============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/9b512edd/tmp/C15MA2_refx/configfile.txt ============================================================================= ----------------------------------------------------------------------------- Warning: Non-parallel version of QRNA cannot spawn threads. Warning: More threads than cores available. Parameters to be used: Number of minimization steps (NSTEPS): 5000 Golden section step sizes: maximal (MAXSTEP): 0.0001 minimal (MINSTEP): 1e-08 Verbosity (VERBOSE): 1 Write output every: 100 steps (WRITEFREQ) Record trajectory (TRAJECTORY): disabled Pedantic treatment of molecules (PEDANTICMOL): disabled Van der Waals cutoff radius (CUTOFF): 12 Born generalized solvent (USEBORN): disabled Constraints on secondary struct. (SSCONSTR): enabled Auto-detection of secondary struct. (SSDETECT): enabled Secondary structure (SECSTRUCT): none specified Hydrogen bonds (HBONDS): enabled Electrostatics (ELECTR): enabled van der Waals interactions (VANDERWAALS): enabled Anti-blow-up protection (BLOWGUARD): enabled Occupancy as positional restraint (POSRESTRAINTS): disabled Restraints description (RESTRFILE): none Number of parallel threads: 1 ----------------------------------------------------------------------------- Internal Warning: unknown atom type(s) in bond: C2 H5 Internal Warning: unknown atom type(s) in bond: C2 N* Internal Warning: unknown atom type(s) in bond: C2 NB Internal Warning: unknown atom type(s) in bond: C C1 Internal Warning: unknown atom type(s) in bond: CA C1 Internal Warning: unknown atom type(s) in bond: C1 C1 Internal Warning: unknown atom type(s) in bond: C1 CT Internal Warning: unknown atom type(s) in bond: C1 HA Internal Warning: unknown atom type(s) in bond: C1 H4 Internal Warning: unknown atom type(s) in bond: C1 N* Internal Warning: unknown atoms in angle: H5 C2 N* Internal Warning: unknown atoms in angle: H5 C2 NB Internal Warning: unknown atoms in angle: N* C2 NB Internal Warning: unknown atoms in angle: CB N* C2 Internal Warning: unknown atoms in angle: C2 N* CT Internal Warning: unknown atoms in angle: CB NB C2 Internal Warning: unknown atoms in angle: C1 C NA Internal Warning: unknown atoms in angle: C1 C O Internal Warning: unknown atoms in angle: C1 CA N2 Internal Warning: unknown atoms in angle: C1 CA NC Internal Warning: unknown atoms in angle: C C1 C1 Internal Warning: unknown atoms in angle: C C1 CT Internal Warning: unknown atoms in angle: C C1 HA Internal Warning: unknown atoms in angle: C C1 H4 Internal Warning: unknown atoms in angle: CA C1 C1 Internal Warning: unknown atoms in angle: CA C1 HA Internal Warning: unknown atoms in angle: CA C1 H4 Internal Warning: unknown atoms in angle: C1 C1 CT Internal Warning: unknown atoms in angle: C1 C1 HA Internal Warning: unknown atoms in angle: C1 C1 H4 Internal Warning: unknown atoms in angle: C1 C1 N* Internal Warning: unknown atoms in angle: H4 C1 N* Internal Warning: unknown atoms in angle: H1 CT C1 Internal Warning: unknown atoms in angle: HC CT C1 Internal Warning: unknown atoms in angle: C N* C1 Internal Warning: unknown atoms in angle: C1 N* CT Internal Warning: unknown atom(s) in dihedral: X C2 N* X Internal Warning: unknown atom(s) in dihedral: X C2 NB X Internal Warning: unknown atom(s) in dihedral: X C C1 X Internal Warning: unknown atom(s) in dihedral: X CA C1 X Internal Warning: unknown atom(s) in dihedral: X C1 C1 X Internal Warning: unknown atom(s) in dihedral: X C1 CT X Internal Warning: unknown atom(s) in dihedral: X C1 N* X Internal Warning: unknown atom(s) in dihedral: HC CT C1 C1 Internal Warning: unknown atom(s) in dihedral: HC CT C1 C1 Internal Warning: unknown atom(s) in dihedral: C1 C1 C O Internal Warning: unknown atom(s) in dihedral: C1 C1 C O Internal Warning: unknown atom(s) in dihedral: OS CT N* C2 Internal Warning: unknown atom(s) in dihedral: OS CT N* C2 Internal Warning: unknown atom(s) in dihedral: OS CT N* C2 Internal Warning: unknown atom(s) in dihedral: OS CT N* C1 Internal Warning: unknown atom(s) in dihedral: OS CT N* C1 Internal Warning: unknown atom(s) in dihedral: OS CT N* C1 Internal Warning: unknown atom(s) in dihedral: OS CT N* C1 Internal Warning: unknown atom(s) in improper: C C1 N* CT Internal Warning: unknown atom(s) in improper: C C1 C1 CT Internal Warning: unknown atom(s) in improper: C1 N2 CA NC Initializing... Generic atom descriptions read: 47 Generic bond descriptions read: 199 Generic angle descriptions read: 567 Generic dihedral descriptions read: 812 Generic improper descriptions read: 116 Generic vdW descriptions read: 47 ----------------------------------------------------------------------------- ============================================================================= Reading PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/9b512edd/tmp/C15MA2_refx/C15MA2.pdb ============================================================================= Error: recognition of atom ATOM 19 'H5' DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 20 'HO5 DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 24 1H2' DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 25 2H2' DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 47 C5M DT A 2 ... failed. Atom erased. Error: recognition of atom ATOM 51 HN3 DT A 2 ... failed. Atom erased. Error: recognition of atom ATOM 52 1HM5 DT A 2 ... failed. Atom erased. Error: recognition of atom ATOM 53 2HM5 DT A 2 ... failed. Atom erased. Error: recognition of atom ATOM 54 3HM5 DT A 2 ... failed. Atom erased. Error: