Starting phenix.real_space_refine on Fri Oct 30 05:21:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tu9_56253/10_2026/9tu9_56253.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tu9_56253/10_2026/9tu9_56253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tu9_56253/10_2026/9tu9_56253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tu9_56253/10_2026/9tu9_56253.map" model { file = "/net/cci-nas-00/data/ceres_data/9tu9_56253/10_2026/9tu9_56253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tu9_56253/10_2026/9tu9_56253.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 10 6.06 5 P 47 5.49 5 S 146 5.16 5 C 21066 2.51 5 N 6021 2.21 5 O 6373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.03s 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: 33663 Number of models: 1 Model: "" Number of chains: 6 Chain: "Y" Number of atoms: 16471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2075, 16471 Classifications: {'peptide': 2075} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 98, 'TRANS': 1976} Chain breaks: 2 Chain: "y" Number of atoms: 16275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2050, 16275 Classifications: {'peptide': 2050} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 98, 'TRANS': 1951} Chain breaks: 3 Chain: "G" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 497 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "I" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 348 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "Y" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' ZN': 5, 'AGS': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "y" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' ZN': 5, 'AGS': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3468 SG CYS Y 437 23.097 59.331 119.871 1.00124.49 S ATOM 3506 SG CYS Y 442 24.180 56.513 121.779 1.00130.11 S ATOM 3727 SG CYS Y 467 22.991 56.118 117.898 1.00128.64 S ATOM 3741 SG CYS Y 469 20.932 55.972 120.850 1.00134.94 S ATOM 3832 SG CYS Y 482 41.255 69.314 125.419 1.00132.50 S ATOM 4643 SG CYS Y 586 39.024 72.374 126.333 1.00134.57 S ATOM 4656 SG CYS Y 588 40.942 70.250 128.830 1.00138.60 S ATOM 4662 SG CYS Y 589 42.534 72.936 126.507 1.00137.97 S ATOM 11183 SG CYS Y1423 20.887 76.386 77.963 1.00134.46 S ATOM 11209 SG CYS Y1426 21.893 73.693 75.536 1.00141.05 S ATOM 11293 SG CYS Y1439 22.036 77.336 74.661 1.00139.26 S ATOM 11315 SG CYS Y1442 18.511 75.429 75.298 1.00142.82 S ATOM 11988 SG CYS Y1526 47.516 96.812 86.073 1.00124.23 S ATOM 12008 SG CYS Y1529 50.361 94.648 87.492 1.00127.01 S ATOM 12342 SG CYS Y1571 50.979 98.178 85.871 1.00133.90 S ATOM 13205 SG CYS Y1681 27.579 52.304 101.805 1.00117.57 S ATOM 13217 SG CYS Y1683 26.419 54.996 103.817 1.00114.13 S ATOM 13251 SG CYS Y1687 30.248 53.993 103.801 1.00111.58 S ATOM 13277 SG CYS Y1690 28.750 55.802 100.855 1.00118.52 S ATOM 19939 SG CYS y 437 144.006 68.174 101.104 1.00245.31 S ATOM 19977 SG CYS y 442 146.100 69.416 104.085 1.00259.93 S ATOM 20198 SG CYS y 467 146.021 71.372 101.001 1.00253.24 S ATOM 20212 SG CYS y 469 147.764 68.039 100.824 1.00231.21 S ATOM 20287 SG CYS y 479 122.859 64.415 106.508 1.00212.46 S ATOM 20303 SG CYS y 482 122.180 64.138 110.045 1.00187.64 S ATOM 20897 SG CYS y 586 122.948 60.940 107.907 1.00233.14 S ATOM 20916 SG CYS y 589 119.659 62.328 107.677 1.00245.75 S ATOM 27458 SG CYS y1423 135.616 83.047 55.287 1.00322.27 S ATOM 27484 SG CYS y1426 136.507 86.218 57.128 1.00325.33 S ATOM 27568 SG CYS y1439 134.051 86.426 54.212 1.00327.07 S ATOM 27590 SG CYS y1442 137.641 85.580 53.487 1.00327.05 S ATOM 28263 SG CYS y1526 104.249 73.168 61.286 1.00331.79 S ATOM 28283 SG CYS y1529 103.371 73.225 64.929 1.00377.37 S ATOM 28617 SG CYS y1571 100.644 72.002 62.361 1.00389.09 S ATOM 29480 SG CYS y1681 142.498 85.673 92.653 1.00321.90 S ATOM 29492 SG CYS y1683 142.344 82.093 92.263 1.00311.12 S ATOM 29526 SG CYS y1687 139.304 83.718 93.890 1.00260.90 S ATOM 29552 SG CYS y1690 139.786 83.964 90.270 1.00266.70 S Time building chain proxies: 7.33, per 1000 atoms: 0.22 Number of scatterers: 33663 At special positions: 0 Unit cell: (169.728, 151.979, 178.603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 10 29.99 S 146 16.00 P 47 15.00 O 6373 8.00 N 6021 7.00 C 21066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y2201 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 442 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 469 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 467 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 437 " pdb=" ZN Y2202 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 589 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 586 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 588 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 482 " pdb=" ZN Y2203 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1423 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1426 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1439 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1442 " pdb=" ZN Y2204 " pdb="ZN ZN Y2204 " - pdb=" NE2 HIS Y1554 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1526 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1571 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1529 " pdb=" ZN Y2205 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1681 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1687 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1683 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1690 " pdb=" ZN y2201 " pdb="ZN ZN y2201 " - pdb=" SG CYS y 467 " pdb="ZN ZN y2201 " - pdb=" SG CYS y 437 " pdb="ZN ZN y2201 " - pdb=" SG CYS y 442 " pdb="ZN ZN y2201 " - pdb=" SG CYS y 469 " pdb=" ZN y2202 " pdb="ZN ZN y2202 " - pdb=" SG CYS y 586 " pdb="ZN ZN y2202 " - pdb=" SG CYS y 479 " pdb="ZN ZN y2202 " - pdb=" SG CYS y 482 " pdb="ZN ZN y2202 " - pdb=" SG CYS y 589 " pdb=" ZN y2203 " pdb="ZN ZN y2203 " - pdb=" SG CYS y1442 " pdb="ZN ZN y2203 " - pdb=" SG CYS y1423 " pdb="ZN ZN y2203 " - pdb=" SG CYS y1426 " pdb="ZN ZN y2203 " - pdb=" SG CYS y1439 " pdb=" ZN y2204 " pdb="ZN ZN y2204 " - pdb=" NE2 HIS y1554 " pdb="ZN ZN y2204 " - pdb=" SG CYS y1526 " pdb="ZN ZN y2204 " - pdb=" SG CYS y1529 " pdb="ZN ZN y2204 " - pdb=" SG CYS y1571 " pdb=" ZN y2205 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1683 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1687 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1690 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1681 " Number of angles added : 54 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7722 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 30 sheets defined 42.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'Y' and resid 7 through 28 Processing helix chain 'Y' and resid 31 through 43 Processing helix chain 'Y' and resid 70 through 78 removed outlier: 3.795A pdb=" N LEU Y 74 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 87 removed outlier: 3.675A pdb=" N VAL Y 84 " --> pdb=" O SER Y 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 106 Processing helix chain 'Y' and resid 120 through 141 removed outlier: 3.900A pdb=" N PHE Y 125 " --> pdb=" O LYS Y 121 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL Y 127 " --> pdb=" O GLU Y 123 " (cutoff:3.500A) Proline residue: Y 128 - end of helix Processing helix chain 'Y' and resid 156 through 170 removed outlier: 3.982A pdb=" N ARG Y 165 " --> pdb=" O SER Y 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 200 removed outlier: 4.471A pdb=" N GLU Y 195 " --> pdb=" O TYR Y 191 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP Y 196 " --> pdb=" O GLU Y 192 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS Y 199 " --> pdb=" O GLU Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 213 Processing helix chain 'Y' and resid 222 through 231 Processing helix chain 'Y' and resid 234 through 245 removed outlier: 3.625A pdb=" N GLU Y 239 " --> pdb=" O ALA Y 235 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS Y 240 " --> pdb=" O PRO Y 236 " (cutoff:3.500A) Processing helix chain 'Y' and resid 258 through 275 removed outlier: 3.696A pdb=" N ALA Y 262 " --> pdb=" O GLY Y 258 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 314 Processing helix chain 'Y' and resid 345 through 351 removed outlier: 3.724A pdb=" N LEU Y 351 " --> pdb=" O SER Y 347 " (cutoff:3.500A) Processing helix chain 'Y' and resid 352 through 363 removed outlier: 3.563A pdb=" N TYR Y 357 " --> pdb=" O PRO Y 353 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN Y 358 " --> pdb=" O GLN Y 354 " (cutoff:3.500A) Processing helix chain 'Y' and resid 363 through 374 removed outlier: 3.723A pdb=" N GLN Y 367 " --> pdb=" O TYR Y 363 " (cutoff:3.500A) Processing helix chain 'Y' and resid 383 through 394 removed outlier: 3.799A pdb=" N THR Y 393 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 398 through 411 Processing helix chain 'Y' and resid 446 through 450 Processing helix chain 'Y' and resid 529 through 535 removed outlier: 4.039A pdb=" N SER Y 533 " --> pdb=" O LEU Y 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 606 through 622 Proline residue: Y 616 - end of helix Processing helix chain 'Y' and resid 627 through 632 removed outlier: 3.803A pdb=" N LEU Y 632 " --> pdb=" O GLU Y 629 " (cutoff:3.500A) Processing helix chain 'Y' and resid 647 through 674 Processing helix chain 'Y' and resid 685 through 700 removed outlier: 3.688A pdb=" N CYS Y 689 " --> pdb=" O SER Y 685 " (cutoff:3.500A) Processing helix chain 'Y' and resid 705 through 716 Processing helix chain 'Y' and resid 722 through 732 Processing helix chain 'Y' and resid 732 through 740 removed outlier: 3.508A pdb=" N VAL Y 736 " --> pdb=" O ILE Y 732 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER Y 740 " --> pdb=" O VAL Y 736 " (cutoff:3.500A) Processing helix chain 'Y' and resid 740 through 756 removed outlier: 3.560A pdb=" N ASN Y 756 " --> pdb=" O ALA Y 752 " (cutoff:3.500A) Processing helix chain 'Y' and resid 764 through 773 Processing helix chain 'Y' and resid 776 through 790 Processing helix chain 'Y' and resid 794 through 808 Processing helix chain 'Y' and resid 817 through 821 Processing helix chain 'Y' and resid 827 through 833 Processing helix chain 'Y' and resid 837 through 844 Processing helix chain 'Y' and resid 849 through 869 removed outlier: 3.885A pdb=" N ILE Y 866 " --> pdb=" O LEU Y 862 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG Y 867 " --> pdb=" O ASP Y 863 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN Y 869 " --> pdb=" O PHE Y 865 " (cutoff:3.500A) Processing helix chain 'Y' and resid 877 through 882 Processing helix chain 'Y' and resid 910 through 916 removed outlier: 4.150A pdb=" N HIS Y 915 " --> pdb=" O ARG Y 912 " (cutoff:3.500A) Processing helix chain 'Y' and resid 917 through 927 Processing helix chain 'Y' and resid 934 through 953 Processing helix chain 'Y' and resid 954 through 956 No H-bonds generated for 'chain 'Y' and resid 954 through 956' Processing helix chain 'Y' and resid 966 through 971 removed outlier: 3.560A pdb=" N GLN Y 970 " --> pdb=" O ASP Y 966 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA Y 971 " --> pdb=" O ILE Y 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 966 through 971' Processing helix chain 'Y' and resid 1021 through 1025 removed outlier: 3.583A pdb=" N TRP Y1024 " --> pdb=" O VAL Y1021 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1033 through 1044 removed outlier: 4.031A pdb=" N ARG Y1037 " --> pdb=" O ALA Y1033 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1044 through 1054 Processing helix chain 'Y' and resid 1057 through 1065 Processing helix chain 'Y' and resid 1080 through 1093 removed outlier: 3.844A pdb=" N SER Y1093 " --> pdb=" O LYS Y1089 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1125 through 1134 Processing helix chain 'Y' and resid 1135 through 1137 No H-bonds generated for 'chain 'Y' and resid 1135 through 1137' Processing helix chain 'Y' and resid 1153 through 1162 Processing helix chain 'Y' and resid 1164 through 1169 Processing helix chain 'Y' and resid 1180 through 1201 removed outlier: 4.157A pdb=" N VAL Y1184 " --> pdb=" O SER Y1180 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL Y1201 " --> pdb=" O LEU Y1197 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1219 through 1230 Processing helix chain 'Y' and resid 1233 through 1242 removed outlier: 4.726A pdb=" N LYS Y1237 " --> pdb=" O GLN Y1233 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1245 through 1249 removed outlier: 4.184A pdb=" N SER Y1249 " --> pdb=" O VAL Y1246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1253 through 1288 removed outlier: 3.515A pdb=" N THR Y1257 " --> pdb=" O THR Y1253 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1294 through 1310 Processing helix chain 'Y' and resid 1311 through 1318 Processing helix chain 'Y' and resid 1338 through 1348 Processing helix chain 'Y' and resid 1374 through 1381 removed outlier: 4.133A pdb=" N ARG Y1379 " --> pdb=" O PRO Y1375 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1445 through 1447 No H-bonds generated for 'chain 'Y' and resid 1445 through 1447' Processing helix chain 'Y' and resid 1547 through 1551 Processing helix chain 'Y' and resid 1604 through 1623 Processing helix chain 'Y' and resid 1626 through 1630 removed outlier: 3.695A pdb=" N GLU Y1629 " --> pdb=" O GLU Y1626 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU Y1630 " --> pdb=" O ASN Y1627 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 1626 through 1630' Processing helix chain 'Y' and resid 1662 through 1666 Processing helix chain 'Y' and resid 1667 through 1680 Processing helix chain 'Y' and resid 1695 through 1703 removed outlier: 4.231A pdb=" N VAL Y1700 " --> pdb=" O GLN Y1697 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASN Y1701 " --> pdb=" O HIS Y1698 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1704 through 1712 removed outlier: 3.703A pdb=" N ALA Y1708 " --> pdb=" O ASP Y1704 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1713 through 1720 Processing helix chain 'Y' and resid 1739 through 1750 removed outlier: 3.507A pdb=" N SER Y1750 " --> pdb=" O GLN Y1746 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1773 through 1784 Processing helix chain 'Y' and resid 1800 through 1812 Processing helix chain 'Y' and resid 1887 through 1892 Processing helix chain 'Y' and resid 1911 through 1927 Processing helix chain 'Y' and resid 1927 through 1937 Processing helix chain 'Y' and resid 1952 through 1970 Processing helix chain 'Y' and resid 1971 through 1974 removed outlier: 3.517A pdb=" N ARG Y1974 " --> pdb=" O MET Y1971 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 1971 through 1974' Processing helix chain 'Y' and resid 2000 through 2013 Processing helix chain 'Y' and resid 2075 through 2086 Processing helix chain 'y' and resid 7 through 28 Processing helix chain 'y' and resid 32 through 44 Processing helix chain 'y' and resid 70 through 75 Processing helix chain 'y' and resid 80 through 88 Processing helix chain 'y' and resid 94 through 103 removed outlier: 3.617A pdb=" N THR y 103 " --> pdb=" O THR y 99 " (cutoff:3.500A) Processing helix chain 'y' and resid 116 through 119 Processing helix chain 'y' and resid 120 through 141 Proline residue: y 128 - end of helix Processing helix chain 'y' and resid 155 through 167 Processing helix chain 'y' and resid 194 through 200 Processing helix chain 'y' and resid 206 through 213 Processing helix chain 'y' and resid 221 through 231 Processing helix chain 'y' and resid 234 through 241 Processing helix chain 'y' and resid 257 through 276 removed outlier: 3.518A pdb=" N ALA y 261 " --> pdb=" O ILE y 257 " (cutoff:3.500A) Processing helix chain 'y' and resid 298 through 314 Processing helix chain 'y' and resid 333 through 337 removed outlier: 3.660A pdb=" N ILE y 337 " --> pdb=" O GLU y 334 " (cutoff:3.500A) Processing helix chain 'y' and resid 345 through 351 Processing helix chain 'y' and resid 352 through 362 Processing helix chain 'y' and resid 363 through 