A 1576 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 1597 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: A 1687 MET cc_start: 0.9001 (mtm) cc_final: 0.8598 (mtm) REVERT: A 1884 CYS cc_start: 0.7652 (t) cc_final: 0.7362 (p) REVERT: B 114 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8654 (mmt-90) REVERT: B 374 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7827 (mtt180) REVERT: B 452 LYS cc_start: 0.6494 (pttp) cc_final: 0.5726 (pttm) REVERT: B 485 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8643 (mttt) REVERT: B 513 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8540 (mp0) REVERT: B 635 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7630 (ptt-90) REVERT: B 761 GLN cc_start: 0.7859 (mt0) cc_final: 0.7309 (mm-40) REVERT: B 813 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7737 (t-90) REVERT: B 1047 GLN cc_start: 0.9524 (OUTLIER) cc_final: 0.8399 (mt0) REVERT: B 1313 LEU cc_start: 0.9141 (tp) cc_final: 0.8788 (tp) REVERT: B 1315 GLU cc_start: 0.8497 (mp0) cc_final: 0.8170 (mp0) REVERT: B 1637 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.6787 (mm-40) REVERT: B 1869 LYS cc_start: 0.8951 (tppp) cc_final: 0.8715 (ttpt) outliers start: 67 outliers final: 34 residues processed: 392 average time/residue: 0.2411 time to fit residues: 141.5992 Evaluate side-chains 387 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 341 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1771 LEU Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1932 LEU Chi-restraints excluded: chain A residue 1934 ARG Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1372 GLU Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1481 THR Chi-restraints excluded: chain B residue 1497 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1767 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [14, 240, 177, 313, 351, 107, 91, 52, 309, 364, 229] chunk 14 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 351 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 309 optimal weight: 0.9980 chunk 364 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.051913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2323 r_free = 0.2323 target = 0.040219 restraints weight = 81375.271| |-----------------------------------------------------------------------------| r_work (start): 0.2320 rms_B_bonded: 2.05 r_work: 0.2228 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2123 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31828 Z= 0.128 Angle : 0.556 15.829 43270 Z= 0.285 Chirality : 0.040 0.192 4715 Planarity : 0.005 0.121 5552 Dihedral : 9.735 73.577 4669 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.55 % Allowed : 16.40 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3794 helix: 2.05 (0.13), residues: 1506 sheet: 0.59 (0.22), residues: 597 loop : -0.80 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1854 TYR 0.015 0.001 TYR B1070 PHE 0.024 0.001 PHE B 144 TRP 0.018 0.001 TRP A1920 HIS 0.005 0.001 HIS A1879 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (31796) covalent geometry : angle 0.53286 / 0.28 (43228) hydrogen bonds : bond 0.05247 / 3.61 ( 1184) hydrogen bonds : angle 4.08046 / 2.89 ( 3369) metal coordination : bond 0.00514 / 0.32 ( 32) metal coordination : angle 5.16677 / 4.19 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 343 time to evaluate : 1.047 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 187 LYS cc_start: 0.8453 (mptt) cc_final: 0.8196 (mmtm) REVERT: A 252 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8091 (mtm180) REVERT: A 504 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 636 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6437 (mtt180) REVERT: A 696 GLU cc_start: 0.8891 (mp0) cc_final: 0.8344 (mp0) REVERT: A 787 ARG cc_start: 0.8604 (mmt180) cc_final: 0.8227 (mmm-85) REVERT: A 871 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8853 (tm-30) REVERT: A 874 GLU cc_start: 0.9094 (pp20) cc_final: 0.8815 (pp20) REVERT: A 897 LYS cc_start: 0.9550 (mttt) cc_final: 0.9291 (mtpp) REVERT: A 1012 MET cc_start: 0.8480 (ppp) cc_final: 0.7862 (ppp) REVERT: A 1047 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.8860 (mt0) REVERT: A 1084 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 1180 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8212 (mmt-90) REVERT: A 1251 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: A 1321 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8719 (pp) REVERT: A 1561 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8170 (pp20) REVERT: A 1565 MET cc_start: 0.8727 (ppp) cc_final: 0.8288 (ppp) REVERT: A 1597 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: A 1620 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8581 (mt0) REVERT: A 1687 MET cc_start: 0.9065 (mtm) cc_final: 0.8651 (mtm) REVERT: A 1884 CYS cc_start: 0.7613 (t) cc_final: 0.7318 (p) REVERT: B 256 ASP cc_start: 0.6694 (t0) cc_final: 0.6374 (t0) REVERT: B 300 