recognition of atom ATOM 81 'H5' DA A 3 ... failed. Atom erased. Error: recognition of atom ATOM 85 1H2' DA A 3 ... failed. Atom erased. Error: recognition of atom ATOM 86 2H2' DA A 3 ... failed. Atom erased. Error: recognition of atom ATOM 114 'H5' DG A 4 ... failed. Atom erased. Error: recognition of atom ATOM 118 1H2' DG A 4 ... failed. Atom erased. Error: recognition of atom ATOM 119 2H2' DG A 4 ... failed. Atom erased. Error: recognition of atom ATOM 144 'H5' DC A 5 ... failed. Atom erased. Error: recognition of atom ATOM 148 1H2' DC A 5 ... failed. Atom erased. Error: recognition of atom ATOM 149 2H2' DC A 5 ... failed. Atom erased. Error: recognition of atom ATOM 176 'H5' DA A 6 ... failed. Atom erased. Error: recognition of atom ATOM 180 1H2' DA A 6 ... failed. Atom erased. Error: recognition of atom ATOM 181 2H2' DA A 6 ... failed. Atom erased. Error: recognition of atom ATOM 203 C5M DT A 7 ... failed. Atom erased. Error: recognition of atom ATOM 207 HN3 DT A 7 ... failed. Atom erased. Error: recognition of atom ATOM 208 1HM5 DT A 7 ... failed. Atom erased. Error: recognition of atom ATOM 209 2HM5 DT A 7 ... failed. Atom erased. Error: recognition of atom ATOM 210 3HM5 DT A 7 ... failed. Atom erased. Error: recognition of atom ATOM 238 'H5' DG A 8 ... failed. Atom erased. Error: recognition of atom ATOM 242 1H2' DG A 8 ... failed. Atom erased. Error: recognition of atom ATOM 243 2H2' DG A 8 ... failed. Atom erased. Error: recognition of atom ATOM 270 'H5' DA A 9 ... failed. Atom erased. Error: recognition of atom ATOM 274 1H2' DA A 9 ... failed. Atom erased. Error: recognition of atom ATOM 275 2H2' DA A 9 ... failed. Atom erased. Error: recognition of atom ATOM 302 'H5' DA A 10 ... failed. Atom erased. Error: recognition of atom ATOM 306 1H2' DA A 10 ... failed. Atom erased. Error: recognition of atom ATOM 307 2H2' DA A 10 ... failed. Atom erased. Error: recognition of atom ATOM 329 C5M DT A 11 ... failed. Atom erased. Error: recognition of atom ATOM 333 HN3 DT A 11 ... failed. Atom erased. Error: recognition of atom ATOM 334 1HM5 DT A 11 ... failed. Atom erased. Error: recognition of atom ATOM 335 2HM5 DT A 11 ... failed. Atom erased. Error: recognition of atom ATOM 336 3HM5 DT A 11 ... failed. Atom erased. Error: recognition of atom ATOM 358 C5M DT A 12 ... failed. Atom erased. Error: recognition of atom ATOM 362 HN3 DT A 12 ... failed. Atom erased. Error: recognition of atom ATOM 363 1HM5 DT A 12 ... failed. Atom erased. Error: recognition of atom ATOM 364 2HM5 DT A 12 ... failed. Atom erased. Error: recognition of atom ATOM 365 3HM5 DT A 12 ... failed. Atom erased. Error: recognition of atom ATOM 390 'H5' DC A 13 ... failed. Atom erased. Error: recognition of atom ATOM 394 1H2' DC A 13 ... failed. Atom erased. Error: recognition of atom ATOM 395 2H2' DC A 13 ... failed. Atom erased. Error: recognition of atom ATOM 420 'H5' DC A 14 ... failed. Atom erased. Error: recognition of atom ATOM 424 1H2' DC A 14 ... failed. Atom erased. Error: recognition of atom ATOM 425 2H2' DC A 14 ... failed. Atom erased. Error: recognition of atom ATOM 450 'H5' DC A 15 ... failed. Atom erased. Error: recognition of atom ATOM 454 1H2' DC A 15 ... failed. Atom erased. Error: recognition of atom ATOM 455 2H2' DC A 15 ... failed. Atom erased. Error: recognition of atom ATOM 483 'H5' DG A 16 ... failed. Atom erased. Error: recognition of atom ATOM 487 1H2' DG A 16 ... failed. Atom erased. Error: recognition of atom ATOM 488 2H2' DG A 16 ... failed. Atom erased. Error: recognition of atom ATOM 515 'H5' DA A 17 ... failed. Atom erased. Error: recognition of atom ATOM 519 1H2' DA A 17 ... failed. Atom erased. Error: recognition of atom ATOM 520 2H2' DA A 17 ... failed. Atom erased. Error: recognition of atom ATOM 547 'H5' DA A 18 ... failed. Atom erased. Error: recognition of atom ATOM 551 1H2' DA A 18 ... failed. Atom erased. Error: recognition of atom ATOM 552 2H2' DA A 18 ... failed. Atom erased. Error: recognition of atom ATOM 580 'H5' DG A 19 ... failed. Atom erased. Error: recognition of atom ATOM 584 1H2' DG A 19 ... failed. Atom erased. Error: recognition of atom ATOM 585 2H2' DG A 19 ... failed. Atom erased. Error: recognition of atom ATOM 612 'H5' DA A 20 ... failed. Atom erased. Error: recognition of atom ATOM 616 1H2' DA A 20 ... failed. Atom erased. Error: recognition of atom ATOM 617 2H2' DA A 20 ... failed. Atom erased. Error: recognition of atom ATOM 642 'H5' DC A 21 ... failed. Atom erased. Error: recognition of atom ATOM 646 1H2' DC A 21 ... failed. Atom erased. Error: recognition of atom ATOM 647 2H2' DC A 21 ... failed. Atom erased. Error: recognition of atom ATOM 675 'H5' DG A 22 ... failed. Atom erased. Error: recognition of atom ATOM 679 1H2' DG A 22 ... failed. Atom erased. Error: recognition of atom ATOM 680 2H2' DG A 22 ... failed. Atom erased. Error: recognition of atom ATOM 705 'H5' DC A 23 ... failed. Atom erased. Error: recognition of atom ATOM 709 1H2' DC A 23 ... failed. Atom erased. Error: recognition of atom ATOM 710 2H2' DC A 23 ... failed. Atom erased. Error: recognition of atom ATOM 732 C5M DT A 24 ... failed. Atom erased. Error: recognition of atom ATOM 736 HN3 DT A 24 ... failed. Atom erased. Error: recognition of atom ATOM 737 1HM5 DT A 24 ... failed. Atom erased. Error: recognition of atom ATOM 738 2HM5 DT A 24 ... failed. Atom erased. Error: recognition of atom ATOM 739 3HM5 DT A 24 ... failed. Atom erased. Error: recognition of atom ATOM 767 'H5' DG A 25 ... failed. Atom erased. Error: recognition of atom ATOM 