374 Processing helix chain 'y' and resid 383 through 394 Processing helix chain 'y' and resid 398 through 411 Processing helix chain 'y' and resid 446 through 450 Processing helix chain 'y' and resid 606 through 620 removed outlier: 4.459A pdb=" N ASN y 612 " --> pdb=" O PRO y 608 " (cutoff:3.500A) Proline residue: y 616 - end of helix removed outlier: 4.137A pdb=" N GLU y 620 " --> pdb=" O PRO y 616 " (cutoff:3.500A) Processing helix chain 'y' and resid 627 through 633 removed outlier: 3.909A pdb=" N LEU y 632 " --> pdb=" O GLU y 629 " (cutoff:3.500A) Processing helix chain 'y' and resid 648 through 673 removed outlier: 4.639A pdb=" N ARG y 652 " --> pdb=" O GLN y 648 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU y 673 " --> pdb=" O LEU y 669 " (cutoff:3.500A) Processing helix chain 'y' and resid 685 through 700 removed outlier: 3.705A pdb=" N GLU y 693 " --> pdb=" O CYS y 689 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS y 694 " --> pdb=" O ALA y 690 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE y 699 " --> pdb=" O VAL y 695 " (cutoff:3.500A) Processing helix chain 'y' and resid 704 through 716 removed outlier: 3.908A pdb=" N ALA y 716 " --> pdb=" O LYS y 712 " (cutoff:3.500A) Processing helix chain 'y' and resid 722 through 740 Proline residue: y 734 - end of helix Processing helix chain 'y' and resid 740 through 753 removed outlier: 3.794A pdb=" N ALA y 744 " --> pdb=" O SER y 740 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU y 745 " --> pdb=" O THR y 741 " (cutoff:3.500A) Processing helix chain 'y' and resid 764 through 773 Processing helix chain 'y' and resid 775 through 790 removed outlier: 4.748A pdb=" N MET y 781 " --> pdb=" O LEU y 777 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ARG y 782 " --> pdb=" O ALA y 778 " (cutoff:3.500A) Processing helix chain 'y' and resid 794 through 808 Processing helix chain 'y' and resid 816 through 821 Processing helix chain 'y' and resid 827 through 833 removed outlier: 3.645A pdb=" N ASP y 831 " --> pdb=" O TYR y 827 " (cutoff:3.500A) Processing helix chain 'y' and resid 837 through 844 Processing helix chain 'y' and resid 849 through 869 removed outlier: 3.950A pdb=" N ILE y 866 " --> pdb=" O LEU y 862 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG y 867 " --> pdb=" O ASP y 863 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN y 869 " --> pdb=" O PHE y 865 " (cutoff:3.500A) Processing helix chain 'y' and resid 879 through 884 removed outlier: 3.746A pdb=" N GLY y 884 " --> pdb=" O PRO y 880 " (cutoff:3.500A) Processing helix chain 'y' and resid 910 through 914 removed outlier: 3.566A pdb=" N ARG y 914 " --> pdb=" O ILE y 911 " (cutoff:3.500A) Processing helix chain 'y' and resid 917 through 927 removed outlier: 4.261A pdb=" N LYS y 921 " --> pdb=" O ASN y 917 " (cutoff:3.500A) Processing helix chain 'y' and resid 934 through 953 Processing helix chain 'y' and resid 1033 through 1042 removed outlier: 3.623A pdb=" N ARG y1037 " --> pdb=" O ALA y1033 " (cutoff:3.500A) Processing helix chain 'y' and resid 1044 through 1053 removed outlier: 4.080A pdb=" N GLN y1048 " --> pdb=" O ASN y1044 " (cutoff:3.500A) Processing helix chain 'y' and resid 1057 through 1065 Processing helix chain 'y' and resid 1080 through 1093 Processing helix chain 'y' and resid 1125 through 1135 removed outlier: 3.789A pdb=" N TYR y1129 " --> pdb=" O ALA y1125 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG y1135 " --> pdb=" O GLN y1131 " (cutoff:3.500A) Processing helix chain 'y' and resid 1153 through 1162 removed outlier: 3.651A pdb=" N PHE y1160 " --> pdb=" O GLY y1156 " (cutoff:3.500A) Processing helix chain 'y' and resid 1164 through 1169 Processing helix chain 'y' and resid 1182 through 1200 Processing helix chain 'y' and resid 1218 through 1230 removed outlier: 3.674A pdb=" N GLN y1230 " --> pdb=" O TRP y1226 " (cutoff:3.500A) Processing helix chain 'y' and resid 1231 through 1243 Processing helix chain 'y' and resid 1251 through 1288 removed outlier: 3.832A pdb=" N LEU y1255 " --> pdb=" O THR y1251 " (cutoff:3.500A) Processing helix chain 'y' and resid 1294 through 1309 Processing helix chain 'y' and resid 1311 through 1319 Processing helix chain 'y' and resid 1338 through 1342 removed outlier: 3.677A pdb=" N LEU y1342 " --> pdb=" O ALA y1339 " (cutoff:3.500A) Processing helix chain 'y' and resid 1373 through 1381 Processing helix chain 'y' and resid 1445 through 1447 No H-bonds generated for 'chain 'y' and resid 1445 through 1447' Processing helix chain 'y' and resid 1604 through 1623 Processing helix chain 'y' and resid 1626 through 1630 Processing helix chain 'y' and resid 1659 through 1666 removed outlier: 4.258A pdb=" N GLN y1663 " --> pdb=" O GLY y1659 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP y1666 " --> pdb=" O VAL y1662 " (cutoff:3.500A) Processing helix chain 'y' and resid 1668 through 1680 Processing helix chain 'y' and resid 1695 through 1703 removed outlier: 4.192A pdb=" N VAL y1700 " --> pdb=" O GLN y1697 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN y1701 " --> pdb=" O HIS y1698 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU y1703 " --> pdb=" O VAL y1700 " (cutoff:3.500A) Processing helix chain 'y' and resid 1704 through 1712 removed outlier: 3.723A pdb=" N ALA y1708 " --> pdb=" O ASP y1704 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU y1711 " --> pdb=" O HIS y1707 " (cutoff:3.500A) Processing helix chain 'y' and resid 1713 through 1720 Processing helix chain 'y' and resid 1739 through 1751 Processing helix chain 'y' and resid 1772 through 1785 removed outlier: 3.691A pdb=" N LYS y1776 " --> pdb=" O TRP y1772 " (cutoff:3.500A) Processing helix chain 'y' and resid 1800 through 1812 Processing helix chain 'y' and resid 1824 through 1828 removed outlier: 3.794A pdb=" N LEU y1828 " --> pdb=" O ALA y1824 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 1824 through 1828' Processing helix chain 'y' and resid 1913 through 1927 removed outlier: 4.111A pdb=" N SER y1917 " --> pdb=" O GLU y1913 " (cutoff:3.500A) Processing helix chain 'y' and resid 1927 through 1937 Processing helix chain 'y' and resid 1952 through 1969 removed outlier: 4.166A pdb=" N GLN y1969 " --> pdb=" O GLU y1965 " (cutoff:3.500A) Processing helix chain 'y' and resid 1970 through 1974 removed outlier: 3.850A pdb=" N GLU y1973 " --> pdb=" O GLY y1970 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG y1974 " --> pdb=" O MET y1971 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 1970 through 1974' Processing helix chain 'y' and resid 2000 through 2013 removed outlier: 4.095A pdb=" N LEU y2012 " --> pdb=" O VAL y2008 " (cutoff:3.500A) Processing helix chain 'y' and resid 2076 through 2086 Processing sheet with id=AA1, first strand: chain 'Y' and resid 380 through 382 removed outlier: 6.401A pdb=" N LEU Y 422 " --> pdb=" O SER Y1144 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ALA Y1146 " --> pdb=" O LEU Y 422 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N MET Y 424 " --> pdb=" O ALA Y1146 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR Y1148 " --> pdb=" O MET Y 424 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY Y 426 " --> pdb=" O THR Y1148 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N CYS Y1150 " --> pdb=" O GLY Y 426 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE Y 428 " --> pdb=" O CYS Y1150 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL Y1117 " --> pdb=" O ILE Y1147 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LEU Y1149 " --> pdb=" O VAL Y1117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 179 through 182 removed outlier: 6.432A pdb=" N ALA Y 180 " --> pdb=" O VAL Y 219 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ASN Y 221 " --> pdb=" O ALA Y 180 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N TYR Y 182 " --> pdb=" O ASN Y 221 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE Y 150 " --> pdb=" O VAL Y 249 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU Y 111 " --> pdb=" O ALA Y 289 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N SER Y 291 " --> pdb=" O LEU Y 111 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL Y 113 " --> pdb=" O SER Y 291 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER Y 110 " --> pdb=" O LYS Y 321 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL Y 323 " --> pdb=" O SER Y 110 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU Y 112 " --> pdb=" O VAL Y 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 435 through 436 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 459 through 460 current: chain 'Y' and resid 485 through 493 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 499 through 503 current: chain 'Y' and resid 565 through 571 Processing sheet with id=AA4, first strand: chain 'Y' and resid 762 through 763 Processing sheet with id=AA5, first strand: chain 'Y' and resid 957 through 958 Processing sheet with id=AA6, first strand: chain 'Y' and resid 988 through 989 removed outlier: 3.670A pdb=" N VAL Y1012 " --> pdb=" O ARG Y 981 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 1072 through 1075 removed outlier: 6.697A pdb=" N GLU Y1073 " --> pdb=" O ASN Y1100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'Y' and resid 1371 through 1373 removed outlier: 3.570A pdb=" N PHE Y1460 " --> pdb=" O ASN Y1333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY Y1459 " --> pdb=" O MET Y1400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 1386 through 1389 Processing sheet with id=AB1, first strand: chain 'Y' and resid 1419 through 1423 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 1429 through 1432 current: chain 'Y' and resid 1501 through 1515 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 1501 through 1515 current: chain 'Y' and resid 1532 through 1534 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 1532 through 1534 current: chain 'Y' and resid 1647 through 1651 Processing sheet with id=AB2, first strand: chain 'Y' and resid 1734 through 1735 removed outlier: 6.192A pdb=" N ALA Y1850 " --> pdb=" O TRP Y1835 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TRP Y1835 " --> pdb=" O ALA Y1850 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU Y1836 " --> pdb=" O VAL Y1759 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS Y1756 " --> pdb=" O GLU Y1789 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU Y1791 " --> pdb=" O CYS Y1756 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU Y1758 " --> pdb=" O LEU Y1791 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Y' and resid 1940 through 1942 removed outlier: 3.548A pdb=" N HIS Y1942 " --> pdb=" O THR Y2044 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR Y2044 " --> pdb=" O HIS Y1942 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'Y' and resid 1944 through 1946 removed outlier: 6.025A pdb=" N VAL Y1979 " --> pdb=" O LEU Y2028 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 2054 through 2055 removed outlier: 3.572A pdb=" N LEU Y2054 " --> pdb=" O ILE Y2102 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE Y2102 " --> pdb=" O LEU Y2054 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'y' and resid 380 through 382 removed outlier: 6.309A pdb=" N VAL y1117 " --> pdb=" O ILE y1147 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU y1149 " --> pdb=" O VAL y1117 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET y1119 " --> pdb=" O LEU y1149 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU y 641 " --> pdb=" O LEU y1116 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU y 640 " --> pdb=" O LEU y1099 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS y1101 " --> pdb=" O LEU y 640 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR y 642 " --> pdb=" O CYS y1101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'y' and resid 179 through 182 removed outlier: 6.602A pdb=" N ALA y 149 " --> pdb=" O MET y 218 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR y 220 " --> pdb=" O ALA y 149 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE y 151 " --> pdb=" O THR y 220 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE y 150 " --> pdb=" O VAL y 249 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP y 251 " --> pdb=" O ILE y 150 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU y 152 " --> pdb=" O ASP y 251 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE y 248 " --> pdb=" O ILE y 288 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR y 290 " --> pdb=" O ILE y 248 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU y 250 " --> pdb=" O THR y 290 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER y 110 " --> pdb=" O LYS y 321 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL y 323 " --> pdb=" O SER y 110 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU y 112 " --> pdb=" O VAL y 323 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'y' and resid 435 through 437 removed outlier: 3.554A pdb=" N ALA y 436 " --> pdb=" O PHE y 474 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N VAL y 473 " --> pdb=" O LYS y 490 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N LYS y 490 " --> pdb=" O VAL y 473 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU y 475 " --> pdb=" O SER y 488 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 499 through 502 current: chain 'y' and resid 565 through 571 Processing sheet with id=AB9, first strand: chain 'y' and resid 762 through 763 Processing sheet with id=AC1, first strand: chain 'y' and resid 891 through 892 removed outlier: 5.621A pdb=" N MET y 891 " --> pdb=" O GLN y 906 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'y' and resid 957 through 959 Processing sheet with id=AC3, first strand: chain 'y' and resid 988 through 989 removed outlier: 3.834A pdb=" N VAL y1012 " --> pdb=" O ARG y 981 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'y' and resid 1333 through 1335 removed outlier: 6.505A pdb=" N ASN y1333 " --> pdb=" O PHE y1460 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'y' and resid 1385 through 1389 removed outlier: 3.988A pdb=" N ALA y1385 " --> pdb=" O SER y1396 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'y' and resid 1428 through 1432 Processing sheet with id=AC7, first strand: chain 'y' and resid 1484 through 1486 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 1484 through 1486 current: chain 'y' and resid 1501 through 1514 removed outlier: 4.220A pdb=" N SER y1508 " --> pdb=" O THR y1587 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR y1587 " --> pdb=" O SER y1508 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU y1510 " --> pdb=" O SER y1585 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER y1585 " --> pdb=" O GLU y1510 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE y1512 " --> pdb=" O TYR y1583 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR y1583 " --> pdb=" O PHE y1512 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 1582 through 1594 current: chain 'y' and resid 1647 through 1651 Processing sheet with id=AC8, first strand: chain 'y' and resid 1532 through 1535 removed outlier: 3.746A pdb=" N GLY y1522 " --> pdb=" O GLN y1535 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR y1523 " --> pdb=" O ASP y1578 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP y1578 " --> pdb=" O TYR y1523 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'y' and resid 1734 through 1735 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 1734 through 1735 current: chain 'y' and resid 1787 through 1792 removed outlier: 6.130A pdb=" N VAL y1788 " --> pdb=" O GLN y1819 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LYS y1821 " --> pdb=" O VAL y1788 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU y1790 " --> pdb=" O LYS y1821 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 1818 through 1822 current: chain 'y' and resid 1833 through 1840 removed outlier: 7.010A pdb=" N TRP y1848 " --> pdb=" O LEU y1836 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN y1838 " --> pdb=" O GLN y1846 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN y1846 " --> pdb=" O GLN y1838 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'y' and resid 1901 through 1903 removed outlier: 3.593A pdb=" N ILE y2102 " --> pdb=" O LEU y2054 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL y2043 " --> pdb=" O HIS y2051 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'y' and resid 1943 through 1946 Processing sheet with id=AD3, first strand: chain 'y' and resid 2063 through 2064 1247 hydrogen bonds defined for protein. 