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8787 (pm20) REVERT: B 374 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.7859 (mtt180) REVERT: B 452 LYS cc_start: 0.6510 (pttp) cc_final: 0.5824 (pttm) REVERT: B 485 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8721 (mttt) REVERT: B 513 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8491 (mp0) REVERT: B 635 ARG cc_start: 0.7938 (ttp-110) cc_final: 0.7681 (ptp90) REVERT: B 761 GLN cc_start: 0.7856 (mt0) cc_final: 0.7322 (mm-40) REVERT: B 813 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7733 (t-90) REVERT: B 828 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5741 (ptp90) REVERT: B 880 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8298 (tm-30) REVERT: B 1047 GLN cc_start: 0.9522 (OUTLIER) cc_final: 0.8411 (mt0) REVERT: B 1306 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8233 (mp) REVERT: B 1313 LEU cc_start: 0.9142 (tp) cc_final: 0.8868 (tp) REVERT: B 1315 GLU cc_start: 0.8529 (mp0) cc_final: 0.8310 (mp0) REVERT: B 1637 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.6863 (mm-40) REVERT: B 1869 LYS cc_start: 0.8936 (tppp) cc_final: 0.8702 (ttpt) outliers start: 82 outliers final: 39 residues processed: 400 average time/residue: 0.2391 time to fit residues: 143.3172 Evaluate side-chains 390 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 333 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1396 HIS Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1620 GLN Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1771 LEU Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1932 LEU Chi-restraints excluded: chain A residue 1934 ARG Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1306 LEU Chi-restraints excluded: chain B residue 1372 GLU Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1481 THR Chi-restraints excluded: chain B residue 1497 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1767 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [336, 140, 89, 297, 323, 2, 236, 315, 39, 64, 274] chunk 336 optimal weight: 0.3980 chunk 140 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 297 optimal weight: 0.9980 chunk 323 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 236 optimal weight: 0.7980 chunk 315 optimal weight: 0.0030 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 829 GLN A1173 GLN A1471 HIS B 281 GLN B 898 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.052265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.040619 restraints weight = 81628.090| |-----------------------------------------------------------------------------| r_work (start): 0.2330 rms_B_bonded: 2.04 r_work: 0.2240 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2136 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31828 Z= 0.117 Angle : 0.545 14.154 43270 Z= 0.280 Chirality : 0.040 0.193 4715 Planarity : 0.004 0.063 5552 Dihedral : 9.696 74.640 4669 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.61 % Allowed : 16.50 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.93 (0.14), residues: 3794 helix: 2.11 (0.14), residues: 1506 sheet: 0.57 (0.21), residues: 598 loop : -0.76 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1854 TYR 0.014 0.001 TYR A1007 PHE 0.023 0.001 PHE B 144 TRP 0.020 0.001 TRP A1920 HIS 0.004 0.001 HIS A1879 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (31796) covalent geometry : angle 0.52431 / 0.28 (43228) hydrogen bonds : bond 0.04903 / 3.37 ( 1184) hydrogen bonds : angle 4.00049 / 2.84 ( 3369) metal coordination : bond 0.00459 / 0.29 ( 32) metal coordination : angle 4.83111 / 3.81 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 343 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8426 (mptt) cc_final: 0.8170 (mmtm) REVERT: A 252 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8151 (mtm180) REVERT: A 504 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7985 (tm-30) REVERT: A 696 GLU cc_start: 0.8881 (mp0) cc_final: 0.8353 (mp0) REVERT: A 787 ARG cc_start: 0.8594 (mmt180) cc_final: 0.8217 (mmm-85) REVERT: A 871 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8841 (tm-30) REVERT: A 874 GLU cc_start: 0.9111 (pp20) cc_final: 0.8844 (pp20) REVERT: A 897 LYS cc_start: 0.9544 (mttt) cc_final: 0.9276 (mtpp) REVERT: A 923 ILE cc_start: 0.9067 (mm) cc_final: 0.8849 (mm) REVERT: A 1012 MET cc_start: 0.8463 (ppp) cc_final: 0.7849 (ppp) REVERT: A 1015 ASP cc_start: 0.8100 (p0) cc_final: 0.7777 (p0) REVERT: A 1047 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.8852 (mt0) REVERT: A 1084 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8288 (mm) REVERT: A 1180 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8300 (mmt-90) REVERT: A 1251 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: A 1321 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8721 (pp) REVERT: A 1561 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8181 (pp20) REVERT: A 1565 MET cc_start: 0.8721 (ppp) cc_final: 