771 1H2' DG A 25 ... failed. Atom erased. Error: recognition of atom ATOM 772 2H2' DG A 25 ... failed. Atom erased. Error: recognition of atom ATOM 794 C5M DT A 26 ... failed. Atom erased. Error: recognition of atom ATOM 798 HN3 DT A 26 ... failed. Atom erased. Error: recognition of atom ATOM 799 1HM5 DT A 26 ... failed. Atom erased. Error: recognition of atom ATOM 800 2HM5 DT A 26 ... failed. Atom erased. Error: recognition of atom ATOM 801 3HM5 DT A 26 ... failed. Atom erased. Error: recognition of atom ATOM 829 'H5' DG A 27 ... failed. Atom erased. Error: recognition of atom ATOM 833 1H2' DG A 27 ... failed. Atom erased. Error: recognition of atom ATOM 834 2H2' DG A 27 ... failed. Atom erased. Error: recognition of atom ATOM 862 'H5' DG A 28 ... failed. Atom erased. Error: recognition of atom ATOM 866 1H2' DG A 28 ... failed. Atom erased. Error: recognition of atom ATOM 867 2H2' DG A 28 ... failed. Atom erased. Error: recognition of atom ATOM 889 C5M DT A 29 ... failed. Atom erased. Error: recognition of atom ATOM 893 HN3 DT A 29 ... failed. Atom erased. Error: recognition of atom ATOM 894 1HM5 DT A 29 ... failed. Atom erased. Error: recognition of atom ATOM 895 2HM5 DT A 29 ... failed. Atom erased. Error: recognition of atom ATOM 896 3HM5 DT A 29 ... failed. Atom erased. Error: recognition of atom ATOM 923 'H5' DA A 30 ... failed. Atom erased. Error: recognition of atom ATOM 927 1H2' DA A 30 ... failed. Atom erased. Error: recognition of atom ATOM 928 2H2' DA A 30 ... failed. Atom erased. Error: recognition of atom ATOM 953 'H5' DC A 31 ... failed. Atom erased. Error: recognition of atom ATOM 957 1H2' DC A 31 ... failed. Atom erased. Error: recognition of atom ATOM 958 2H2' DC A 31 ... failed. Atom erased. Error: recognition of atom ATOM 986 'H5' DG A 32 ... failed. Atom erased. Error: recognition of atom ATOM 990 1H2' DG A 32 ... failed. Atom erased. Error: recognition of atom ATOM 991 2H2' DG A 32 ... failed. Atom erased. Error: recognition of atom ATOM 1016 'H5' DC A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1020 1H2' DC A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1021 2H2' DC A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1048 'H5' DA A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1052 1H2' DA A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1053 2H2' DA A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1075 C5M DT A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1079 HN3 DT A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1080 1HM5 DT A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1081 2HM5 DT A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1082 3HM5 DT A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1107 'H5' DC A 36 ... failed. Atom erased. Error: recognition of atom ATOM 1111 1H2' DC A 36 ... failed. Atom erased. Error: recognition of atom ATOM 1112 2H2' DC A 36 ... failed. Atom erased. Error: recognition of atom ATOM 1137 'H5' DC A 37 ... failed. Atom erased. Error: recognition of atom ATOM 1141 1H2' DC A 37 ... failed. Atom erased. Error: recognition of atom ATOM 1142 2H2' DC A 37 ... failed. Atom erased. Error: recognition of atom ATOM 1170 'H5' DG A 38 ... failed. Atom erased. Error: recognition of atom ATOM 1174 1H2' DG A 38 ... failed. Atom erased. Error: recognition of atom ATOM 1175 2H2' DG A 38 ... failed. Atom erased. Error: recognition of atom ATOM 1197 C5M DT A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1201 HN3 DT A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1202 1HM5 DT A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1203 2HM5 DT A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1204 3HM5 DT A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1231 'H5' DA A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1235 1H2' DA A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1236 2H2' DA A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1263 'H5' DA A 41 ... failed. Atom erased. Error: recognition of atom ATOM 1267 1H2' DA A 41 ... failed. Atom erased. Error: recognition of atom ATOM 1268 2H2' DA A 41 ... failed. Atom erased. Error: recognition of atom ATOM 1293 'H5' DC A 42 ... failed. Atom erased. Error: recognition of atom ATOM 1297 1H2' DC A 42 ... failed. Atom erased. Error: recognition of atom ATOM 1298 2H2' DC A 42 ... failed. Atom erased. Error: recognition of atom ATOM 1325 'H5' DA A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1329 1H2' DA A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1330 2H2' DA A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1352 C5M DT A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1356 HN3 DT A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1357 1HM5 DT A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1358 2HM5 DT A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1359 3HM5 DT A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1387 'H5' DG A 45 ... failed. Atom erased. Error: recognition of atom ATOM 1391 1H2' DG A 45 ... failed. Atom erased. Error: recognition of atom ATOM 1392 2H2' DG A 45 ... failed. Atom erased. Error: recognition of atom ATOM 1417 'H5' DC A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1421 1H2' DC A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1422 2H2' DC A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1444 C5M DT A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1448 HN3 DT A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1449 1HM5 DT A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1450 