3540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.81 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 11437 1.36 - 1.51: 10292 1.51 - 1.65: 12550 1.65 - 1.80: 152 1.80 - 1.95: 64 Bond restraints: 34495 Sorted by residual: bond pdb=" O3B AGS Y2206 " pdb=" PB AGS Y2206 " ideal model delta sigma weight residual 1.673 1.563 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" O3B AGS y2206 " pdb=" PB AGS y2206 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" O3A AGS Y2206 " pdb=" PA AGS Y2206 " ideal model delta sigma weight residual 1.664 1.574 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" O3A AGS y2206 " pdb=" PA AGS y2206 " ideal model delta sigma weight residual 1.664 1.583 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" O3B AGS Y2206 " pdb=" PG AGS Y2206 " ideal model delta sigma weight residual 1.614 1.546 0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 34490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 46427 2.86 - 5.73: 440 5.73 - 8.59: 67 8.59 - 11.46: 15 11.46 - 14.32: 3 Bond angle restraints: 46952 Sorted by residual: angle pdb=" O4' DA G 17 " pdb=" C4' DA G 17 " pdb=" C3' DA G 17 " ideal model delta sigma weight residual 106.00 102.63 3.37 6.00e-01 2.78e+00 3.15e+01 angle pdb=" O4' DG G 19 " pdb=" C4' DG G 19 " pdb=" C3' DG G 19 " ideal model delta sigma weight residual 106.00 102.64 3.36 6.00e-01 2.78e+00 3.13e+01 angle pdb=" C4' DA G 17 " pdb=" C3' DA G 17 " pdb=" C2' DA G 17 " ideal model delta sigma weight residual 103.10 98.98 4.12 9.00e-01 1.23e+00 2.09e+01 angle pdb=" N3 DT I 11 " pdb=" C4 DT I 11 " pdb=" O4 DT I 11 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" CB MET y 747 " pdb=" CG MET y 747 " pdb=" SD MET y 747 " ideal model delta sigma weight residual 112.70 99.51 13.19 3.00e+00 1.11e-01 1.93e+01 ... (remaining 46947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.80: 19214 28.80 - 57.60: 1327 57.60 - 86.41: 159 86.41 - 115.21: 9 115.21 - 144.01: 9 Dihedral angle restraints: 20718 sinusoidal: 8755 harmonic: 11963 Sorted by residual: dihedral pdb=" CA THR Y1251 " pdb=" C THR Y1251 " pdb=" N ALA Y1252 " pdb=" CA ALA Y1252 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA PHE Y1213 " pdb=" C PHE Y1213 " pdb=" N GLU Y1214 " pdb=" CA GLU Y1214 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA GLU Y 868 " pdb=" C GLU Y 868 " pdb=" N ASN Y 869 " pdb=" CA ASN Y 869 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 20715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4354 0.061 - 0.121: 708 0.121 - 0.182: 46 0.182 - 0.242: 4 0.242 - 0.303: 3 Chirality restraints: 5115 Sorted by residual: chirality pdb=" CB VAL Y1967 " pdb=" CA VAL Y1967 " pdb=" CG1 VAL Y1967 " pdb=" CG2 VAL Y1967 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' AGS Y2206 " pdb=" C2' AGS Y2206 " pdb=" C4' AGS Y2206 " pdb=" O3' AGS Y2206 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C3' AGS y2206 " pdb=" C2' AGS y2206 " pdb=" C4' AGS y2206 " pdb=" O3' AGS y2206 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 5112 not shown) Planarity restraints: 5978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY y1910 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO y1911 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO y1911 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO y1911 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG Y 269 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C ARG Y 269 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG Y 269 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG Y 270 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN y1884 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" CD GLN y1884 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLN y1884 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN y1884 " -0.011 2.00e-02 2.50e+03 ... (remaining 5975 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 647 2.58 - 3.16: 31433 3.16 - 3.74: 59817 3.74 - 4.32: 76830 4.32 - 4.90: 119811 Nonbonded interactions: 288538 Sorted by model distance: nonbonded pdb=" N2 DG G 21 " pdb=" O2 DC I 10 " model vdw 2.001 3.120 nonbonded pdb=" O SER Y1115 " pdb=" OG SER Y1144 " model vdw 2.028 3.040 nonbonded pdb=" N2 DG G 28 " pdb=" O2 DC I 3 " model vdw 2.036 3.120 nonbonded pdb=" O ILE y 104 " pdb=" OH TYR y 247 " model vdw 2.088 3.040 nonbonded pdb=" O ALA Y1382 " pdb=" OG SER Y1396 " model vdw 2.104 3.040 ... (remaining 288533 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 'Y' and (resid 4 through 505 or resid 534 through 2206)) selection = (chain 'y' and (resid 4 through 1349 or resid 1369 through 2206)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.800 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 34535 Z= 0.300 Angle : 0.783 16.303 47006 Z= 0.398 Chirality : 0.043 0.303 5115 Planarity : 0.004 0.054 5978 Dihedral : 18.537 144.012 12996 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 25.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.25 % Favored : 93.72 % Rotamer: Outliers : 4.04 % Allowed : 24.25 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.13), residues: 4111 helix: 0.33 (0.13), residues: 1592 sheet: -1.12 (0.21), residues: 584 loop : -1.55 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 594 TYR 0.023 0.001 TYR y1466 PHE 0.016 0.002 PHE Y1519 TRP 0.026 0.002 TRP Y 101 HIS 0.012 0.001 HIS Y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.30 (34495) covalent geometry : angle 0.75378 / 0.40 (46952) hydrogen bonds : bond 0.14887 / 10.28 ( 1247) hydrogen bonds : angle 6.38380 / 4.55 ( 3540) metal coordination : bond 0.01276 / 0.72 ( 40) metal coordination : angle 6.27072 / 4.13 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 138 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 407 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8623 (t70) REVERT: Y 698 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: Y 945 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8618 (tpp) REVERT: Y 1760 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8782 (mt) REVERT: Y 1950 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8287 (tp) REVERT: Y 1995 TYR cc_start: -0.0189 (OUTLIER) cc_final: -0.1667 (p90) REVERT: Y 1998 TRP cc_start: 0.7535 (t-100) cc_final: 0.7247 (t60) REVERT: Y 2079 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6253 (mt0) REVERT: y 641 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8410 (mm) REVERT: y 1105 MET cc_start: 0.6062 (tpt) cc_final: 0.5704 (tpt) REVERT: y 1823 ILE cc_start: 0.5649 (OUTLIER) cc_final: 0.5261 (tp) REVERT: y 2097 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.5370 (pt) outliers start: 142 outliers final: 119 residues processed: 266 average time/residue: 0.1823 time to fit residues: 84.5266 Evaluate side-chains 265 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 136 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 41 GLN Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain Y residue 103 THR Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 206 SER Chi-restraints excluded: chain Y residue 309 VAL Chi-restraints excluded: chain Y residue 312 LEU Chi-restraints excluded: chain Y residue 355 ASP Chi-restraints excluded: chain Y residue 396 ASP Chi-restraints excluded: chain Y residue 407 ASP Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 467 CYS Chi-restraints excluded: chain Y residue 517 VAL Chi-restraints excluded: chain Y residue 532 ASN Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 551 GLU Chi-restraints excluded: chain Y residue 559 ASP Chi-restraints excluded: chain Y residue 568 ILE Chi-restraints excluded: chain Y residue 582 ASN Chi-restraints excluded: chain Y residue 592 THR Chi-restraints excluded: chain Y residue 594 ARG Chi-restraints excluded: chain Y residue 695 VAL Chi-restraints excluded: chain Y residue 698 GLN Chi-restraints excluded: chain Y residue 761 THR Chi-restraints excluded: chain Y residue 794 THR Chi-restraints excluded: chain Y residue 803 LEU Chi-restraints excluded: chain Y residue 813 ASN Chi-restraints excluded: chain Y residue 823 VAL Chi-restraints excluded: chain Y residue 829 PHE Chi-restraints excluded: chain Y residue 835 THR Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 936 HIS Chi-restraints excluded: chain Y residue 941 VAL Chi-restraints excluded: chain Y residue 945 MET Chi-restraints excluded: chain Y residue 948 VAL Chi-restraints excluded: chain Y residue 982 CYS Chi-restraints excluded: chain Y residue 1058 THR Chi-restraints excluded: chain Y residue 1107 MET Chi-restraints excluded: chain Y residue 1130 LEU Chi-restraints excluded: chain Y residue 1153 THR Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1210 LYS Chi-restraints excluded: chain Y residue 1242 THR Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1373 ASP Chi-restraints excluded: chain Y residue 1399 ILE Chi-restraints excluded: chain Y residue 1423 CYS Chi-restraints excluded: chain Y residue 1426 CYS Chi-restraints excluded: chain Y residue 1431 THR Chi-restraints excluded: chain Y residue 1432 SER Chi-restraints excluded: chain Y residue 1458 VAL Chi-restraints excluded: chain Y residue 1464 ILE Chi-restraints excluded: chain Y residue 1487 VAL Chi-restraints excluded: chain Y residue 1536 THR Chi-restraints excluded: chain Y residue 1541 THR Chi-restraints excluded: chain Y residue 1587 THR Chi-restraints excluded: chain Y residue 1652 ASP Chi-restraints excluded: chain Y residue 1664 LEU Chi-restraints excluded: chain Y residue 1666 ASP Chi-restraints excluded: chain Y residue 1689 HIS Chi-restraints excluded: chain Y residue 1715 VAL Chi-restraints excluded: chain Y residue 1760 LEU Chi-restraints excluded: chain Y residue 1788 VAL Chi-restraints excluded: chain Y residue 1792 VAL Chi-restraints excluded: chain Y residue 1841 ARG Chi-restraints excluded: chain Y residue 1874 LYS Chi-restraints excluded: chain Y residue 1890 ASP Chi-restraints excluded: chain Y residue 1915 PHE Chi-restraints excluded: chain Y residue 1919 PHE Chi-restraints excluded: chain Y residue 1950 LEU Chi-restraints excluded: chain Y residue 1995 TYR Chi-restraints excluded: chain Y residue 2016 TYR Chi-restraints excluded: chain Y residue 2079 GLN Chi-restraints excluded: chain y residue 13 ASN Chi-restraints excluded: chain y residue 22 SER Chi-restraints excluded: chain y residue 29 LEU Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain y residue 189 THR Chi-restraints excluded: chain y residue 193 ILE Chi-restraints excluded: chain y residue 271 VAL Chi-restraints excluded: chain y residue 308 PHE Chi-restraints excluded: chain y residue 383 LEU Chi-restraints excluded: chain y residue 571 LEU Chi-restraints excluded: chain y residue 641 LEU Chi-restraints excluded: chain y residue 650 THR Chi-restraints excluded: chain y residue 670 CYS Chi-restraints excluded: chain y residue 700 SER Chi-restraints excluded: chain y residue 709 ASP Chi-restraints excluded: chain y residue 730 LYS Chi-restraints excluded: chain y residue 736 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 806 GLU Chi-restraints excluded: chain y residue 833 VAL Chi-restraints excluded: chain y residue 862 LEU Chi-restraints excluded: chain y residue 936 HIS Chi-restraints excluded: chain y residue 1014 ILE Chi-restraints excluded: chain y residue 1047 ILE Chi-restraints excluded: chain y residue 1052 GLU Chi-restraints excluded: chain y residue 1122 VAL Chi-restraints excluded: chain y residue 1128 ASN Chi-restraints excluded: chain y residue 1169 THR Chi-restraints excluded: chain y residue 1216 ASP Chi-restraints excluded: chain y residue 1232 ASP Chi-restraints excluded: chain y residue 1238 LEU Chi-restraints excluded: chain y residue 1251 THR Chi-restraints excluded: chain y residue 1292 GLU Chi-restraints excluded: chain y residue 1348 ILE Chi-restraints excluded: chain y residue 1387 VAL Chi-restraints excluded: chain y residue 1404 VAL Chi-restraints excluded: chain y residue 1437 VAL Chi-restraints excluded: chain y residue 1441 HIS Chi-restraints excluded: chain y residue 1493 VAL Chi-restraints excluded: chain y residue 1519 PHE Chi-restraints excluded: chain y residue 1541 THR Chi-restraints excluded: chain y residue 1553 THR Chi-restraints excluded: chain y residue 1574 HIS Chi-restraints excluded: chain y residue 1590 VAL Chi-restraints excluded: chain y residue 1641 ASN Chi-restraints excluded: chain y residue 1740 LEU Chi-restraints excluded: chain y residue 1823 ILE Chi-restraints excluded: chain y residue 1870 VAL Chi-restraints excluded: chain y residue 2041 LEU Chi-restraints excluded: chain y residue 2097 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 155, 244] chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.5766 > 50:) overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 626 GLN ** Y 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 970 GLN ** Y1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1636 GLN ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 359 GLN ** y 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 856 ASN ** y 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y1128 ASN y1228 ASN y1229 HIS y1230 GLN ** y1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1654 ASN ** y1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y1884 GLN ** y2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.106486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.077867 restraints weight = 220809.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.076090 restraints weight = 109270.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.076251 restraints weight = 65893.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.076521 restraints weight = 48563.