0.8265 (ppp) REVERT: A 1576 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7961 (tm-30) REVERT: A 1597 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: A 1687 MET cc_start: 0.9031 (mtm) cc_final: 0.8672 (mtm) REVERT: A 1884 CYS cc_start: 0.7595 (t) cc_final: 0.7291 (p) REVERT: A 1927 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7951 (mm) REVERT: B 70 GLU cc_start: 0.7912 (pm20) cc_final: 0.7625 (pm20) REVERT: B 300 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8798 (pm20) REVERT: B 374 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7842 (mtt180) REVERT: B 452 LYS cc_start: 0.6491 (pttp) cc_final: 0.5805 (pttm) REVERT: B 513 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8469 (mp0) REVERT: B 635 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7657 (ptt-90) REVERT: B 761 GLN cc_start: 0.7855 (mt0) cc_final: 0.7329 (mm-40) REVERT: B 785 ARG cc_start: 0.8893 (mtp180) cc_final: 0.8612 (mtp180) REVERT: B 813 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7723 (t-90) REVERT: B 828 ARG cc_start: 0.6193 (OUTLIER) cc_final: 0.5754 (ptp90) REVERT: B 880 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8375 (tm-30) REVERT: B 1047 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.8409 (mt0) REVERT: B 1241 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8786 (mmt180) REVERT: B 1306 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8282 (mp) REVERT: B 1313 LEU cc_start: 0.9140 (tp) cc_final: 0.8872 (tp) REVERT: B 1315 GLU cc_start: 0.8534 (mp0) cc_final: 0.8310 (mp0) REVERT: B 1637 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.6853 (mm-40) REVERT: B 1869 LYS cc_start: 0.8920 (tppp) cc_final: 0.8712 (ttpt) outliers start: 84 outliers final: 51 residues processed: 403 average time/residue: 0.2358 time to fit residues: 143.5253 Evaluate side-chains 404 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 336 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1396 HIS Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1771 LEU Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1932 LEU Chi-restraints excluded: chain A residue 1934 ARG Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1241 ARG Chi-restraints excluded: chain B residue 1306 LEU Chi-restraints excluded: chain B residue 1372 GLU Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1434 LYS Chi-restraints excluded: chain B residue 1481 THR Chi-restraints excluded: chain B residue 1497 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1767 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [162, 250, 254, 61, 191, 190, 63, 367, 361, 373, 210] chunk 162 optimal weight: 0.9990 chunk 250 optimal weight: 0.7980 chunk 254 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 367 optimal weight: 4.9990 chunk 361 optimal weight: 2.9990 chunk 373 optimal weight: 0.5980 chunk 210 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 165 ASN B1355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.052158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.040496 restraints weight = 81821.473| |-----------------------------------------------------------------------------| r_work (start): 0.2329 rms_B_bonded: 2.03 r_work: 0.2238 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2134 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31828 Z= 0.121 Angle : 0.551 16.624 43270 Z= 0.281 Chirality : 0.040 0.198 4715 Planarity : 0.004 0.113 5552 Dihedral : 9.692 76.287 4669 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.58 % Allowed : 17.05 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.95 (0.14), residues: 3794 helix: 2.13 (0.13), residues: 1504 sheet: 0.60 (0.21), residues: 593 loop : -0.75 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1854 TYR 0.015 0.001 TYR A1007 PHE 0.024 0.001 PHE B 144 TRP 0.021 0.001 TRP A1920 HIS 0.007 0.001 HIS B1339 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (31796) covalent geometry : angle 0.53202 / 0.28 (43228) hydrogen bonds : bond 0.04945 / 3.40 ( 1184) hydrogen bonds : angle 3.98243 / 2.83 ( 3369) metal coordination : bond 0.00454 / 0.29 ( 32) metal coordination : angle 4.62581 / 3.69 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 342 time to evaluate : 1.205 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 187 LYS cc_start: 0.8445 (mptt) cc_final: 0.8171 (mmtm) REVERT: A 252 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8139 (mtm180) REVERT: A 504 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7986 (tm-30) REVERT: A 696 GLU cc_start: 0.8883 (mp0) cc_final: 0.8335 (mp0) REVERT: A 787 ARG cc_start: 0.8586 (mmt180) cc_final: 0.8219 (mmm-85) REVERT: A 865 GLU cc_start: 0.8642 (tp30) cc_final: 0.8436 (tm-30) REVERT: A 871 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8807 (tm-30) REVERT: A 874 GLU cc_start: 0.9109 (pp20) cc_final: 0.8877 (pp20) REVERT: A 897 LYS cc_start: 0.9536 (mttt) cc_final: 0.9268 (mtpp) REVERT: A 923 ILE cc_start: 0.9059 (mm) cc_final: 0.8846 (mm) REVERT: A 1012 MET cc_start: 0.8443 (ppp) cc_final: 0.7929 (ppp) REVERT: A 1015 ASP cc_start: 0.8024 (p0) cc_final: 0.7692 (p0) REVERT: A 1047 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.8863 (mt0) REVERT: A 1084 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8291 (mm) REVERT: A 1180 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8285 (mmt-90) REVERT: A 1251 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: A 1321 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8717 (pp) REVERT: A 1561 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8186 (pp20) REVERT: A 1565 MET cc_start: 0.8755 (ppp) cc_final: 0.8287 (ppp) REVERT: A 1576 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 1620 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8570 (mt0) REVERT: A 1687 MET cc_start: 0.9027 (mtm) cc_final: 0.8671 (mtm) REVERT: A 1884 CYS cc_start: 0.7610 (t) cc_final: 0.7284 (p) REVERT: A 1927 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7958 (mm) REVERT: B 70 GLU cc_start: 0.7868 (pm20) cc_final: 0.7560 (pm20) REVERT: B 256 ASP cc_start: 0.6580 (t0) cc_final: 0.6344 (t0) REVERT: B 300 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8801 (pm20) REVERT: B 374 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7833 (mtt180) REVERT: B 452 LYS cc_start: 0.6460 (pttp) cc_final: 0.5782 (pttm) REVERT: B 513 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8467 (mp0) REVERT: B 635 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7663 (ptt-90) REVERT: B 761 GLN cc_start: 0.7872 (mt0) cc_final: 0.7330 (mm-40) REVERT: B 813 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7704 (t-90) REVERT: B 828 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5745 (ptp90) REVERT: B 1047 GLN cc_start: 0.9514 (OUTLIER) cc_final: 0.8409 (mt0) REVERT: B 1241 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8780 (mmt180) REVERT: B 1306 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8274 (mp) REVERT: B 1637 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.6838 (mm-40) REVERT: B 1869 LYS cc_start: 0.8913 (tppp) cc_final: 0.8696 (ttpt) outliers start: 83 outliers final: 54 residues processed: 402 average time/residue: 0.2286 time to fit residues: 138.8533 Evaluate side-chains 409 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 338 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1396 HIS Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1620 GLN Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1934 ARG Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1241 ARG Chi-restraints excluded: chain B residue 1270 GLN Chi-restraints excluded: chain B residue 1306 LEU Chi-restraints excluded: chain B residue 1372 GLU Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1434 LYS Chi-restraints excluded: chain B residue 1481 THR Chi-restraints excluded: chain B residue 1497 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1767 LEU Chi-restraints excluded: chain B residue 1888 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [295, 215, 60, 382, 357, 274, 147, 369, 330, 209, 160] chunk 295 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 382 optimal weight: 10.0000 chunk 357 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 369 optimal weight: 4.9990 chunk 330 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS A1371 GLN A1906 HIS B1355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.049514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2254 r_free = 0.2254 target = 0.037890 restraints weight = 83295.022| |-----------------------------------------------------------------------------| r_work (start): 0.2248 rms_B_bonded: 2.03 r_work: 0.2155 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2051 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31828 Z= 0.225 Angle : 0.657 14.648 43270 Z= 0.339 Chirality : 0.044 0.205 4715 Planarity : 0.005 0.099 5552 Dihedral : 9.850 79.130 4666 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.89 % Allowed : 17.30 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.61 (0.14), residues: 3794 helix: 1.76 (0.13), residues: 1501 sheet: 0.55 (0.22), residues: 599 loop : -0.90 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1854 TYR 0.028 0.002 TYR B1070 PHE 0.033 0.002 PHE B 144 TRP 0.022 0.002 TRP A1920 HIS 0.010 0.002 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (31796) covalent geometry : angle 0.63706 / 0.34 (43228) hydrogen bonds : bond 0.07056 / 4.85 ( 1184) hydrogen bonds : angle 4.22746 / 3.00 ( 3369) metal coordination : bond 0.00782 / 0.49 ( 32) metal coordination : angle 5.14354 / 4.03 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 337 time to evaluate : 1.206 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 187 LYS cc_start: 0.8494 (mptt) cc_final: 0.8233 (mmtm) REVERT: A 252 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8053 (mtm180) REVERT: A 504 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 696 GLU cc_start: 0.8869 (mp0) cc_final: 