2HM5 DT A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1451 3HM5 DT A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1476 'H5' DC A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1480 1H2' DC A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1481 2H2' DC A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1506 'H5' DC A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1510 1H2' DC A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1511 2H2' DC A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1538 'H5' DA A 50 ... failed. Atom erased. Error: recognition of atom ATOM 1542 1H2' DA A 50 ... failed. Atom erased. Error: recognition of atom ATOM 1543 2H2' DA A 50 ... failed. Atom erased. Error: recognition of atom ATOM 1571 'H5' DG A 51 ... failed. Atom erased. Error: recognition of atom ATOM 1575 1H2' DG A 51 ... failed. Atom erased. Error: recognition of atom ATOM 1576 2H2' DG A 51 ... failed. Atom erased. Error: recognition of atom ATOM 1601 'H5' DC A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1605 1H2' DC A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1606 2H2' DC A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1628 C5M DT A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1632 HN3 DT A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1633 1HM5 DT A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1634 2HM5 DT A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1635 3HM5 DT A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1663 'H5' DG A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1667 1H2' DG A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1668 2H2' DG A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1690 C5M DT A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1694 HN3 DT A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1695 1HM5 DT A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1696 2HM5 DT A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1697 3HM5 DT A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1724 'H5' DA A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1728 1H2' DA A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1729 2H2' DA A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1751 C5M DT A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1755 HN3 DT A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1756 1HM5 DT A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1757 2HM5 DT A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1758 3HM5 DT A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1786 'H5' DG A 58 ... failed. Atom erased. Error: recognition of atom ATOM 1790 1H2' DG A 58 ... failed. Atom erased. Error: recognition of atom ATOM 1791 2H2' DG A 58 ... failed. Atom erased. Error: recognition of atom ATOM 1813 C5M DT A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1817 HN3 DT A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1818 1HM5 DT A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1819 2HM5 DT A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1820 3HM5 DT A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1847 'H5' DA A 60 ... failed. Atom erased. Error: recognition of atom ATOM 1851 1H2' DA A 60 ... failed. Atom erased. Error: recognition of atom ATOM 1852 2H2' DA A 60 ... failed. Atom erased. Error: recognition of atom ATOM 1874 C5M DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1878 HN3 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1879 1HM5 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1880 2HM5 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1881 3HM5 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1909 'H5' DG A 62 ... failed. Atom erased. Error: recognition of atom ATOM 1913 1H2' DG A 62 ... failed. Atom erased. Error: recognition of atom ATOM 1914 2H2' DG A 62 ... failed. Atom erased. Error: recognition of atom ATOM 1942 'H5' DG A 63 ... failed. Atom erased. Error: recognition of atom ATOM 1946 1H2' DG A 63 ... failed. Atom erased. Error: recognition of atom ATOM 1947 2H2' DG A 63 ... failed. Atom erased. Error: recognition of atom ATOM 1975 'H5' DG A 64 ... failed. Atom erased. Error: recognition of atom ATOM 1979 1H2' DG A 64 ... failed. Atom erased. Error: recognition of atom ATOM 1980 2H2' DG A 64 ... failed. Atom erased. Error: recognition of atom ATOM 2002 C5M DT A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2006 HN3 DT A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2007 1HM5 DT A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2008 2HM5 DT A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2009 3HM5 DT A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2034 'H5' DC A 66 ... failed. Atom erased. Error: recognition of atom ATOM 2038 1H2' DC A 66 ... failed. Atom erased. Error: recognition of atom ATOM 2039 2H2' DC A 66 ... failed. Atom erased. Error: recognition of atom ATOM 2067 'H5' DG A 67 ... failed. Atom erased. Error: recognition of atom ATOM 2071 1H2' DG A 67 ... failed. Atom erased. Error: recognition of atom ATOM 2072 2H2' DG A 67 ... failed. Atom erased. Error: recognition of atom ATOM 2099 'H5' DA A 68 ... failed. Atom erased. Error: recognition of atom ATOM 2103 1H2' DA A 68 ... failed. Atom erased. Error: recognition of atom ATOM 2104 2H2' DA A 68 ... failed. Atom erased. Error: recognition of atom ATOM 2129 'H5' DC A 69 ... failed. Atom erased. Error: recognition of atom ATOM 2133 1H2' DC A 69 ... failed. Atom erased. Error: recognition of atom ATOM 2134 2H2' DC A 69 ... failed. Atom erased. Error: recognition of atom ATOM 2162 'H5' DG A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2166 1H2' DG A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2167 2H2' DG A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2194 'H5' DA A 71 ... failed. Atom erased. Error: recognition of atom ATOM 2198 1H2' DA A 71 ... failed. Atom erased. Error: recognition of atom ATOM 2199 2H2' DA A 71 ... failed. Atom erased. Error: recognition of atom ATOM 2227 'H5' DG A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2231 1H2' DG A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2232 2H2' DG A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2260 'H5' DG A 73 ... failed. Atom erased. Error: recognition of atom ATOM 2264 1H2' DG A 73 ... failed. Atom erased. Error: recognition of atom ATOM 2265 2H2' DG A 73 ... failed. Atom erased. Error: recognition of atom ATOM 2287 C5M DT A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2291 HN3 DT A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2292 1HM5 DT A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2293 2HM5 DT A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2294 3HM5 DT A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2319 'H5' DC A 75 ... failed. Atom erased. Error: recognition of atom ATOM 2323 1H2' DC A 75 ... failed. Atom erased. Error: recognition of atom ATOM 2324 2H2' DC A 75 ... failed. Atom erased. Error: recognition of atom ATOM 2346 C5M DT A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2350 HN3 DT A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2351 1HM5 DT A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2352 2HM5 DT A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2353 3HM5 DT A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2380 'H5' DA A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2384 1H2' DA A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2385 2H2' DA A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2413 'H5' DG A 78 ... failed. Atom erased. Error: recognition of atom ATOM 2417 1H2' DG A 78 ... failed. Atom erased. Error: recognition of atom ATOM 2418 2H2' DG A 78 ... failed. Atom erased. Error: recognition of atom ATOM 2445 'H5' DA A 79 ... failed. Atom erased. Error: recognition of atom ATOM 2449 1H2' DA A 79 ... failed. Atom erased. Error: recognition of atom ATOM 2450 2H2' DA A 79 ... failed. Atom erased. Error: recognition of atom ATOM 2477 'H5' DA A 80 ... failed. Atom erased. Error: recognition of atom ATOM 2481 1H2' DA A 80 ... failed. Atom erased. Error: recognition of atom ATOM 2482 2H2' DA A 80 ... failed. Atom erased. Error: recognition of atom ATOM 2504 C5M DT A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2508 HN3 DT A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2509 1HM5 DT A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2510 2HM5 DT A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2511 3HM5 DT A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2538 'H5' DA A 82 ... failed. Atom erased. Error: recognition of atom ATOM 2542 1H2' DA A 82 ... failed. Atom erased. Error: recognition of atom ATOM 2543 2H2' DA A 82 ... failed. Atom erased. Error: recognition of atom ATOM 2568 'H5' DC A 83 ... failed. Atom erased. Error: recognition of atom ATOM 2572 1H2' DC A 83 ... failed. Atom erased. Error: recognition of atom ATOM 2573 2H2' DC A 83 ... failed. Atom erased. Error: recognition of atom ATOM 2598 'H5' DC A 84 ... failed. Atom erased. Error: recognition of atom ATOM 2602 1H2' DC A 84 ... failed. Atom erased. Error: recognition of atom ATOM 2603 2H2' DC A 84 ... failed. Atom erased. Error: recognition of atom ATOM 2630 'H5' DA A 85 ... failed. Atom erased. Error: recognition of atom ATOM 2634 1H2' DA A 85 ... failed. Atom erased. Error: recognition of atom ATOM 2635 2H2' DA A 85 ... failed. Atom erased. Error: recognition of atom ATOM 2663 'H5' DG A 86 ... failed. Atom erased. Error: recognition of atom ATOM 2664 'HO3 DG A 86 ... failed. Atom erased. Error: recognition of atom ATOM 2668 1H2' DG A 86 ... failed. Atom erased. Error: recognition of atom ATOM 2669 2H2' DG A 86 ... failed. Atom erased. Missing atom added: HETATM 1 P DA A 1 0.929 -0.142 -2.420 1.00 0.00 P Missing atom added: HETATM 24 H5'2 DA A 1 2.027 -1.865 -0.308 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 1 1.498 0.469 3.742 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 1 1.747 -1.416 4.361 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 2 6.472 -0.850 4.592 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 2 4.315 -5.016 6.513 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 2 5.703 -5.171 7.582 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 2 0.912 -7.225 4.419 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 2 4.341 -6.051 1.588 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 2 3.678 -5.723 0.779 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 2 4.650 -7.084 1.388 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 2 5.234 -5.416 1.584 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 3 8.644 -6.969 7.700 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 3 7.117 -10.815 8.761 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 3 7.487 -11.158 6.826 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 4 10.588 -13.008 7.872 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 4 10.354 -16.369 5.264 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 4 11.793 -15.387 4.282 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 