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.076829 restraints weight = 40186.372| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34535 Z= 0.204 Angle : 0.695 16.313 47006 Z= 0.340 Chirality : 0.042 0.218 5115 Planarity : 0.005 0.068 5978 Dihedral : 14.973 150.543 5274 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.87 % Allowed : 22.60 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4111 helix: 0.50 (0.13), residues: 1597 sheet: -1.02 (0.21), residues: 548 loop : -1.54 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG y 987 TYR 0.020 0.001 TYR y 916 PHE 0.019 0.001 PHE y 125 TRP 0.018 0.001 TRP y1291 HIS 0.009 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (34495) covalent geometry : angle 0.66161 / 0.34 (46952) hydrogen bonds : bond 0.04745 / 3.20 ( 1247) hydrogen bonds : angle 5.52693 / 3.91 ( 3540) metal coordination : bond 0.01362 / 0.79 ( 40) metal coordination : angle 6.32881 / 4.28 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 146 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: Y 224 MET cc_start: 0.9400 (mmp) cc_final: 0.9046 (tpp) REVERT: Y 443 SER cc_start: 0.9399 (OUTLIER) cc_final: 0.9184 (p) REVERT: Y 945 MET cc_start: 0.9186 (mmp) cc_final: 0.8767 (tpp) REVERT: Y 1303 GLN cc_start: 0.9356 (tp-100) cc_final: 0.8796 (tm-30) REVERT: y 641 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8526 (mm) REVERT: y 791 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8804 (mp) REVERT: y 804 TYR cc_start: 0.9402 (OUTLIER) cc_final: 0.9062 (m-80) REVERT: y 1016 MET cc_start: 0.8659 (mmp) cc_final: 0.8295 (mmp) REVERT: y 1904 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5234 (tt) REVERT: y 1919 PHE cc_start: 0.6063 (t80) cc_final: 0.5822 (t80) outliers start: 171 outliers final: 94 residues processed: 307 average time/residue: 0.1696 time to fit residues: 90.9826 Evaluate side-chains 236 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 137 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 73 ASP Chi-restraints excluded: chain Y residue 103 THR Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 206 SER Chi-restraints excluded: chain Y residue 219 VAL Chi-restraints excluded: chain Y residue 298 SER Chi-restraints excluded: chain Y residue 312 LEU Chi-restraints excluded: chain Y residue 396 ASP Chi-restraints excluded: chain Y residue 403 LEU Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 443 SER Chi-restraints excluded: chain Y residue 517 VAL Chi-restraints excluded: chain Y residue 532 ASN Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 551 GLU Chi-restraints excluded: chain Y residue 559 ASP Chi-restraints excluded: chain Y residue 565 HIS Chi-restraints excluded: chain Y residue 568 ILE Chi-restraints excluded: chain Y residue 580 ARG Chi-restraints excluded: chain Y residue 620 GLU Chi-restraints excluded: chain Y residue 683 LYS Chi-restraints excluded: chain Y residue 695 VAL Chi-restraints excluded: chain Y residue 794 THR Chi-restraints excluded: chain Y residue 829 PHE Chi-restraints excluded: chain Y residue 835 THR Chi-restraints excluded: chain Y residue 863 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 936 HIS Chi-restraints excluded: chain Y residue 948 VAL Chi-restraints excluded: chain Y residue 992 THR Chi-restraints excluded: chain Y residue 1058 THR Chi-restraints excluded: chain Y residue 1130 LEU Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1210 LYS Chi-restraints excluded: chain Y residue 1234 LEU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1399 ILE Chi-restraints excluded: chain Y residue 1431 THR Chi-restraints excluded: chain Y residue 1541 THR Chi-restraints excluded: chain Y residue 1564 ARG Chi-restraints excluded: chain Y residue 1689 HIS Chi-restraints excluded: chain Y residue 1715 VAL Chi-restraints excluded: chain Y residue 1788 VAL Chi-restraints excluded: chain Y residue 1845 SER Chi-restraints excluded: chain Y residue 1915 PHE Chi-restraints excluded: chain Y residue 1919 PHE Chi-restraints excluded: chain Y residue 2008 VAL Chi-restraints excluded: chain Y residue 2016 TYR Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain y residue 117 THR Chi-restraints excluded: chain y residue 189 THR Chi-restraints excluded: chain y residue 193 ILE Chi-restraints excluded: chain y residue 210 ILE Chi-restraints excluded: chain y residue 271 VAL Chi-restraints excluded: chain y residue 332 VAL Chi-restraints excluded: chain y residue 383 LEU Chi-restraints excluded: chain y residue 578 GLU Chi-restraints excluded: chain y residue 641 LEU Chi-restraints excluded: chain y residue 709 ASP Chi-restraints excluded: chain y residue 730 LYS Chi-restraints excluded: chain y residue 736 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 766 THR Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 804 TYR Chi-restraints excluded: chain y residue 833 VAL Chi-restraints excluded: chain y residue 862 LEU Chi-restraints excluded: chain y residue 887 PHE Chi-restraints excluded: chain y residue 936 HIS Chi-restraints excluded: chain y residue 1014 ILE Chi-restraints excluded: chain y residue 1047 ILE Chi-restraints excluded: chain y residue 1052 GLU Chi-restraints excluded: chain y residue 1122 VAL Chi-restraints excluded: chain y residue 1161 LYS Chi-restraints excluded: chain y residue 1169 THR Chi-restraints excluded: chain y residue 1232 ASP Chi-restraints excluded: chain y residue 1238 LEU Chi-restraints excluded: chain y residue 1387 VAL Chi-restraints excluded: chain y residue 1404 VAL Chi-restraints excluded: chain y residue 1441 HIS Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1519 PHE Chi-restraints excluded: chain y residue 1525 ILE Chi-restraints excluded: chain y residue 1541 THR Chi-restraints excluded: chain y residue 1574 HIS Chi-restraints excluded: chain y residue 1590 VAL Chi-restraints excluded: chain y residue 1621 HIS Chi-restraints excluded: chain y residue 1641 ASN Chi-restraints excluded: chain y residue 1648 ILE Chi-restraints excluded: chain y residue 1740 LEU Chi-restraints excluded: chain y residue 1870 VAL Chi-restraints excluded: chain y residue 1904 LEU Chi-restraints excluded: chain y residue 1943 VAL Chi-restraints excluded: chain y residue 1998 TRP Chi-restraints excluded: chain y residue 2006 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: [323, 290, 397, 35, 185, 64, 84, 126, 414, 136, 275] chunk 323 optimal weight: 9.9990 chunk 290 optimal weight: 0.6980 chunk 397 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 414 optimal weight: 50.0000 chunk 136 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 26 GLN Y 658 GLN ** Y 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1572 HIS ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y2079 GLN ** y 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 869 ASN ** y1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y1884 GLN ** y2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.107050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.078214 restraints weight = 221101.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.077024 restraints weight = 108350.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.077542 restraints weight = 67063.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.077708 restraints weight = 49104.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.077708 restraints weight = 40954.930| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34535 Z= 0.168 Angle : 0.656 16.412 47006 Z= 0.318 Chirality : 0.041 0.176 5115 Planarity : 0.004 0.053 5978 Dihedral : 14.315 150.994 5158 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.70 % Allowed : 23.51 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.13), residues: 4111 helix: 0.58 (0.13), residues: 1605 sheet: -0.99 (0.22), residues: 531 loop : -1.51 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG y 987 TYR 0.017 0.001 TYR y 916 PHE 0.018 0.001 PHE y 125 TRP 0.017 0.001 TRP y1291 HIS 0.007 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (34495) covalent geometry : angle 0.62521 / 0.32 (46952) hydrogen bonds : bond 0.04233 / 2.84 ( 1247) hydrogen bonds : angle 5.32737 / 3.76 ( 3540) metal coordination : bond 0.01126 / 0.63 ( 40) metal coordination : angle 5.91425 / 3.99 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 146 time to evaluate : 1.265 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: Y 224 MET cc_start: 0.9448 (OUTLIER) cc_final: 0.8999 (tpp) REVERT: Y 228 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8454 (ptm) REVERT: Y 443 SER cc_start: 0.9356 (OUTLIER) cc_final: 0.9132 (p) REVERT: Y 945 MET cc_start: 0.9158 (mmp) cc_final: 0.8748 (tpp) REVERT: Y 1105 MET cc_start: 0.0802 (mtm) cc_final: -0.0490 (ttt) REVERT: Y 1157 MET cc_start: 0.8979 (mmm) cc_final: 0.8672 (mmm) REVERT: Y 1303 GLN cc_start: 0.9323 (tp-100) cc_final: 0.8777 (tm-30) REVERT: Y 1505 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7942 (t80) REVERT: y 641 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8504 (mm) REVERT: y 791 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8810 (mp) REVERT: y 804 TYR cc_start: 0.9419 (OUTLIER) cc_final: 0.9063 (m-80) REVERT: y 1016 MET cc_start: 0.8704 (mmp) cc_final: 0.8440 (mmp) outliers start: 165 outliers final: 112 residues processed: 295 average time/residue: 0.1767 time to fit residues: 90.1354 Evaluate side-chains 254 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 135 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 73 ASP Chi-restraints excluded: chain Y residue 103 THR Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 206 SER Chi-restraints excluded: chain Y residue 212 GLU Chi-restraints excluded: chain Y residue 219 VAL Chi-restraints excluded: chain Y residue 224 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 298 SER Chi-restraints excluded: chain Y residue 312 LEU Chi-restraints excluded: chain Y residue 396 ASP Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 443 SER Chi-restraints excluded: chain Y residue 467 CYS Chi-restraints excluded: chain Y residue 517 VAL Chi-restraints excluded: chain Y residue 532 ASN Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 551 GLU Chi-restraints excluded: chain Y residue 559 ASP Chi-restraints excluded: chain Y residue 565 HIS Chi-restraints excluded: chain Y residue 568 ILE Chi-restraints excluded: chain Y residue 580 ARG Chi-restraints excluded: chain Y residue 683 LYS Chi-restraints excluded: chain Y residue 695 VAL Chi-restraints excluded: chain Y residue 735 MET Chi-restraints excluded: chain Y residue 829 PHE Chi-restraints excluded: chain Y residue 835 THR Chi-restraints excluded: chain Y residue 863 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 936 HIS Chi-restraints excluded: chain Y residue 1058 THR Chi-restraints excluded: chain Y residue 1107 MET Chi-restraints excluded: chain Y residue 1130 LEU Chi-restraints excluded: chain Y residue 1153 THR Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1210 LYS Chi-restraints excluded: chain Y residue 1234 LEU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1389 LEU Chi-restraints excluded: chain Y residue 1399 ILE Chi-restraints excluded: chain Y residue 1431 THR Chi-restraints excluded: chain Y residue 1441 HIS Chi-restraints excluded: chain Y residue 1485 VAL Chi-restraints excluded: chain Y residue 1505 PHE Chi-restraints excluded: chain Y residue 1536 THR Chi-restraints excluded: chain Y residue 1541 THR Chi-restraints excluded: chain Y residue 1564 ARG Chi-restraints excluded: chain Y residue 1664 LEU Chi-restraints excluded: chain Y residue 1715 VAL Chi-restraints excluded: chain Y residue 1788 VAL Chi-restraints excluded: chain Y residue 1845 SER Chi-restraints excluded: chain Y residue 1897 THR Chi-restraints excluded: chain Y residue 1915 PHE Chi-restraints excluded: chain Y residue 1919 PHE Chi-restraints excluded: chain Y residue 1991 HIS Chi-restraints excluded: chain Y residue 2008 VAL Chi-restraints excluded: chain Y residue 2016 TYR Chi-restraints excluded: chain y residue 29 LEU Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 117 THR Chi-restraints excluded: chain y residue 189 THR Chi-restraints excluded: chain y residue 193 ILE Chi-restraints excluded: chain y residue 220 THR Chi-restraints excluded: chain y residue 271 VAL Chi-restraints excluded: chain y residue 332 VAL Chi-restraints excluded: chain y residue 383 LEU Chi-restraints excluded: chain y residue 641 LEU Chi-restraints excluded: chain y residue 670 CYS Chi-restraints excluded: chain y residue 705 LYS Chi-restraints excluded: chain y residue 709 ASP Chi-restraints excluded: chain y residue 722 SER Chi-restraints excluded: chain y residue 730 LYS Chi-restraints excluded: chain y residue 733 GLU Chi-restraints excluded: chain y residue 736 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 766 THR Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 804 TYR Chi-restraints excluded: chain y residue 830 ILE Chi-restraints excluded: chain y residue 833 VAL Chi-restraints excluded: chain y residue 862 LEU Chi-restraints excluded: chain y residue 887 PHE Chi-restraints excluded: chain y residue 915 HIS Chi-restraints excluded: chain y residue 936 HIS Chi-restraints excluded: chain y residue 1014 ILE Chi-restraints excluded: chain y residue 1047 ILE Chi-restraints excluded: chain y residue 1122 VAL Chi-restraints excluded: chain y residue 1164 LEU Chi-restraints excluded: chain y residue 1169 THR Chi-restraints excluded: chain y residue 1232 ASP Chi-restraints excluded: chain y residue 1238 LEU Chi-restraints excluded: chain y residue 1348 ILE Chi-restraints excluded: chain y residue 1387 VAL Chi-restraints excluded: chain y residue 1404 VAL Chi-restraints excluded: chain y residue 1441 HIS Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1519 PHE Chi-restraints excluded: chain y residue 1525 ILE Chi-restraints excluded: chain y residue 1541 THR Chi-restraints excluded: chain y residue 1574 HIS Chi-restraints excluded: chain y residue 1590 VAL Chi-restraints excluded: chain y residue 1621 HIS Chi-restraints excluded: chain y residue 1648 ILE Chi-restraints excluded: chain y residue 1740 LEU Chi-restraints excluded: chain y residue 1870 VAL Chi-restraints excluded: chain y residue 1943 VAL Chi-restraints excluded: chain y residue 1998 TRP Chi-restraints excluded: chain y residue 2006 GLN Chi-restraints excluded: chain y residue 2041 LEU Chi-restraints excluded: chain y residue 2068 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: [61, 99, 150, 414, 156, 333, 199, 76, 284, 183, 391] chunk 61 optimal weight: 0.0980 chunk 99 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 414 optimal weight: 50.0000 chunk 156 optimal weight: 0.5980 chunk 333 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 284 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 391 optimal weight: 0.0870 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1100 ASN Y1535 GLN ** Y1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 160 ASN y 302 ASN ** y 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 676 ASN ** y 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y1805 HIS y1884 GLN ** y2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.108074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.081616 restraints weight = 219002.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.080969 restraints weight = 128646.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.081378 restraints weight = 87910.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.081393 restraints weight = 60063.