0.8332 (mp0) REVERT: A 787 ARG cc_start: 0.8675 (mmt180) cc_final: 0.8303 (mmm-85) REVERT: A 865 GLU cc_start: 0.8642 (tp30) cc_final: 0.8422 (tm-30) REVERT: A 897 LYS cc_start: 0.9545 (mttt) cc_final: 0.9265 (mtpp) REVERT: A 1012 MET cc_start: 0.8541 (ppp) cc_final: 0.8112 (ppp) REVERT: A 1015 ASP cc_start: 0.8057 (p0) cc_final: 0.7685 (p0) REVERT: A 1047 GLN cc_start: 0.9410 (OUTLIER) cc_final: 0.8891 (mt0) REVERT: A 1084 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8751 (mm) REVERT: A 1180 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8235 (mmt-90) REVERT: A 1321 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8756 (pp) REVERT: A 1561 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8189 (pp20) REVERT: A 1565 MET cc_start: 0.8763 (ppp) cc_final: 0.8278 (ppp) REVERT: A 1597 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: A 1620 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8648 (mt0) REVERT: A 1687 MET cc_start: 0.9166 (mtm) cc_final: 0.8674 (mtm) REVERT: A 1884 CYS cc_start: 0.7659 (t) cc_final: 0.7383 (p) REVERT: A 1927 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7928 (mm) REVERT: B 70 GLU cc_start: 0.8008 (pm20) cc_final: 0.7633 (pm20) REVERT: B 256 ASP cc_start: 0.6739 (t0) cc_final: 0.6314 (t0) REVERT: B 374 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8037 (mtt180) REVERT: B 452 LYS cc_start: 0.6680 (pttp) cc_final: 0.6066 (pttm) REVERT: B 513 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8571 (mp0) REVERT: B 635 ARG cc_start: 0.8050 (ttp-110) cc_final: 0.7742 (ptt-90) REVERT: B 761 GLN cc_start: 0.7857 (mt0) cc_final: 0.7302 (mm-40) REVERT: B 976 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8475 (mp) REVERT: B 1047 GLN cc_start: 0.9547 (OUTLIER) cc_final: 0.8391 (mt0) REVERT: B 1051 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8711 (m-30) REVERT: B 1341 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8233 (tp-100) REVERT: B 1637 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.6859 (mm-40) REVERT: B 1869 LYS cc_start: 0.9051 (tppp) cc_final: 0.8794 (ttpt) outliers start: 93 outliers final: 58 residues processed: 405 average time/residue: 0.2353 time to fit residues: 143.7950 Evaluate side-chains 403 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 331 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1396 HIS Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1620 GLN Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1880 SER Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1932 LEU Chi-restraints excluded: chain A residue 1934 ARG Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1270 GLN Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1434 LYS Chi-restraints excluded: chain B residue 1481 THR Chi-restraints excluded: chain B residue 1589 SER Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1653 SER Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1767 LEU Chi-restraints excluded: chain B residue 1888 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [350, 177, 332, 144, 70, 334, 137, 87, 7, 234, 212] chunk 350 optimal weight: 0.8980 chunk 177 optimal weight: 0.3980 chunk 332 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 334 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 7 optimal weight: 0.0030 chunk 234 optimal weight: 0.0370 chunk 212 optimal weight: 0.7980 overall best weight: 0.3068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.051834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2319 r_free = 0.2319 target = 0.040042 restraints weight = 81952.413| |-----------------------------------------------------------------------------| r_work (start): 0.2317 rms_B_bonded: 2.09 r_work: 0.2224 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2119 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 31828 Z= 0.116 Angle : 0.568 14.918 43270 Z= 0.293 Chirality : 0.039 0.214 4715 Planarity : 0.004 0.111 5552 Dihedral : 9.679 78.000 4664 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.08 % Allowed : 18.39 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.83 (0.14), residues: 3794 helix: 1.99 (0.13), residues: 1504 sheet: 0.50 (0.21), residues: 606 loop : -0.77 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1700 TYR 0.015 0.001 TYR B1007 PHE 0.019 0.001 PHE A 144 TRP 0.024 0.001 TRP A1920 HIS 0.003 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (31796) covalent geometry : angle 0.55058 / 0.29 (43228) hydrogen bonds : bond 0.05029 / 3.46 ( 1184) hydrogen bonds : angle 4.01646 / 2.85 ( 3369) metal coordination : bond 0.00416 / 0.26 ( 32) metal coordination : angle 4.46584 / 3.48 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 1.178 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 176 LYS cc_start: 0.9112 (mmmt) cc_final: 0.8808 (mmmt) REVERT: A 187 LYS cc_start: 0.8439 (mptt) cc_final: 0.8214 (mmtm) REVERT: A 252 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8160 (mtm180) REVERT: A 504 