5 15.343 -15.586 5.062 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 5 13.166 -18.991 2.076 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 5 14.746 -18.370 1.019 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 6 17.496 -20.952 2.098 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 6 17.862 -21.510 -2.408 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 6 19.251 -20.084 -2.217 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 7 21.617 -23.675 -1.911 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 7 23.208 -20.758 -5.269 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 7 24.553 -21.891 -5.234 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 7 22.064 -16.308 -5.057 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 7 21.838 -18.063 -0.877 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 7 20.812 -17.766 -0.667 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 7 22.523 -17.302 -0.502 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 7 22.049 -19.012 -0.388 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 8 26.420 -20.207 -2.891 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 8 27.648 -16.598 -1.110 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 8 28.199 -18.034 0.167 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 9 28.355 -16.276 -5.645 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 9 27.486 -12.059 -4.551 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 9 29.092 -12.268 -3.379 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 10 28.839 -13.982 -9.140 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 10 26.546 -15.245 -11.403 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 10 28.064 -16.452 -11.892 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 11 28.227 -17.927 -8.379 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 11 24.555 -20.662 -9.223 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 11 25.655 -21.766 -10.038 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 11 20.313 -20.124 -10.056 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 11 22.829 -16.353 -10.942 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 11 22.079 -15.633 -10.588 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 11 22.736 -16.437 -12.035 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 11 23.825 -15.949 -10.715 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 12 26.756 -21.778 -13.848 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 12 24.233 -23.330 -13.542 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 12 24.731 -24.747 -14.458 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 12 20.546 -21.586 -14.369 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 12 23.441 -18.199 -13.371 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 12 22.785 -17.763 -12.619 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 12 23.275 -17.705 -14.329 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 12 24.479 -18.063 -13.070 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 13 30.080 -22.479 -16.931 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 13 32.122 -23.006 -20.937 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 13 32.473 -24.974 -20.985 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 14 26.684 -24.527 -20.453 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 14 23.881 -24.804 -21.098 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 14 23.917 -24.549 -19.116 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 15 24.272 -18.587 -19.613 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 15 25.237 -17.544 -16.833 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 15 24.675 -15.975 -17.937 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 16 18.875 -19.078 -16.006 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 16 16.684 -19.551 -19.991 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 16 15.675 -20.517 -18.561 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 17 12.836 -20.112 -16.410 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 17 12.381 -23.979 -16.675 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 17 13.078 -23.401 -14.892 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 18 10.636 -23.949 -12.390 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 18 12.859 -26.614 -9.883 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 18 13.448 -24.893 -9.054 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 19 10.727 -24.646 -6.112 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 19 13.094 -23.719 -2.916 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 19 13.087 -21.896 -3.737 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 20 8.981 -22.748 -1.576 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 20 7.391 -21.685 1.454 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 20 6.668 -20.266 0.245 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 21 3.704 -22.642 -0.943 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 21 1.822 -18.767 1.773 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 21 1.462 -17.819 0.051 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 22 -1.425 -20.039 -2.709 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 22 -2.428 -17.085 -5.311 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 22 -1.527 -17.956 -6.869 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 23 -5.907 -20.453 -6.424 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 