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.081462 restraints weight = 62242.989| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34535 Z= 0.118 Angle : 0.641 16.035 47006 Z= 0.306 Chirality : 0.041 0.299 5115 Planarity : 0.004 0.062 5978 Dihedral : 14.034 153.653 5149 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.10 % Allowed : 24.22 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.13), residues: 4111 helix: 0.68 (0.13), residues: 1605 sheet: -0.90 (0.22), residues: 518 loop : -1.49 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG Y2087 TYR 0.018 0.001 TYR y1583 PHE 0.017 0.001 PHE y 125 TRP 0.019 0.001 TRP y1291 HIS 0.006 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (34495) covalent geometry : angle 0.61376 / 0.30 (46952) hydrogen bonds : bond 0.03786 / 2.55 ( 1247) hydrogen bonds : angle 5.11843 / 3.60 ( 3540) metal coordination : bond 0.00939 / 0.52 ( 40) metal coordination : angle 5.48267 / 3.64 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 151 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 224 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.9078 (tpp) REVERT: Y 228 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8603 (ptm) REVERT: Y 443 SER cc_start: 0.9322 (OUTLIER) cc_final: 0.9092 (p) REVERT: Y 945 MET cc_start: 0.9180 (mmp) cc_final: 0.8722 (tpp) REVERT: Y 1105 MET cc_start: 0.1311 (mtm) cc_final: -0.0336 (ttt) REVERT: Y 1157 MET cc_start: 0.9085 (mmm) cc_final: 0.8746 (mmm) REVERT: Y 1303 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8785 (tm-30) REVERT: y 182 TYR cc_start: 0.6450 (t80) cc_final: 0.5969 (t80) REVERT: y 423 ARG cc_start: 0.5252 (OUTLIER) cc_final: 0.4997 (ptt180) REVERT: y 641 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8578 (mm) REVERT: y 715 MET cc_start: 0.4354 (mpp) cc_final: 0.3984 (mpp) REVERT: y 1016 MET cc_start: 0.8793 (mmp) cc_final: 0.8498 (mmp) REVERT: y 1291 TRP cc_start: 0.8065 (p-90) cc_final: 0.7748 (p-90) outliers start: 144 outliers final: 95 residues processed: 281 average time/residue: 0.1893 time to fit residues: 91.6978 Evaluate side-chains 242 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 141 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 73 ASP Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 212 GLU Chi-restraints excluded: chain Y residue 219 VAL Chi-restraints excluded: chain Y residue 224 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 298 SER Chi-restraints excluded: chain Y residue 312 LEU Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 443 SER Chi-restraints excluded: chain Y residue 448 GLU Chi-restraints excluded: chain Y residue 467 CYS Chi-restraints excluded: chain Y residue 517 VAL Chi-restraints excluded: chain Y residue 532 ASN Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 551 GLU Chi-restraints excluded: chain Y residue 559 ASP Chi-restraints excluded: chain Y residue 568 ILE Chi-restraints excluded: chain Y residue 580 ARG Chi-restraints excluded: chain Y residue 646 SER Chi-restraints excluded: chain Y residue 735 MET Chi-restraints excluded: chain Y residue 794 THR Chi-restraints excluded: chain Y residue 829 PHE Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 936 HIS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1130 LEU Chi-restraints excluded: chain Y residue 1210 LYS Chi-restraints excluded: chain Y residue 1234 LEU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1303 GLN Chi-restraints excluded: chain Y residue 1389 LEU Chi-restraints excluded: chain Y residue 1399 ILE Chi-restraints excluded: chain Y residue 1431 THR Chi-restraints excluded: chain Y residue 1441 HIS Chi-restraints excluded: chain Y residue 1535 GLN Chi-restraints excluded: chain Y residue 1541 THR Chi-restraints excluded: chain Y residue 1664 LEU Chi-restraints excluded: chain Y residue 1689 HIS Chi-restraints excluded: chain Y residue 1788 VAL Chi-restraints excluded: chain Y residue 1792 VAL Chi-restraints excluded: chain Y residue 1845 SER Chi-restraints excluded: chain Y residue 1915 PHE Chi-restraints excluded: chain Y residue 1919 PHE Chi-restraints excluded: chain Y residue 1991 HIS Chi-restraints excluded: chain Y residue 2008 VAL Chi-restraints excluded: chain Y residue 2016 TYR Chi-restraints excluded: chain Y residue 2028 LEU Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 117 THR Chi-restraints excluded: chain y residue 189 THR Chi-restraints excluded: chain y residue 193 ILE Chi-restraints excluded: chain y residue 220 THR Chi-restraints excluded: chain y residue 271 VAL Chi-restraints excluded: chain y residue 332 VAL Chi-restraints excluded: chain y residue 383 LEU Chi-restraints excluded: chain y residue 423 ARG Chi-restraints excluded: chain y residue 587 VAL Chi-restraints excluded: chain y residue 605 LEU Chi-restraints excluded: chain y residue 641 LEU Chi-restraints excluded: chain y residue 705 LYS Chi-restraints excluded: chain y residue 722 SER Chi-restraints excluded: chain y residue 730 LYS Chi-restraints excluded: chain y residue 736 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 766 THR Chi-restraints excluded: chain y residue 830 ILE Chi-restraints excluded: chain y residue 833 VAL Chi-restraints excluded: chain y residue 862 LEU Chi-restraints excluded: chain y residue 887 PHE Chi-restraints excluded: chain y residue 915 HIS Chi-restraints excluded: chain y residue 1047 ILE Chi-restraints excluded: chain y residue 1122 VAL Chi-restraints excluded: chain y residue 1153 THR Chi-restraints excluded: chain y residue 1161 LYS Chi-restraints excluded: chain y residue 1164 LEU Chi-restraints excluded: chain y residue 1169 THR Chi-restraints excluded: chain y residue 1232 ASP Chi-restraints excluded: chain y residue 1238 LEU Chi-restraints excluded: chain y residue 1348 ILE Chi-restraints excluded: chain y residue 1387 VAL Chi-restraints excluded: chain y residue 1404 VAL Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1519 PHE Chi-restraints excluded: chain y residue 1541 THR Chi-restraints excluded: chain y residue 1574 HIS Chi-restraints excluded: chain y residue 1590 VAL Chi-restraints excluded: chain y residue 1621 HIS Chi-restraints excluded: chain y residue 1648 ILE Chi-restraints excluded: chain y residue 1740 LEU Chi-restraints excluded: chain y residue 1870 VAL Chi-restraints excluded: chain y residue 1943 VAL Chi-restraints excluded: chain y residue 1998 TRP Chi-restraints excluded: chain y residue 2006 GLN Chi-restraints excluded: chain y residue 2041 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: [313, 292, 248, 149, 153, 262, 157, 361, 85, 242, 202] chunk 313 optimal weight: 9.9990 chunk 292 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 361 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1303 GLN ** Y1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y2078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y1100 ASN ** y1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1884 GLN ** y2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.105171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.075571 restraints weight = 221526.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.074080 restraints weight = 105373.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.074177 restraints weight = 65181.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.074431 restraints weight = 50175.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.074681 restraints weight = 43448.443| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 34535 Z= 0.331 Angle : 0.760 15.060 47006 Z= 0.372 Chirality : 0.043 0.281 5115 Planarity : 0.005 0.083 5978 Dihedral : 13.959 156.215 5130 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 5.49 % Allowed : 23.65 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.13), residues: 4111 helix: 0.55 (0.13), residues: 1606 sheet: -1.00 (0.22), residues: 531 loop : -1.49 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG y1372 TYR 0.019 0.002 TYR Y 341 PHE 0.018 0.002 PHE y 865 TRP 0.019 0.002 TRP y1419 HIS 0.008 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.33 (34495) covalent geometry : angle 0.73377 / 0.37 (46952) hydrogen bonds : bond 0.04175 / 2.78 ( 1247) hydrogen bonds : angle 5.38089 / 3.80 ( 3540) metal coordination : bond 0.01675 / 0.97 ( 40) metal coordination : angle 5.85505 / 4.02 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 141 time to evaluate : 1.533 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: Y 218 MET cc_start: 0.8749 (tpp) cc_final: 0.8499 (tpp) REVERT: Y 443 SER cc_start: 0.9406 (OUTLIER) cc_final: 0.9205 (p) REVERT: Y 945 MET cc_start: 0.9185 (mmp) cc_final: 0.8716 (tpp) REVERT: Y 1105 MET cc_start: 0.1159 (mtm) cc_final: -0.0166 (ttt) REVERT: Y 1157 MET cc_start: 0.9150 (mmm) cc_final: 0.8876 (mmm) REVERT: Y 1458 VAL cc_start: 0.9687 (OUTLIER) cc_final: 0.9451 (m) REVERT: Y 1505 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7997 (t80) REVERT: Y 1683 CYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7255 (p) REVERT: Y 1950 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8403 (tp) REVERT: Y 1998 TRP cc_start: 0.6796 (t60) cc_final: 0.6372 (t60) REVERT: y 182 TYR cc_start: 0.6423 (t80) cc_final: 0.6196 (t80) REVERT: y 641 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8506 (mm) REVERT: y 715 MET cc_start: 0.3906 (mpp) cc_final: 0.3706 (mpp) REVERT: y 791 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8830 (mp) REVERT: y 804 TYR cc_start: 0.9422 (OUTLIER) cc_final: 0.9045 (m-80) REVERT: y 1048 GLN cc_start: 0.9566 (OUTLIER) cc_final: 0.9118 (mp10) REVERT: y 1226 TRP cc_start: 0.4550 (t60) cc_final: 0.4286 (t60) outliers start: 193 outliers final: 136 residues processed: 317 average time/residue: 0.1920 time to fit residues: 105.2606 Evaluate side-chains 285 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 140 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 73 ASP Chi-restraints excluded: chain Y residue 103 THR Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 206 SER Chi-restraints excluded: chain Y residue 219 VAL Chi-restraints excluded: chain Y residue 298 SER Chi-restraints excluded: chain Y residue 396 ASP Chi-restraints excluded: chain Y residue 403 LEU Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 443 SER Chi-restraints excluded: chain Y residue 448 GLU Chi-restraints excluded: chain Y residue 467 CYS Chi-restraints excluded: chain Y residue 510 VAL Chi-restraints excluded: chain Y residue 517 VAL Chi-restraints excluded: chain Y residue 532 ASN Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 551 GLU Chi-restraints excluded: chain Y residue 559 ASP Chi-restraints excluded: chain Y residue 568 ILE Chi-restraints excluded: chain Y residue 580 ARG Chi-restraints excluded: chain Y residue 609 PHE Chi-restraints excluded: chain Y residue 620 GLU Chi-restraints excluded: chain Y residue 646 SER Chi-restraints excluded: chain Y residue 683 LYS Chi-restraints excluded: chain Y residue 695 VAL Chi-restraints excluded: chain Y residue 735 MET Chi-restraints excluded: chain Y residue 794 THR Chi-restraints excluded: chain Y residue 803 LEU Chi-restraints excluded: chain Y residue 813 ASN Chi-restraints excluded: chain Y residue 823 VAL Chi-restraints excluded: chain Y residue 829 PHE Chi-restraints excluded: chain Y residue 835 THR Chi-restraints excluded: chain Y residue 863 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 936 HIS Chi-restraints excluded: chain Y residue 941 VAL Chi-restraints excluded: chain Y residue 948 VAL Chi-restraints excluded: chain Y residue 992 THR Chi-restraints excluded: chain Y residue 1052 GLU Chi-restraints excluded: chain Y residue 1107 MET Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1130 LEU Chi-restraints excluded: chain Y residue 1153 THR Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1210 LYS Chi-restraints excluded: chain Y residue 1234 LEU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1257 THR Chi-restraints excluded: chain Y residue 1399 ILE Chi-restraints excluded: chain Y residue 1431 THR Chi-restraints excluded: chain Y residue 1441 HIS Chi-restraints excluded: chain Y residue 1458 VAL Chi-restraints excluded: chain Y residue 1505 PHE Chi-restraints excluded: chain Y residue 1536 THR Chi-restraints excluded: chain Y residue 1541 THR Chi-restraints excluded: chain Y residue 1564 ARG Chi-restraints excluded: chain Y residue 1587 THR Chi-restraints excluded: chain Y residue 1633 THR Chi-restraints excluded: chain Y residue 1664 LEU Chi-restraints excluded: chain Y residue 1683 CYS Chi-restraints excluded: chain Y residue 1689 HIS Chi-restraints excluded: chain Y residue 1700 VAL Chi-restraints excluded: chain Y residue 1715 VAL Chi-restraints excluded: chain Y residue 1741 SER Chi-restraints excluded: chain Y residue 1788 VAL Chi-restraints excluded: chain Y residue 1845 SER Chi-restraints excluded: chain Y residue 1897 THR Chi-restraints excluded: chain Y residue 1915 PHE Chi-restraints excluded: chain Y residue 1919 PHE Chi-restraints excluded: chain Y residue 1950 LEU Chi-restraints excluded: chain Y residue 1991 HIS Chi-restraints excluded: chain Y residue 1995 TYR Chi-restraints excluded: chain Y residue 2008 VAL Chi-restraints excluded: chain Y residue 2016 TYR Chi-restraints excluded: chain Y residue 2028 LEU Chi-restraints excluded: chain Y residue 2083 LEU Chi-restraints excluded: chain y residue 29 LEU Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 117 THR Chi-restraints excluded: chain y residue 189 THR Chi-restraints excluded: chain y residue 193 ILE Chi-restraints excluded: chain y residue 210 ILE Chi-restraints excluded: chain y residue 218 MET Chi-restraints excluded: chain y residue 271 VAL Chi-restraints excluded: chain y residue 332 VAL Chi-restraints excluded: chain y residue 587 VAL Chi-restraints excluded: chain y residue 605 LEU Chi-restraints excluded: chain y residue 641 LEU Chi-restraints excluded: chain y residue 670 CYS Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 705 LYS Chi-restraints excluded: chain y residue 722 SER Chi-restraints excluded: chain y residue 730 LYS Chi-restraints excluded: chain y residue 736 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 766 THR Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 804 TYR Chi-restraints excluded: chain y residue 833 VAL Chi-restraints excluded: chain y residue 862 LEU Chi-restraints excluded: chain y residue 866 ILE Chi-restraints excluded: chain y residue 887 PHE Chi-restraints excluded: chain y residue 915 HIS Chi-restraints excluded: chain y residue 936 HIS Chi-restraints excluded: chain y residue 1014 ILE Chi-restraints excluded: chain y residue 1047 ILE Chi-restraints excluded: chain y residue 1048 GLN Chi-restraints excluded: chain y residue 1052 GLU Chi-restraints excluded: chain y residue 1122 VAL Chi-restraints excluded: chain y residue 1161 LYS Chi-restraints excluded: chain y residue 1164 LEU Chi-restraints excluded: chain y residue 1169 THR Chi-restraints excluded: chain y residue 1232 ASP Chi-restraints excluded: chain y residue 1238 LEU Chi-restraints excluded: chain y residue 1348 ILE Chi-restraints excluded: chain y residue 1351 THR Chi-restraints excluded: chain y residue 1387 VAL Chi-restraints excluded: chain y residue 1404 VAL Chi-restraints excluded: chain y residue 1437 VAL Chi-restraints excluded: chain y residue 1441 HIS Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1519 PHE Chi-restraints excluded: chain y residue 1525 ILE Chi-restraints excluded: chain y residue 1541 THR Chi-restraints excluded: chain y residue 1574 HIS Chi-restraints excluded: chain y residue 1590 VAL Chi-restraints excluded: chain y residue 1621 HIS Chi-restraints excluded: chain y residue 1648 ILE Chi-restraints excluded: chain y residue 1740 LEU Chi-restraints excluded: chain y residue 1799 LEU Chi-restraints excluded: chain y residue 1800 THR Chi-restraints excluded: chain y residue 1870 VAL Chi-restraints excluded: chain y residue 1943 VAL Chi-restraints excluded: chain y residue 1998 TRP Chi-restraints excluded: chain y residue 2006 GLN Chi-restraints excluded: chain y residue 2041 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: [262, 164, 7, 37, 252, 347, 385, 369, 271, 10, 67] chunk 262 optimal weight: 20.0000 chunk 164 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 347 optimal weight: 6.9990 chunk 385 optimal weight: 0.9990 chunk 369 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1303 GLN ** Y1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y2050 GLN ** Y2078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1884 GLN ** y2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.106857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.077953 restraints weight = 219799.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.076730 restraints weight = 104401.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.077088 restraints weight = 63498.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.077306 restraints weight = 47921.