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 696 GLU cc_start: 0.8883 (mp0) cc_final: 0.8341 (mp0) REVERT: A 865 GLU cc_start: 0.8662 (tp30) cc_final: 0.8460 (tm-30) REVERT: A 871 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8832 (tm-30) REVERT: A 874 GLU cc_start: 0.9031 (pp20) cc_final: 0.8792 (pp20) REVERT: A 897 LYS cc_start: 0.9494 (mttt) cc_final: 0.9198 (ttmm) REVERT: A 1012 MET cc_start: 0.8494 (ppp) cc_final: 0.8058 (ppp) REVERT: A 1015 ASP cc_start: 0.8013 (p0) cc_final: 0.7602 (p0) REVERT: A 1047 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.8872 (mt0) REVERT: A 1084 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8463 (mm) REVERT: A 1180 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8296 (mmt-90) REVERT: A 1251 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: A 1321 LEU cc_start: 0.9022 (mp) cc_final: 0.8746 (pp) REVERT: A 1446 MET cc_start: 0.9038 (ptp) cc_final: 0.8797 (ptm) REVERT: A 1560 ASP cc_start: 0.8279 (m-30) cc_final: 0.7571 (p0) REVERT: A 1565 MET cc_start: 0.8747 (ppp) cc_final: 0.8283 (ppp) REVERT: A 1620 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8616 (mt0) REVERT: A 1687 MET cc_start: 0.9020 (mtm) cc_final: 0.8618 (mtm) REVERT: A 1884 CYS cc_start: 0.7656 (t) cc_final: 0.7310 (p) REVERT: A 1927 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 66 ASP cc_start: 0.7765 (t0) cc_final: 0.7547 (t0) REVERT: B 70 GLU cc_start: 0.7942 (pm20) cc_final: 0.7580 (pm20) REVERT: B 290 ASP cc_start: 0.8681 (t0) cc_final: 0.8404 (t0) REVERT: B 374 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7834 (mtt180) REVERT: B 452 LYS cc_start: 0.6477 (pttp) cc_final: 0.5818 (pttm) REVERT: B 513 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8511 (mp0) REVERT: B 635 ARG cc_start: 0.8053 (ttp-110) cc_final: 0.7738 (ptt-90) REVERT: B 761 GLN cc_start: 0.7847 (mt0) cc_final: 0.7325 (mm-40) REVERT: B 807 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7886 (mm-30) REVERT: B 1047 GLN cc_start: 0.9519 (OUTLIER) cc_final: 0.8378 (mt0) REVERT: B 1306 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8302 (mp) REVERT: B 1637 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.6851 (mm-40) REVERT: B 1869 LYS cc_start: 0.8943 (tppp) cc_final: 0.8701 (ttpt) outliers start: 67 outliers final: 44 residues processed: 387 average time/residue: 0.2359 time to fit residues: 137.3491 Evaluate side-chains 388 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 333 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1251 PHE Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1372 GLU Chi-restraints excluded: chain A residue 1396 HIS Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1620 GLN Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1934 ARG Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1270 GLN Chi-restraints excluded: chain B residue 1306 LEU Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1434 LYS Chi-restraints excluded: chain B residue 1481 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1767 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [0, 166, 321, 235, 307, 144, 224, 223, 189, 232, 146] chunk 0 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 307 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 chunk 146 optimal weight: 0.1980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1341 GLN B1355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.051332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.039536 restraints weight = 82133.223| |-----------------------------------------------------------------------------| r_work (start): 0.2302 rms_B_bonded: 2.09 r_work: 0.2209 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2104 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31828 Z= 0.139 Angle : 0.588 14.718 43270 Z= 0.302 Chirality : 0.041 0.201 4715 Planarity : 0.005 0.107 5552 Dihedral : 9.681 78.580 4664 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.02 % Allowed : 18.76 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.83 (0.14), residues: 3794 helix: 1.99 (0.13), residues: 1502 sheet: 0.54 (0.21), residues: 601 loop : -0.78 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1854 TYR 0.017 0.001 TYR B1070 PHE 0.025 0.001 PHE B 144 TRP 0.026 0.001 TRP A1920 HIS 0.010 0.001 HIS B1339 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (31796) covalent geometry : angle 0.57201 / 0.30 (43228) hydrogen bonds : bond 0.05404 / 3.72 ( 1184) hydrogen bonds : angle 4.02584 / 2.86 ( 3369) metal coordination : bond 0.00501 / 0.31 ( 32) metal coordination : angle 4.42145 / 3.45 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 333 time to evaluate : 1.203 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 187 LYS cc_start: 0.8447 (mptt) cc_final: 0.8224 (mmtm) REVERT: A 504 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 696 GLU cc_start: 0.8867 (mp0) cc_final: 0.8338 (mp0) REVERT: A 787 ARG cc_start: 0.8590 (mmt180) cc_final: 0.8148 (mmm-85) REVERT: A 865 GLU cc_start: 0.8683 (tp30) cc_final: 0.8442 (tm-30) REVERT: A 897 LYS cc_start: 0.9467 (mttt) cc_final: 0.9179 (ttmm) REVERT: A 1012 MET cc_start: 0.8474 (ppp) cc_final: 0.8041 (ppp) REVERT: A 1015 ASP cc_start: 0.8067 (p0) cc_final: 0.7665 (p0) REVERT: A 1047 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8863 (mt0) REVERT: A 1084 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 1180 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8260 (mmt-90) REVERT: A 1321 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8766 (pp) REVERT: A 1560 ASP cc_start: 0.8235 (m-30) cc_final: 0.7402 (p0) REVERT: A 1565 MET cc_start: 0.8727 (ppp) cc_final: 0.8231 (ppp) REVERT: A 1597 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: A 1620 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8645 (mt0) REVERT: A 1687 MET cc_start: 0.9073 (mtm) cc_final: 0.8669 (mtm) REVERT: A 1884 CYS cc_start: 0.7626 (t) cc_final: 0.7300 (p) REVERT: A 1927 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7945 (mm) REVERT: B 66 ASP cc_start: 0.7842 (t0) cc_final: 0.7615 (t0) REVERT: B 70 GLU cc_start: 0.7986 (pm20) cc_final: 0.7544 (pm20) REVERT: B 290 ASP cc_start: 0.8702 (t0) cc_final: 0.8389 (t0) REVERT: B 374 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.7880 (mtt180) REVERT: B 452 LYS cc_start: 0.6535 (pttp) cc_final: 0.5878 (pttm) REVERT: B 485 LYS cc_start: 0.9039 (mttt) cc_final: 0.8646 (mmtm) REVERT: B 513 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8531 (mp0) REVERT: B 635 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7836 (ptp90) REVERT: B 761 GLN cc_start: 0.7850 (mt0) cc_final: 0.7337 (mm-40) REVERT: B 807 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7872 (mm-30) REVERT: B 1047 GLN cc_start: 0.9527 (OUTLIER) cc_final: 0.8388 (mt0) REVERT: B 1306 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8326 (mp) REVERT: B 1637 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.6851 (mm-40) REVERT: B 1869 LYS cc_start: 0.8950 (tppp) cc_final: 0.8712 (ttpt) outliers start: 65 outliers final: 48 residues processed: 385 average time/residue: 0.2419 time to fit residues: 139.8720 Evaluate side-chains 388 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1396 HIS Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1620 GLN Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1934 ARG Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1270 GLN Chi-restraints excluded: chain B residue 1306 LEU Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1434 LYS Chi-restraints excluded: chain B residue 1481 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1653 SER Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1767 LEU Chi-restraints excluded: chain B residue 1888 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [336, 245, 255, 301, 114, 366, 20, 94, 263, 163, 360] chunk 336 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 255 optimal weight: 0.4980 chunk 301 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 366 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.050541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2280 r_free = 0.2280 target = 0.038749 restraints weight = 82797.592| |-----------------------------------------------------------------------------| r_work (start): 0.2276 rms_B_bonded: 2.11 r_work: 0.2182 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2076 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31828 Z= 0.165 Angle : 0.615 14.755 43270 Z= 0.318 Chirality : 0.042 0.207 4715 Planarity : 0.005 0.090 5552 Dihedral : 9.735 80.012 4662 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.08 % Allowed : 18.64 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.72 (0.14), residues: 3794 helix: 1.89 (0.13), residues: 1496 sheet: 0.55 (0.22), residues: 599 loop : -0.85 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1854 TYR 0.021 0.002 TYR B1070 PHE 0.027 0.002 PHE B 144 TRP 0.026 0.001 TRP A1920 HIS 0.007 0.001 HIS B1339 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (31796) covalent geometry : angle 0.59917 / 0.32 (43228) hydrogen bonds : bond 0.05997 / 4.13 ( 1184) hydrogen bonds : angle 4.11292 / 2.92 ( 3369) metal coordination : bond 0.00586 / 0.36 ( 32) metal coordination : angle 4.53487 / 3.49 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 330 time to evaluate : 1.174 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: A 187 LYS cc_start: 0.8496 (mptt) cc_final: 0.8219 (mmtm) REVERT: A 504 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 696 GLU cc_start: 0.8874 (mp0) cc_final: 0.8291 (mp0) REVERT: A 865 GLU cc_start: 0.8715 (tp30) cc_final: 0.8441 (tm-30) REVERT: A 896 LYS cc_start: 0.9344 (ptpp) cc_final: 0.9080 (pttm) REVERT: A 897 LYS cc_start: 0.9474 (mttt) cc_final: 0.9171 (ttmm) REVERT: A 1012 MET cc_start: 0.8518 (ppp) cc_final: 0.8098 (ppp) REVERT: A 1015 ASP cc_start: 0.8155 (p0) cc_final: 0.7771 (p0) REVERT: A 1047 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.8893 (mt0) REVERT: A 1084 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 1151 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8397 (ttt-90) REVERT: A 1180 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8241 (mmt-90) REVERT: A 1321 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8775 (pp) REVERT: A 1560 ASP cc_start: 0.8299 (m-30) cc_final: 0.7484 (p0) REVERT: A 1565 MET cc_start: 0.8779 (ppp) cc_final: 0.8283 (ppp) REVERT: A 1597 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.7119 (mp10) REVERT: A 1620 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8645 (mt0) REVERT: A 1687 MET cc_start: 0.9069 (mtm) cc_final: 0.8640 (mtm) REVERT: A 1690 ARG cc_start: 0.7100 (tpp80) cc_final: 0.6598 (tpp80) REVERT: A 1884 CYS cc_start: 0.7686 (t) cc_final: 0.7354 (p) REVERT: A 1927 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7934 (mm) REVERT: B 66 ASP cc_start: 0.7898 (t0) cc_final: 0.7652 (t0) REVERT: B 70 GLU cc_start: 0.8012 (pm20) cc_final: 0.7554 (pm20) REVERT: B 256 ASP cc_start: 0.6578 (t0) cc_final: 0.6298 (t0) REVERT: B 290 ASP cc_start: 0.8591 (t0) cc_final: 0.8303 (t0) REVERT: B 374 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7890 (mtt180) REVERT: B 452 LYS cc_start: 0.6637 (pttp) cc_final: 0.6005 (pttm) REVERT: B 485 LYS cc_start: 0.9113 (mttt) cc_final: 0.8763 (mmtm) REVERT: B 513 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8600 (mp0) REVERT: B 635 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7883 (ptp90) REVERT: B 761 GLN cc_start: 0.7861 (mt0) cc_final: 0.7317 (mm-40) REVERT: B 807 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7871 (mm-30) REVERT: B 1047 GLN cc_start: 0.9532 (OUTLIER) cc_final: 0.8379 (mt0) REVERT: B 1051 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8680 (m-30) REVERT: B 1114 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: B 1306 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8299 (mp) REVERT: B 1637 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.6814 (mm-40) REVERT: B 1869 LYS cc_start: 0.9016 (tppp) cc_final: 0.8760 (ttpt) REVERT: B 1887 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8010 (tt0) outliers start: 67 outliers final: 52 residues processed: 384 average time/residue: 0.2398 time to fit residues: 138.2495 Evaluate side-chains 395 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 328 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1372 GLU Chi-restraints excluded: chain A residue 1396 HIS Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1620 GLN Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1932 LEU Chi-restraints excluded: chain A residue 1934 ARG Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain B residue 1179 ASP Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1270 GLN Chi-restraints excluded: chain B residue 1306 LEU Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1434 LYS Chi-restraints excluded: chain B residue 1481 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1653 SER Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 1767 LEU Chi-restraints excluded: chain B residue 1887 GLU Chi-restraints excluded: chain B residue 1888 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [307, 106, 139, 225, 242, 324, 188, 274, 263, 311, 207] chunk 307 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 139 optimal weight: 0.0010 chunk 225 optimal weight: 4.9990 chunk 242 optimal weight: 0.1980 chunk 324 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 chunk 274 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 311 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1341 GLN B1355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.051965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.040208 restraints weight = 82383.492| |-----------------------------------------------------------------------------| r_work (start): 0.2321 rms_B_bonded: 2.09 r_work: 0.2229 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2125 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31828 Z= 0.119 Angle : 0.572 14.628 43270 Z= 0.295 Chirality : 0.040 0.192 4715 Planarity : 0.004 0.074 5552 Dihedral : 9.651 79.589 4662 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.08 % Allowed : 18.79 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3794 helix: 2.04 (0.13), residues: 1496 sheet: 0.51 (0.21), residues: 603 loop : -0.74 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1854 TYR 0.015 0.001 TYR B1007 PHE 0.021 0.001 PHE B 144 TRP 0.026 0.001 TRP A1920 HIS 0.003 0.001 HIS B1339 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (31796) covalent geometry : angle 0.55786 / 0.29 (43228) hydrogen bonds : bond 0.04905 / 3.38 ( 1184) hydrogen bonds : angle 3.99288 / 2.84 ( 3369) metal coordination : bond 0.00406 / 0.26 ( 32) metal coordination : angle 4.15253 / 3.19 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6798.14 seconds wall clock time: 116 minutes 55.73 seconds (7015.73 seconds total)