23 -7.308 -17.193 -9.608 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 23 -5.856 -17.949 -10.755 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 24 -9.250 -20.994 -10.883 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 24 -7.816 -18.918 -15.253 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 24 -9.300 -19.531 -15.973 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 24 -3.596 -18.403 -16.534 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 24 -4.086 -22.138 -13.844 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 24 -3.196 -21.985 -13.239 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 24 -3.856 -22.803 -14.676 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 24 -4.873 -22.576 -13.234 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 25 -11.626 -22.201 -17.661 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 25 -11.663 -20.232 -21.619 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 25 -9.846 -21.040 -21.821 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 26 -9.934 -24.196 -23.524 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 26 -7.176 -22.949 -24.085 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 26 -7.391 -22.655 -25.806 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 26 -3.552 -24.075 -22.634 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 26 -6.717 -25.718 -19.710 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 26 -6.389 -25.190 -18.817 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 26 -6.277 -26.716 -19.727 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 26 -7.803 -25.801 -19.706 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 27 -11.029 -24.186 -28.907 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 27 -6.793 -26.774 -28.893 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 27 -8.232 -28.153 -29.062 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 28 -7.709 -29.903 -30.021 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 28 -5.756 -31.591 -33.400 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 28 -4.881 -29.948 -32.671 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 29 -2.969 -31.953 -30.724 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 29 -3.172 -34.315 -27.863 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 29 -1.782 -34.587 -26.818 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 29 -4.340 -32.480 -22.051 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 29 -7.189 -31.889 -25.616 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 29 -7.500 -30.864 -25.407 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 29 -7.906 -32.579 -25.163 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 29 -7.180 -32.046 -26.696 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 30 2.722 -33.230 -29.208 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 30 2.746 -28.941 -31.562 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 30 2.693 -27.768 -29.944 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 31 6.118 -27.868 -26.269 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 31 4.839 -24.695 -29.592 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 31 3.967 -23.594 -28.170 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 32 4.581 -21.718 -25.367 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 32 2.278 -20.072 -28.781 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 32 1.199 -19.633 -27.156 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 33 1.654 -16.000 -27.052 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 33 -2.181 -14.554 -26.767 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 33 -1.828 -14.717 -24.806 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 34 1.634 -13.741 -22.789 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 34 -0.165 -10.758 -19.490 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 34 1.021 -11.910 -18.366 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 35 5.364 -12.804 -20.052 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 35 6.772 -16.001 -19.290 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 35 7.906 -15.693 -17.981 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 35 3.103 -19.347 -17.609 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 35 4.268 -18.426 -21.971 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 35 3.259 -18.236 -22.342 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 35 4.528 -19.471 -22.162 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 35 4.971 -17.783 -22.505 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 36 7.499 -10.290 -15.621 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 36 4.617 -6.931 -15.068 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 36 3.762 -8.254 -13.837 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 37 6.687 -7.195 -10.406 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 37 2.276 -7.856 -8.371 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 37 2.603 -9.827 -8.317 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 38 4.956 -5.158 -5.891 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 38 4.017 -7.004 -1.437 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 38 5.671 -8.124 -1.345 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 39 8.775 -5.108 0.545 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 39 9.289 -9.366 2.593 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 39 10.772 -8.705 3.272 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 