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.077634 restraints weight = 42617.711| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34535 Z= 0.164 Angle : 0.660 15.117 47006 Z= 0.316 Chirality : 0.041 0.199 5115 Planarity : 0.004 0.051 5978 Dihedral : 13.911 155.574 5126 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.70 % Allowed : 24.47 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.13), residues: 4111 helix: 0.69 (0.13), residues: 1604 sheet: -0.98 (0.22), residues: 534 loop : -1.48 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG y1372 TYR 0.033 0.001 TYR y1643 PHE 0.017 0.001 PHE y 125 TRP 0.015 0.001 TRP y1419 HIS 0.009 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (34495) covalent geometry : angle 0.63182 / 0.31 (46952) hydrogen bonds : bond 0.03809 / 2.54 ( 1247) hydrogen bonds : angle 5.13120 / 3.62 ( 3540) metal coordination : bond 0.01195 / 0.63 ( 40) metal coordination : angle 5.64910 / 3.83 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 145 time to evaluate : 1.328 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: Y 218 MET cc_start: 0.8690 (tpp) cc_final: 0.8403 (tpp) REVERT: Y 224 MET cc_start: 0.9401 (tpp) cc_final: 0.8847 (tpp) REVERT: Y 228 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8311 (ptm) REVERT: Y 443 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.9120 (p) REVERT: Y 493 MET cc_start: 0.8950 (mmp) cc_final: 0.8727 (mmp) REVERT: Y 660 ASP cc_start: 0.9118 (p0) cc_final: 0.8893 (p0) REVERT: Y 810 ARG cc_start: 0.9402 (OUTLIER) cc_final: 0.9168 (ptm-80) REVERT: Y 945 MET cc_start: 0.9137 (mmp) cc_final: 0.8641 (tpp) REVERT: Y 1105 MET cc_start: 0.1002 (mtm) cc_final: -0.0184 (ttt) REVERT: Y 1157 MET cc_start: 0.9041 (mmm) cc_final: 0.8723 (mmm) REVERT: Y 1303 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8747 (tm-30) REVERT: Y 1505 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7833 (t80) REVERT: Y 1998 TRP cc_start: 0.6670 (t60) cc_final: 0.6369 (t60) REVERT: y 182 TYR cc_start: 0.6351 (t80) cc_final: 0.6117 (t80) REVERT: y 641 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8561 (mm) REVERT: y 747 MET cc_start: 0.8403 (ptm) cc_final: 0.8088 (ppp) REVERT: y 791 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.8857 (mp) REVERT: y 804 TYR cc_start: 0.9397 (OUTLIER) cc_final: 0.9002 (m-80) REVERT: y 1016 MET cc_start: 0.8771 (mmp) cc_final: 0.8458 (mmp) REVERT: y 1226 TRP cc_start: 0.4910 (t60) cc_final: 0.4605 (t60) REVERT: y 1904 LEU cc_start: 0.5623 (OUTLIER) cc_final: 0.5401 (tt) outliers start: 165 outliers final: 127 residues processed: 294 average time/residue: 0.1823 time to fit residues: 92.6870 Evaluate side-chains 275 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 139 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 73 ASP Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 206 SER Chi-restraints excluded: chain Y residue 212 GLU Chi-restraints excluded: chain Y residue 219 VAL Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 298 SER Chi-restraints excluded: chain Y residue 312 LEU Chi-restraints excluded: chain Y residue 396 ASP Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 443 SER Chi-restraints excluded: chain Y residue 448 GLU Chi-restraints excluded: chain Y residue 467 CYS Chi-restraints excluded: chain Y residue 510 VAL Chi-restraints excluded: chain Y residue 517 VAL Chi-restraints excluded: chain Y residue 532 ASN Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 551 GLU Chi-restraints excluded: chain Y residue 559 ASP Chi-restraints excluded: chain Y residue 568 ILE Chi-restraints excluded: chain Y residue 580 ARG Chi-restraints excluded: chain Y residue 609 PHE Chi-restraints excluded: chain Y residue 613 GLU Chi-restraints excluded: chain Y residue 646 SER Chi-restraints excluded: chain Y residue 683 LYS Chi-restraints excluded: chain Y residue 735 MET Chi-restraints excluded: chain Y residue 794 THR Chi-restraints excluded: chain Y residue 810 ARG Chi-restraints excluded: chain Y residue 813 ASN Chi-restraints excluded: chain Y residue 829 PHE Chi-restraints excluded: chain Y residue 835 THR Chi-restraints excluded: chain Y residue 863 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 936 HIS Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1130 LEU Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1210 LYS Chi-restraints excluded: chain Y residue 1234 LEU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1303 GLN Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1389 LEU Chi-restraints excluded: chain Y residue 1399 ILE Chi-restraints excluded: chain Y residue 1431 THR Chi-restraints excluded: chain Y residue 1441 HIS Chi-restraints excluded: chain Y residue 1505 PHE Chi-restraints excluded: chain Y residue 1536 THR Chi-restraints excluded: chain Y residue 1541 THR Chi-restraints excluded: chain Y residue 1564 ARG Chi-restraints excluded: chain Y residue 1587 THR Chi-restraints excluded: chain Y residue 1664 LEU Chi-restraints excluded: chain Y residue 1689 HIS Chi-restraints excluded: chain Y residue 1700 VAL Chi-restraints excluded: chain Y residue 1715 VAL Chi-restraints excluded: chain Y residue 1788 VAL Chi-restraints excluded: chain Y residue 1792 VAL Chi-restraints excluded: chain Y residue 1836 LEU Chi-restraints excluded: chain Y residue 1845 SER Chi-restraints excluded: chain Y residue 1905 CYS Chi-restraints excluded: chain Y residue 1915 PHE Chi-restraints excluded: chain Y residue 1919 PHE Chi-restraints excluded: chain Y residue 1991 HIS Chi-restraints excluded: chain Y residue 2008 VAL Chi-restraints excluded: chain Y residue 2016 TYR Chi-restraints excluded: chain Y residue 2028 LEU Chi-restraints excluded: chain y residue 29 LEU Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 117 THR Chi-restraints excluded: chain y residue 189 THR Chi-restraints excluded: chain y residue 193 ILE Chi-restraints excluded: chain y residue 218 MET Chi-restraints excluded: chain y residue 220 THR Chi-restraints excluded: chain y residue 332 VAL Chi-restraints excluded: chain y residue 571 LEU Chi-restraints excluded: chain y residue 578 GLU Chi-restraints excluded: chain y residue 587 VAL Chi-restraints excluded: chain y residue 641 LEU Chi-restraints excluded: chain y residue 705 LYS Chi-restraints excluded: chain y residue 709 ASP Chi-restraints excluded: chain y residue 722 SER Chi-restraints excluded: chain y residue 730 LYS Chi-restraints excluded: chain y residue 736 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 766 THR Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 804 TYR Chi-restraints excluded: chain y residue 830 ILE Chi-restraints excluded: chain y residue 833 VAL Chi-restraints excluded: chain y residue 862 LEU Chi-restraints excluded: chain y residue 866 ILE Chi-restraints excluded: chain y residue 887 PHE Chi-restraints excluded: chain y residue 915 HIS Chi-restraints excluded: chain y residue 936 HIS Chi-restraints excluded: chain y residue 1042 GLU Chi-restraints excluded: chain y residue 1047 ILE Chi-restraints excluded: chain y residue 1122 VAL Chi-restraints excluded: chain y residue 1161 LYS Chi-restraints excluded: chain y residue 1164 LEU Chi-restraints excluded: chain y residue 1169 THR Chi-restraints excluded: chain y residue 1232 ASP Chi-restraints excluded: chain y residue 1238 LEU Chi-restraints excluded: chain y residue 1250 LEU Chi-restraints excluded: chain y residue 1348 ILE Chi-restraints excluded: chain y residue 1351 THR Chi-restraints excluded: chain y residue 1387 VAL Chi-restraints excluded: chain y residue 1404 VAL Chi-restraints excluded: chain y residue 1441 HIS Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1519 PHE Chi-restraints excluded: chain y residue 1541 THR Chi-restraints excluded: chain y residue 1574 HIS Chi-restraints excluded: chain y residue 1590 VAL Chi-restraints excluded: chain y residue 1621 HIS Chi-restraints excluded: chain y residue 1630 LEU Chi-restraints excluded: chain y residue 1648 ILE Chi-restraints excluded: chain y residue 1726 TYR Chi-restraints excluded: chain y residue 1740 LEU Chi-restraints excluded: chain y residue 1799 LEU Chi-restraints excluded: chain y residue 1800 THR Chi-restraints excluded: chain y residue 1870 VAL Chi-restraints excluded: chain y residue 1904 LEU Chi-restraints excluded: chain y residue 1943 VAL Chi-restraints excluded: chain y residue 1998 TRP Chi-restraints excluded: chain y residue 2006 GLN Chi-restraints excluded: chain y residue 2008 VAL Chi-restraints excluded: chain y residue 2041 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: [132, 87, 101, 186, 67, 155, 140, 45, 5, 313, 66] chunk 132 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 313 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y2050 GLN ** Y2078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 658 GLN ** y 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y1764 GLN y1884 GLN ** y2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.107307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.078970 restraints weight = 219832.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 89)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.077703 restraints weight = 102379.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.077859 restraints weight = 62310.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.078072 restraints weight = 46292.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.078072 restraints weight = 38367.377| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34535 Z= 0.128 Angle : 0.647 14.796 47006 Z= 0.309 Chirality : 0.041 0.233 5115 Planarity : 0.004 0.051 5978 Dihedral : 13.797 157.233 5125 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.47 % Allowed : 24.84 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4111 helix: 0.76 (0.13), residues: 1605 sheet: -0.95 (0.22), residues: 533 loop : -1.43 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG y1372 TYR 0.018 0.001 TYR y1643 PHE 0.016 0.001 PHE y 125 TRP 0.015 0.001 TRP Y 101 HIS 0.006 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (34495) covalent geometry : angle 0.62158 / 0.31 (46952) hydrogen bonds : bond 0.03672 / 2.44 ( 1247) hydrogen bonds : angle 5.01337 / 3.54 ( 3540) metal coordination : bond 0.01002 / 0.54 ( 40) metal coordination : angle 5.29774 / 3.54 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 149 time to evaluate : 1.069 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: Y 224 MET cc_start: 0.9411 (tpp) cc_final: 0.9059 (tpp) REVERT: Y 228 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8634 (ptm) REVERT: Y 273 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8717 (pp30) REVERT: Y 443 SER cc_start: 0.9336 (OUTLIER) cc_final: 0.9111 (p) REVERT: Y 660 ASP cc_start: 0.9087 (p0) cc_final: 0.8870 (p0) REVERT: Y 810 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.9139 (ptm-80) REVERT: Y 945 MET cc_start: 0.9143 (mmp) cc_final: 0.8630 (tpp) REVERT: Y 1047 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9316 (mm) REVERT: Y 1105 MET cc_start: 0.1010 (mtm) cc_final: -0.0195 (ttt) REVERT: Y 1157 MET cc_start: 0.9056 (mmm) cc_final: 0.8829 (mmm) REVERT: Y 1505 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7861 (t80) REVERT: Y 1760 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8689 (mt) REVERT: Y 1998 TRP cc_start: 0.6556 (t60) cc_final: 0.6321 (t60) REVERT: y 182 TYR cc_start: 0.6300 (t80) cc_final: 0.6061 (t80) REVERT: y 641 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8423 (mm) REVERT: y 747 MET cc_start: 0.8446 (ptm) cc_final: 0.8001 (ppp) REVERT: y 791 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8884 (mp) REVERT: y 1226 TRP cc_start: 0.5134 (t60) cc_final: 0.4808 (t60) REVERT: y 1904 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.5895 (tt) outliers start: 157 outliers final: 122 residues processed: 290 average time/residue: 0.1869 time to fit residues: 93.5796 Evaluate side-chains 278 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 146 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 73 ASP Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 206 SER Chi-restraints excluded: chain Y residue 219 VAL Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 273 GLN Chi-restraints excluded: chain Y residue 298 SER Chi-restraints excluded: chain Y residue 312 LEU Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 443 SER Chi-restraints excluded: chain Y residue 448 GLU Chi-restraints excluded: chain Y residue 467 CYS Chi-restraints excluded: chain Y residue 510 VAL Chi-restraints excluded: chain Y residue 517 VAL Chi-restraints excluded: chain Y residue 532 ASN Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 559 ASP Chi-restraints excluded: chain Y residue 580 ARG Chi-restraints excluded: chain Y residue 613 GLU Chi-restraints excluded: chain Y residue 646 SER Chi-restraints excluded: chain Y residue 683 LYS Chi-restraints excluded: chain Y residue 695 VAL Chi-restraints excluded: chain Y residue 735 MET Chi-restraints excluded: chain Y residue 763 SER Chi-restraints excluded: chain Y residue 794 THR Chi-restraints excluded: chain Y residue 810 ARG Chi-restraints excluded: chain Y residue 813 ASN Chi-restraints excluded: chain Y residue 829 PHE Chi-restraints excluded: chain Y residue 835 THR Chi-restraints excluded: chain Y residue 863 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 936 HIS Chi-restraints excluded: chain Y residue 1047 ILE Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1130 LEU Chi-restraints excluded: chain Y residue 1210 LYS Chi-restraints excluded: chain Y residue 1234 LEU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1399 ILE Chi-restraints excluded: chain Y residue 1431 THR Chi-restraints excluded: chain Y residue 1441 HIS Chi-restraints excluded: chain Y residue 1505 PHE Chi-restraints excluded: chain Y residue 1541 THR Chi-restraints excluded: chain Y residue 1564 ARG Chi-restraints excluded: chain Y residue 1587 THR Chi-restraints excluded: chain Y residue 1664 LEU Chi-restraints excluded: chain Y residue 1689 HIS Chi-restraints excluded: chain Y residue 1715 VAL Chi-restraints excluded: chain Y residue 1760 LEU Chi-restraints excluded: chain Y residue 1788 VAL Chi-restraints excluded: chain Y residue 1836 LEU Chi-restraints excluded: chain Y residue 1845 SER Chi-restraints excluded: chain Y residue 1897 THR Chi-restraints excluded: chain Y residue 1905 CYS Chi-restraints excluded: chain Y residue 1915 PHE Chi-restraints excluded: chain Y residue 1919 PHE Chi-restraints excluded: chain Y residue 2004 ARG Chi-restraints excluded: chain Y residue 2008 VAL Chi-restraints excluded: chain Y residue 2009 THR Chi-restraints excluded: chain Y residue 2016 TYR Chi-restraints excluded: chain Y residue 2028 LEU Chi-restraints excluded: chain Y residue 2050 GLN Chi-restraints excluded: chain Y residue 2083 LEU Chi-restraints excluded: chain y residue 29 LEU Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 117 THR Chi-restraints excluded: chain y residue 189 THR Chi-restraints excluded: chain y residue 193 ILE Chi-restraints excluded: chain y residue 218 MET Chi-restraints excluded: chain y residue 220 THR Chi-restraints excluded: chain y residue 332 VAL Chi-restraints excluded: chain y residue 587 VAL Chi-restraints excluded: chain y residue 605 LEU Chi-restraints excluded: chain y residue 641 LEU Chi-restraints excluded: chain y residue 705 LYS Chi-restraints excluded: chain y residue 709 ASP Chi-restraints excluded: chain y residue 722 SER Chi-restraints excluded: chain y residue 730 LYS Chi-restraints excluded: chain y residue 736 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 766 THR Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 862 LEU Chi-restraints excluded: chain y residue 866 ILE Chi-restraints excluded: chain y residue 887 PHE Chi-restraints excluded: chain y residue 915 HIS Chi-restraints excluded: chain y residue 936 HIS Chi-restraints excluded: chain y residue 1014 ILE Chi-restraints excluded: chain y residue 1042 GLU Chi-restraints excluded: chain y residue 1047 ILE Chi-restraints excluded: chain y residue 1122 VAL Chi-restraints excluded: chain y residue 1161 LYS Chi-restraints excluded: chain y residue 1164 LEU Chi-restraints excluded: chain y residue 1169 THR Chi-restraints excluded: chain y residue 1232 ASP Chi-restraints excluded: chain y residue 1238 LEU Chi-restraints excluded: chain y residue 1250 LEU Chi-restraints excluded: chain y residue 1348 ILE Chi-restraints excluded: chain y residue 1351 THR Chi-restraints excluded: chain y residue 1387 VAL Chi-restraints excluded: chain y residue 1388 VAL Chi-restraints excluded: chain y residue 1404 VAL Chi-restraints excluded: chain y residue 1441 HIS Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1519 PHE Chi-restraints excluded: chain y residue 1541 THR Chi-restraints excluded: chain y residue 1574 HIS Chi-restraints excluded: chain y residue 1590 VAL Chi-restraints excluded: chain y residue 1621 HIS Chi-restraints excluded: chain y residue 1630 LEU Chi-restraints excluded: chain y residue 1648 ILE Chi-restraints excluded: chain y residue 1726 TYR Chi-restraints excluded: chain y residue 1740 LEU Chi-restraints excluded: chain y residue 1799 LEU Chi-restraints excluded: chain y residue 1800 THR Chi-restraints excluded: chain y residue 1870 VAL Chi-restraints excluded: chain y residue 1904 LEU Chi-restraints excluded: chain y residue 1943 VAL Chi-restraints excluded: chain y residue 1998 TRP Chi-restraints excluded: chain y residue 2006 GLN Chi-restraints excluded: chain y residue 2041 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: [271, 182, 105, 63, 50, 89, 156, 246, 127, 373, 203] chunk 271 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 373 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 688 HIS ** Y 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1303 GLN ** Y1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y2078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y1749 ASN y1884 GLN ** y2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.106937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.078161 restraints weight = 220031.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 93)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.077000 restraints weight = 105260.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.077352 restraints weight = 63461.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.077694 restraints weight = 49081.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.077843 restraints weight = 41956.085| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34535 Z= 0.170 Angle : 0.662 14.561 47006 Z= 0.317 Chirality : 0.041 0.291 5115 Planarity : 0.004 0.052 5978 Dihedral : 13.731 158.592 5119 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.50 % Allowed : 25.01 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4111 helix: 0.76 (0.13), residues: 1605 sheet: -0.92 (0.22), residues: 541 loop : -1.43 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG y1372 TYR 0.020 0.001 TYR y1466 PHE 0.016 0.001 PHE y 125 TRP 0.014 0.001 TRP y1291 HIS 0.006 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (34495) covalent geometry : angle 0.63768 / 0.32 (46952) hydrogen bonds : bond 0.03682 / 2.44 ( 1247) hydrogen bonds : angle 5.03045 / 3.55 ( 3540) metal coordination : bond 0.01121 / 0.62 ( 40) metal coordination : angle 5.23827 / 3.52 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 148 time to evaluate : 1.118 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: Y 224 MET cc_start: 0.9408 (tpp) cc_final: 0.8841 (tpp) REVERT: Y 228 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8302 (ptm) REVERT: Y 443 SER cc_start: 0.9313 (OUTLIER) cc_final: 0.9084 (p) REVERT: Y 611 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9458 (mm) REVERT: Y 660 ASP cc_start: 0.9078 (p0) cc_final: 0.8868 (p0) REVERT: Y 810 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.9111 (ptm-80) REVERT: Y 945 MET cc_start: 0.9166 (mmp) cc_final: 0.8656 (tpp) REVERT: Y 1047 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9316 (mm) REVERT: Y 1105 MET cc_start: 0.1006 (mtm) cc_final: -0.0136 (ttt) REVERT: Y 1157 MET cc_start: 0.9082 (mmm) cc_final: 0.8842 (mmm) REVERT: Y 1210 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8632 (ptmt) REVERT: Y 1303 GLN cc_start: 0.9328 (tp-100) cc_final: 0.8795 (tm-30) REVERT: Y 1505 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7962 (t80) REVERT: Y 1507 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8304 (t-90) REVERT: Y 1760 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8747 (mt) REVERT: Y 1950 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8366 (tp) REVERT: Y 2050 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7845 (tp40) REVERT: y 182 TYR cc_start: 0.6407 (t80) cc_final: 0.6179 (t80) REVERT: y 641 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8395 (mm) REVERT: y 747 MET cc_start: 0.8520 (ptm) cc_final: 0.8026 (ppp) REVERT: y 1016 MET cc_start: 0.8775 (mmp) cc_final: 0.8530 (mmp) REVERT: y 1048 GLN cc_start: 0.9612 (OUTLIER) cc_final: 0.9116 (mp10) REVERT: y 1226 TRP cc_start: 0.5147 (t60) cc_final: 0.4825 (t60) REVERT: y 1904 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5376 (tt) outliers start: 158 outliers final: 127 residues processed: 288 average time/residue: 0.1846 time to fit residues: 91.7847 Evaluate side-chains 286 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 145 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 73 ASP Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 206 SER Chi-restraints excluded: chain Y residue 219 VAL Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 298 SER Chi-restraints excluded: chain Y residue 312 LEU Chi-restraints excluded: chain Y residue 396 ASP Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 443 SER Chi-restraints excluded: chain Y residue 448 GLU Chi-restraints excluded: chain Y residue 467 CYS Chi-restraints excluded: chain Y residue 510 VAL Chi-restraints excluded: chain Y residue 517 VAL Chi-restraints excluded: chain Y residue 532 ASN Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 559 ASP Chi-restraints excluded: chain Y residue 568 ILE Chi-restraints excluded: chain Y residue 580 ARG Chi-restraints excluded: chain Y residue 611 LEU Chi-restraints excluded: chain Y residue 613 GLU Chi-restraints excluded: chain Y residue 646 SER Chi-restraints excluded: chain Y residue 683 LYS Chi-restraints excluded: chain Y residue 695 VAL Chi-restraints excluded: chain Y residue 735 MET Chi-restraints excluded: chain Y residue 763 SER Chi-restraints excluded: chain Y residue 794 THR Chi-restraints excluded: chain Y residue 810 ARG Chi-restraints excluded: chain Y residue 813 ASN Chi-restraints excluded: chain Y residue 829 PHE Chi-restraints excluded: chain Y residue 835 THR Chi-restraints excluded: chain Y residue 863 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 936 HIS Chi-restraints excluded: chain Y residue 1047 ILE Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1130 LEU Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1210 LYS Chi-restraints excluded: chain Y residue 1234 LEU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1399 ILE Chi-restraints excluded: chain Y residue 1431 THR Chi-restraints excluded: chain Y residue 1441 HIS Chi-restraints excluded: chain Y residue 1505 PHE Chi-restraints excluded: chain Y residue 1507 HIS Chi-restraints excluded: chain Y residue 1541 THR Chi-restraints excluded: chain Y residue 1564 ARG Chi-restraints excluded: chain Y residue 1587 THR Chi-restraints excluded: chain Y residue 1664 LEU Chi-restraints excluded: chain Y residue 1689 HIS Chi-restraints excluded: chain Y residue 1715 VAL Chi-restraints excluded: chain Y residue 1760 LEU Chi-restraints excluded: chain Y residue 1788 VAL Chi-restraints excluded: chain Y residue 1792 VAL Chi-restraints excluded: chain Y residue 1836 LEU Chi-restraints excluded: chain Y residue 1845 SER Chi-restraints excluded: chain Y residue 1897 THR Chi-restraints excluded: chain Y residue 1905 CYS Chi-restraints excluded: chain Y residue 1908 LEU Chi-restraints excluded: chain Y residue 1915 PHE Chi-restraints excluded: chain Y residue 1919 PHE Chi-restraints excluded: chain Y residue 1950 LEU Chi-restraints excluded: chain Y residue 2004 ARG Chi-restraints excluded: chain Y residue 2008 VAL Chi-restraints excluded: chain Y residue 2009 THR Chi-restraints excluded: chain Y residue 2016 TYR Chi-restraints excluded: chain Y residue 2028 LEU Chi-restraints excluded: chain Y residue 2042 THR Chi-restraints excluded: chain Y residue 2050 GLN Chi-restraints excluded: chain Y residue 2083 LEU Chi-restraints excluded: chain y residue 29 LEU Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 117 THR Chi-restraints excluded: chain y residue 189 THR Chi-restraints excluded: chain y residue 193 ILE Chi-restraints excluded: chain y residue 218 MET Chi-restraints excluded: chain y residue 220 THR Chi-restraints excluded: chain y residue 332 VAL Chi-restraints excluded: chain y residue 587 VAL Chi-restraints excluded: chain y residue 593 GLN Chi-restraints excluded: chain y residue 605 LEU Chi-restraints excluded: chain y residue 641 LEU Chi-restraints excluded: chain y residue 670 CYS Chi-restraints excluded: chain y residue 705 LYS Chi-restraints excluded: chain y residue 722 SER Chi-restraints excluded: chain y residue 730 LYS Chi-restraints excluded: chain y residue 736 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 766 THR Chi-restraints excluded: chain y residue 830 ILE Chi-restraints excluded: chain y residue 862 LEU Chi-restraints excluded: chain y residue 866 ILE Chi-restraints excluded: chain y residue 887 PHE Chi-restraints excluded: chain y residue 915 HIS Chi-restraints excluded: chain y residue 936 HIS Chi-restraints excluded: chain y residue 1014 ILE Chi-restraints excluded: chain y residue 1042 GLU Chi-restraints excluded: chain y residue 1047 ILE Chi-restraints excluded: chain y residue 1048 GLN Chi-restraints excluded: chain y residue 1122 VAL Chi-restraints excluded: chain y residue 1161 LYS Chi-restraints excluded: chain y residue 1164 LEU Chi-restraints excluded: chain y residue 1169 THR Chi-restraints excluded: chain y residue 1232 ASP Chi-restraints excluded: chain y residue 1250 LEU Chi-restraints excluded: chain y residue 1348 ILE Chi-restraints excluded: chain y residue 1351 THR Chi-restraints excluded: chain y residue 1387 VAL Chi-restraints excluded: chain y residue 1388 VAL Chi-restraints excluded: chain y residue 1404 VAL Chi-restraints excluded: chain y residue 1441 HIS Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1519 PHE Chi-restraints excluded: chain y residue 1541 THR Chi-restraints excluded: chain y residue 1574 HIS Chi-restraints excluded: chain y residue 1590 VAL Chi-restraints excluded: chain y residue 1621 HIS Chi-restraints excluded: chain y residue 1648 ILE Chi-restraints excluded: chain y residue 1726 TYR Chi-restraints excluded: chain y residue 1740 LEU Chi-restraints excluded: chain y residue 1799 LEU Chi-restraints excluded: chain y residue 1800 THR Chi-restraints excluded: chain y residue 1870 VAL Chi-restraints excluded: chain y residue 1904 LEU Chi-restraints excluded: chain y residue 1943 VAL Chi-restraints excluded: chain y residue 1998 TRP Chi-restraints excluded: chain y residue 2006 GLN Chi-restraints excluded: chain y residue 2041 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: [406, 96, 4, 397, 249, 338, 342, 326, 380, 281, 403] chunk 406 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 397 optimal weight: 8.9990 chunk 249 optimal weight: 30.0000 chunk 338 optimal weight: 0.9990 chunk 342 optimal weight: 0.9990 chunk 326 optimal weight: 20.0000 chunk 380 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 403 optimal weight: 50.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y2050 GLN ** Y2078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y1230 GLN ** y1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y1884 GLN ** y2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.107098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.078484 restraints weight = 219088.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.077931 restraints weight = 102957.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.078225 restraints weight = 62829.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.078412 restraints weight = 48200.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.078580 restraints weight = 41770.006| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34535 Z= 0.156 Angle : 0.657 14.057 47006 Z= 0.315 Chirality : 0.041 0.228 5115 Planarity : 0.004 0.052 5978 Dihedral : 13.650 159.837 5117 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.33 % Allowed : 25.24 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 4111 helix: 0.78 (0.13), residues: 1601 sheet: -0.92 (0.22), residues: 555 loop : -1.38 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG y1372 TYR 0.022 0.001 TYR y1466 PHE 0.016 0.001 PHE y 308 TRP 0.046 0.001 TRP Y1998 HIS 0.006 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (34495) covalent geometry : angle 0.63370 / 0.31 (46952) hydrogen bonds : bond 0.03631 / 2.40 ( 1247) hydrogen bonds : angle 5.00447 / 3.53 ( 3540) metal coordination : bond 0.01084 / 0.59 ( 40) metal coordination : angle 5.19065 / 3.47 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 155 time to evaluate : 1.228 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: Y 224 MET cc_start: 0.9392 (tpp) cc_final: 0.8835 (tpp) REVERT: Y 228 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8297 (ptm) REVERT: Y 273 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8718 (pp30) REVERT: Y 443 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.9074 (p) REVERT: Y 660 ASP cc_start: 0.9059 (p0) cc_final: 0.8851 (p0) REVERT: Y 683 LYS cc_start: 0.1207 (OUTLIER) cc_final: 0.0066 (tptt) REVERT: Y 810 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.9100 (ptm-80) REVERT: Y 945 MET cc_start: 0.9141 (mmp) cc_final: 0.8640 (tpp) REVERT: Y 1047 ILE cc_start: 0.9565 (OUTLIER) cc_final: 0.9312 (mm) REVERT: Y 1105 MET cc_start: 0.0967 (mtm) cc_final: -0.0138 (ttt) REVERT: Y 1157 MET cc_start: 0.9096 (mmm) cc_final: 0.8868 (mmm) REVERT: Y 1210 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8514 (ptmt) REVERT: Y 1303 GLN cc_start: 0.9289 (tp-100) cc_final: 0.8761 (tm-30) REVERT: Y 1505 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7965 (t80) REVERT: Y 1507 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.8330 (t-90) REVERT: Y 1760 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8737 (mt) REVERT: Y 1950 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8376 (tp) REVERT: y 182 TYR cc_start: 0.6427 (t80) cc_final: 0.6173 (t80) REVERT: y 641 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8453 (mm) REVERT: y 747 MET cc_start: 0.8599 (ptm) cc_final: 0.8047 (ppp) REVERT: y 945 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7928 (ttt) REVERT: y 1016 MET cc_start: 0.8811 (mmp) cc_final: 0.8547 (mmp) REVERT: y 1048 GLN cc_start: 0.9611 (OUTLIER) cc_final: 0.9118 (mp10) REVERT: y 1226 TRP cc_start: 0.5640 (t60) cc_final: 0.5192 (t60) REVERT: y 1904 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.5042 (tt) REVERT: y 2041 LEU cc_start: -0.3152 (OUTLIER) cc_final: -0.3391 (tt) outliers start: 152 outliers final: 123 residues processed: 290 average time/residue: 0.1831 time to fit residues: 91.4961 Evaluate side-chains 281 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 142 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 73 ASP Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 206 SER Chi-restraints excluded: chain Y residue 219 VAL Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 273 GLN Chi-restraints excluded: chain Y residue 298 SER Chi-restraints excluded: chain Y residue 312 LEU Chi-restraints excluded: chain Y residue 396 ASP Chi-restraints excluded: chain Y residue 443 SER Chi-restraints excluded: chain Y residue 448 GLU Chi-restraints excluded: chain Y residue 467 CYS Chi-restraints excluded: chain Y residue 510 VAL Chi-restraints excluded: chain Y residue 517 VAL Chi-restraints excluded: chain Y residue 532 ASN Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 559 ASP Chi-restraints excluded: chain Y residue 568 ILE Chi-restraints excluded: chain Y residue 580 ARG Chi-restraints excluded: chain Y residue 613 GLU Chi-restraints excluded: chain Y residue 646 SER Chi-restraints excluded: chain Y residue 683 LYS Chi-restraints excluded: chain Y residue 695 VAL Chi-restraints excluded: chain Y residue 735 MET Chi-restraints excluded: chain Y residue 763 SER Chi-restraints excluded: chain Y residue 794 THR Chi-restraints excluded: chain Y residue 810 ARG Chi-restraints excluded: chain Y residue 813 ASN Chi-restraints excluded: chain Y residue 829 PHE Chi-restraints excluded: chain Y residue 835 THR Chi-restraints excluded: chain Y residue 863 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 936 HIS Chi-restraints excluded: chain Y residue 1047 ILE Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1130 LEU Chi-restraints excluded: chain Y residue 1195 LEU Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1210 LYS Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1257 THR Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1399 ILE Chi-restraints excluded: chain Y residue 1431 THR Chi-restraints excluded: chain Y residue 1441 HIS Chi-restraints excluded: chain Y residue 1505 PHE Chi-restraints excluded: chain Y residue 1507 HIS Chi-restraints excluded: chain Y residue 1536 THR Chi-restraints excluded: chain Y residue 1541 THR Chi-restraints excluded: chain Y residue 1581 LEU Chi-restraints excluded: chain Y residue 1587 THR Chi-restraints excluded: chain Y residue 1664 LEU Chi-restraints excluded: chain Y residue 1689 HIS Chi-restraints excluded: chain Y residue 1715 VAL Chi-restraints excluded: chain Y residue 1741 SER Chi-restraints excluded: chain Y residue 1760 LEU Chi-restraints excluded: chain Y residue 1788 VAL Chi-restraints excluded: chain Y residue 1792 VAL Chi-restraints excluded: chain Y residue 1836 LEU Chi-restraints excluded: chain Y residue 1845 SER Chi-restraints excluded: chain Y residue 1897 THR Chi-restraints excluded: chain Y residue 1905 CYS Chi-restraints excluded: chain Y residue 1908 LEU Chi-restraints excluded: chain Y residue 1915 PHE Chi-restraints excluded: chain Y residue 1919 PHE Chi-restraints excluded: chain Y residue 1950 LEU Chi-restraints excluded: chain Y residue 2004 ARG Chi-restraints excluded: chain Y residue 2008 VAL Chi-restraints excluded: chain Y residue 2016 TYR Chi-restraints excluded: chain Y residue 2028 LEU Chi-restraints excluded: chain Y residue 2083 LEU Chi-restraints excluded: chain y residue 29 LEU Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 189 THR Chi-restraints excluded: chain y residue 193 ILE Chi-restraints excluded: chain y residue 218 MET Chi-restraints excluded: chain y residue 220 THR Chi-restraints excluded: chain y residue 332 VAL Chi-restraints excluded: chain y residue 587 VAL Chi-restraints excluded: chain y residue 593 GLN Chi-restraints excluded: chain y residue 605 LEU Chi-restraints excluded: chain y residue 641 LEU Chi-restraints excluded: chain y residue 670 CYS Chi-restraints excluded: chain y residue 705 LYS Chi-restraints excluded: chain y residue 722 SER Chi-restraints excluded: chain y residue 730 LYS Chi-restraints excluded: chain y residue 736 VAL Chi-restraints excluded: chain y residue 766 THR Chi-restraints excluded: chain y residue 830 ILE Chi-restraints excluded: chain y residue 862 LEU Chi-restraints excluded: chain y residue 866 ILE Chi-restraints excluded: chain y residue 915 HIS Chi-restraints excluded: chain y residue 936 HIS Chi-restraints excluded: chain y residue 945 MET Chi-restraints excluded: chain y residue 1014 ILE Chi-restraints excluded: chain y residue 1042 GLU Chi-restraints excluded: chain y residue 1047 ILE Chi-restraints excluded: chain y residue 1048 GLN Chi-restraints excluded: chain y residue 1122 VAL Chi-restraints excluded: chain y residue 1161 LYS Chi-restraints excluded: chain y residue 1164 LEU Chi-restraints excluded: chain y residue 1169 THR Chi-restraints excluded: chain y residue 1232 ASP Chi-restraints excluded: chain y residue 1250 LEU Chi-restraints excluded: chain y residue 1348 ILE Chi-restraints excluded: chain y residue 1351 THR Chi-restraints excluded: chain y residue 1387 VAL Chi-restraints excluded: chain y residue 1388 VAL Chi-restraints excluded: chain y residue 1404 VAL Chi-restraints excluded: chain y residue 1441 HIS Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1519 PHE Chi-restraints excluded: chain y residue 1541 THR Chi-restraints excluded: chain y residue 1574 HIS Chi-restraints excluded: chain y residue 1590 VAL Chi-restraints excluded: chain y residue 1621 HIS Chi-restraints excluded: chain y residue 1630 LEU Chi-restraints excluded: chain y residue 1726 TYR Chi-restraints excluded: chain y residue 1740 LEU Chi-restraints excluded: chain y residue 1799 LEU Chi-restraints excluded: chain y residue 1800 THR Chi-restraints excluded: chain y residue 1870 VAL Chi-restraints excluded: chain y residue 1904 LEU Chi-restraints excluded: chain y residue 1943 VAL Chi-restraints excluded: chain y residue 1998 TRP Chi-restraints excluded: chain y residue 2006 GLN Chi-restraints excluded: chain y residue 2041 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: [255, 211, 130, 85, 248, 220, 7, 266, 316, 145, 284] chunk 255 optimal weight: 20.0000 chunk 211 optimal weight: 0.0060 chunk 130 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 266 optimal weight: 20.0000 chunk 316 optimal weight: 40.0000 chunk 145 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y2050 GLN ** Y2078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1100 ASN ** y1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1303 GLN y1688 HIS y1884 GLN ** y2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.107005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.078866 restraints weight = 219861.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.079994 restraints weight = 115585.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.079547 restraints weight = 68629.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.079605 restraints weight = 63111.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.079523 restraints weight = 54791.257| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34535 Z= 0.165 Angle : 0.667 13.922 47006 Z= 0.318 Chirality : 0.042 0.510 5115 Planarity : 0.004 0.053 5978 Dihedral : 13.590 160.951 5114 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.30 % Allowed : 25.30 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.13), residues: 4111 helix: 0.77 (0.13), residues: 1601 sheet: -0.92 (0.22), residues: 547 loop : -1.39 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG y1372 TYR 0.038 0.001 TYR y1583 PHE 0.016 0.001 PHE y 125 TRP 0.037 0.001 TRP Y1998 HIS 0.006 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (34495) covalent geometry : angle 0.64307 / 0.32 (46952) hydrogen bonds : bond 0.03574 / 2.37 ( 1247) hydrogen bonds : angle 4.99350 / 3.53 ( 3540) metal coordination : bond 0.01168 / 0.69 ( 40) metal coordination : angle 5.20937 / 3.45 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 146 time to evaluate : 1.295 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: Y 224 MET cc_start: 0.9437 (tpp) cc_final: 0.8827 (tpp) REVERT: Y 228 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8271 (ptm) REVERT: Y 273 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8743 (pp30) REVERT: Y 443 SER cc_start: 0.9322 (OUTLIER) cc_final: 0.9094 (p) REVERT: Y 660 ASP cc_start: 0.9091 (p0) cc_final: 0.8873 (p0) REVERT: Y 683 LYS cc_start: 0.2919 (OUTLIER) cc_final: 0.1830 (tptt) REVERT: Y 810 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.9089 (ptm-80) REVERT: Y 945 MET cc_start: 0.9165 (mmp) cc_final: 0.8649 (tpp) REVERT: Y 1047 ILE cc_start: 0.9570 (OUTLIER) cc_final: 0.9316 (mm) REVERT: Y 1105 MET cc_start: 0.1745 (mtm) cc_final: -0.0023 (ttp) REVERT: Y 1157 MET cc_start: 0.9105 (mmm) cc_final: 0.8872 (mmm) REVERT: Y 1210 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8607 (ptmt) REVERT: Y 1303 GLN cc_start: 0.9303 (tp-100) cc_final: 0.8776 (tm-30) REVERT: Y 1505 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8047 (t80) REVERT: Y 1507 HIS cc_start: 0.8748 (OUTLIER) cc_final: 0.8318 (t-90) REVERT: Y 1617 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8867 (tp30) REVERT: Y 1760 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8715 (mt) REVERT: Y 1950 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8397 (tp) REVERT: y 182 TYR cc_start: 0.6446 (t80) cc_final: 0.6097 (t80) REVERT: y 641 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8441 (mm) REVERT: y 804 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.8923 (m-80) REVERT: y 832 LYS cc_start: 0.9364 (mmtp) cc_final: 0.9153 (mmtp) REVERT: y 945 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7919 (ttt) REVERT: y 1048 GLN cc_start: 0.9586 (OUTLIER) cc_final: 0.9087 (mp10) REVERT: y 1226 TRP cc_start: 0.6662 (t60) cc_final: 0.6182 (t60) REVERT: y 2041 LEU cc_start: -0.3160 (OUTLIER) cc_final: -0.3410 (tt) outliers start: 151 outliers final: 125 residues processed: 281 average time/residue: 0.1893 time to fit residues: 92.0208 Evaluate side-chains 285 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 144 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 73 ASP Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 206 SER Chi-restraints excluded: chain Y residue 219 VAL Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 273 GLN Chi-restraints excluded: chain Y residue 298 SER Chi-restraints excluded: chain Y residue 312 LEU Chi-restraints excluded: chain Y residue 396 ASP Chi-restraints excluded: chain Y residue 443 SER Chi-restraints excluded: chain Y residue 448 GLU Chi-restraints excluded: chain Y residue 467 CYS Chi-restraints excluded: chain Y residue 510 VAL Chi-restraints excluded: chain Y residue 517 VAL Chi-restraints excluded: chain Y residue 532 ASN Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 559 ASP Chi-restraints excluded: chain Y residue 568 ILE Chi-restraints excluded: chain Y residue 580 ARG Chi-restraints excluded: chain Y residue 613 GLU Chi-restraints excluded: chain Y residue 646 SER Chi-restraints excluded: chain Y residue 683 LYS Chi-restraints excluded: chain Y residue 695 VAL Chi-restraints excluded: chain Y residue 735 MET Chi-restraints excluded: chain Y residue 763 SER Chi-restraints excluded: chain Y residue 794 THR Chi-restraints excluded: chain Y residue 810 ARG Chi-restraints excluded: chain Y residue 813 ASN Chi-restraints excluded: chain Y residue 829 PHE Chi-restraints excluded: chain Y residue 835 THR Chi-restraints excluded: chain Y residue 863 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 936 HIS Chi-restraints excluded: chain Y residue 1018 GLU Chi-restraints excluded: chain Y residue 1047 ILE Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1130 LEU Chi-restraints excluded: chain Y residue 1195 LEU Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1210 LYS Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1257 THR Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1389 LEU Chi-restraints excluded: chain Y residue 1399 ILE Chi-restraints excluded: chain Y residue 1431 THR Chi-restraints excluded: chain Y residue 1441 HIS Chi-restraints excluded: chain Y residue 1505 PHE Chi-restraints excluded: chain Y residue 1507 HIS Chi-restraints excluded: chain Y residue 1536 THR Chi-restraints excluded: chain Y residue 1541 THR Chi-restraints excluded: chain Y residue 1581 LEU Chi-restraints excluded: chain Y residue 1587 THR Chi-restraints excluded: chain Y residue 1664 LEU Chi-restraints excluded: chain Y residue 1689 HIS Chi-restraints excluded: chain Y residue 1715 VAL Chi-restraints excluded: chain Y residue 1741 SER Chi-restraints excluded: chain Y residue 1760 LEU Chi-restraints excluded: chain Y residue 1788 VAL Chi-restraints excluded: chain Y residue 1792 VAL Chi-restraints excluded: chain Y residue 1836 LEU Chi-restraints excluded: chain Y residue 1845 SER Chi-restraints excluded: chain Y residue 1897 THR Chi-restraints excluded: chain Y residue 1905 CYS Chi-restraints excluded: chain Y residue 1915 PHE Chi-restraints excluded: chain Y residue 1919 PHE Chi-restraints excluded: chain Y residue 1950 LEU Chi-restraints excluded: chain Y residue 2004 ARG Chi-restraints excluded: chain Y residue 2008 VAL Chi-restraints excluded: chain Y residue 2016 TYR Chi-restraints excluded: chain Y residue 2028 LEU Chi-restraints excluded: chain Y residue 2083 LEU Chi-restraints excluded: chain y residue 29 LEU Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 189 THR Chi-restraints excluded: chain y residue 193 ILE Chi-restraints excluded: chain y residue 218 MET Chi-restraints excluded: chain y residue 220 THR Chi-restraints excluded: chain y residue 332 VAL Chi-restraints excluded: chain y residue 587 VAL Chi-restraints excluded: chain y residue 593 GLN Chi-restraints excluded: chain y residue 605 LEU Chi-restraints excluded: chain y residue 641 LEU Chi-restraints excluded: chain y residue 670 CYS Chi-restraints excluded: chain y residue 705 LYS Chi-restraints excluded: chain y residue 722 SER Chi-restraints excluded: chain y residue 730 LYS Chi-restraints excluded: chain y residue 736 VAL Chi-restraints excluded: chain y residue 766 THR Chi-restraints excluded: chain y residue 804 TYR Chi-restraints excluded: chain y residue 830 ILE Chi-restraints excluded: chain y residue 862 LEU Chi-restraints excluded: chain y residue 866 ILE Chi-restraints excluded: chain y residue 887 PHE Chi-restraints excluded: chain y residue 915 HIS Chi-restraints excluded: chain y residue 936 HIS Chi-restraints excluded: chain y residue 945 MET Chi-restraints excluded: chain y residue 1014 ILE Chi-restraints excluded: chain y residue 1042 GLU Chi-restraints excluded: chain y residue 1047 ILE Chi-restraints excluded: chain y residue 1048 GLN Chi-restraints excluded: chain y residue 1122 VAL Chi-restraints excluded: chain y residue 1161 LYS Chi-restraints excluded: chain y residue 1164 LEU Chi-restraints excluded: chain y residue 1169 THR Chi-restraints excluded: chain y residue 1232 ASP Chi-restraints excluded: chain y residue 1250 LEU Chi-restraints excluded: chain y residue 1348 ILE Chi-restraints excluded: chain y residue 1351 THR Chi-restraints excluded: chain y residue 1387 VAL Chi-restraints excluded: chain y residue 1388 VAL Chi-restraints excluded: chain y residue 1404 VAL Chi-restraints excluded: chain y residue 1437 VAL Chi-restraints excluded: chain y residue 1441 HIS Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1519 PHE Chi-restraints excluded: chain y residue 1541 THR Chi-restraints excluded: chain y residue 1574 HIS Chi-restraints excluded: chain y residue 1590 VAL Chi-restraints excluded: chain y residue 1621 HIS Chi-restraints excluded: chain y residue 1726 TYR Chi-restraints excluded: chain y residue 1740 LEU Chi-restraints excluded: chain y residue 1799 LEU Chi-restraints excluded: chain y residue 1800 THR Chi-restraints excluded: chain y residue 1870 VAL Chi-restraints excluded: chain y residue 1943 VAL Chi-restraints excluded: chain y residue 1998 TRP Chi-restraints excluded: chain y residue 2006 GLN Chi-restraints excluded: chain y residue 2041 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: [192, 336, 330, 198, 159, 272, 305, 99, 166, 410, 400] chunk 192 optimal weight: 6.9990 chunk 336 optimal weight: 30.0000 chunk 330 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 272 optimal weight: 20.0000 chunk 305 optimal weight: 8.9990 chunk 99 optimal weight: 0.3980 chunk 166 optimal weight: 0.8980 chunk 410 optimal weight: 0.0980 chunk 400 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y2050 GLN ** Y2078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1100 ASN ** y1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1884 GLN ** y2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.107272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.079483 restraints weight = 219530.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.079956 restraints weight = 120752.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.079932 restraints weight = 77460.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.079798 restraints weight = 69173.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.079880 restraints weight = 66019.318| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34535 Z= 0.133 Angle : 0.653 13.782 47006 Z= 0.310 Chirality : 0.041 0.213 5115 Planarity : 0.004 0.053 5978 Dihedral : 13.517 161.808 5114 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.13 % Allowed : 25.50 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.13), residues: 4111 helix: 0.83 (0.13), residues: 1598 sheet: -0.88 (0.22), residues: 538 loop : -1.38 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 639 TYR 0.054 0.001 TYR y1583 PHE 0.016 0.001 PHE y 308 TRP 0.029 0.001 TRP Y1998 HIS 0.007 0.001 HIS y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (34495) covalent geometry : angle 0.63052 / 0.31 (46952) hydrogen bonds : bond 0.03452 / 2.28 ( 1247) hydrogen bonds : angle 4.90691 / 3.47 ( 3540) metal coordination : bond 0.00985 / 0.56 ( 40) metal coordination : angle 5.04379 / 3.32 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9275.98 seconds wall clock time: 159 minutes 15.01 seconds (9555.01 seconds total)