39 8.537 -12.954 0.602 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 39 8.213 -9.271 -2.219 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 39 7.324 -9.579 -2.744 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 39 9.103 -9.534 -2.772 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 39 8.190 -8.216 -1.999 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 40 13.390 -6.136 3.119 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 40 16.526 -9.647 2.474 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 40 17.261 -8.748 0.847 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 41 19.329 -7.789 1.234 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 41 22.018 -10.990 0.083 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 41 20.479 -12.123 0.668 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 42 22.613 -7.248 -1.412 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 42 25.073 -7.050 0.722 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 42 25.975 -7.912 -0.840 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 43 24.741 -5.695 -5.741 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 43 24.844 -8.622 -8.779 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 43 23.594 -9.630 -7.588 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 44 20.569 -7.693 -10.003 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 44 19.608 -12.282 -8.995 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 44 18.248 -12.050 -10.086 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 44 18.948 -13.495 -4.780 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 44 21.349 -9.602 -4.767 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 44 22.121 -9.979 -4.089 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 44 20.602 -9.056 -4.178 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 44 21.813 -8.903 -5.471 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 45 14.202 -9.954 -10.675 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 45 13.007 -14.083 -9.541 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 45 13.468 -13.541 -7.673 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 46 9.665 -10.707 -10.764 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 46 8.196 -14.353 -7.551 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 46 7.927 -13.153 -5.975 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 47 3.305 -12.833 -7.700 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 47 1.199 -12.403 -3.787 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 47 -0.140 -12.463 -4.926 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 47 1.776 -12.161 0.551 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 47 1.355 -8.428 -2.122 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 47 2.203 -7.905 -1.679 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 47 0.434 -8.103 -1.632 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 47 1.300 -8.189 -3.184 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 48 -2.483 -11.294 -6.787 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 48 -5.980 -12.708 -4.471 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 48 -5.797 -10.893 -3.654 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 49 -8.067 -8.179 -5.482 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 49 -9.711 -6.283 -1.901 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 49 -7.977 -5.290 -1.931 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 50 -9.742 -2.727 -4.684 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 50 -9.897 0.249 -1.510 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 50 -8.237 0.949 -2.376 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 51 -9.927 3.453 -4.649 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 51 -7.422 6.254 -2.395 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 51 -6.076 6.005 -3.852 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 52 -7.131 8.811 -6.377 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 52 -2.932 10.096 -5.723 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 52 -2.477 8.808 -7.181 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 53 -3.311 12.130 -9.861 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 53 -0.015 9.428 -11.344 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 53 0.462 10.769 -12.377 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 53 0.305 5.225 -12.221 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 53 -3.921 6.159 -10.715 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 53 -3.950 5.434 -9.903 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 53 -4.354 5.716 -11.614 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 53 -4.497 7.040 -10.434 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 54 0.022 12.520 -15.322 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 54 3.249 9.930 -16.786 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 54 1.809 8.767 -17.542 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 55 1.823 10.604 -20.860 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 55 0.773 6.086 -21.332 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 55 1.264 6.314 -23.006 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 55 -2.533 3.964 -19.630 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 55 -2.785 8.335 -18.191 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 55 -2.954 8.095 -17.139 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 55 -3.751 8.496 -18.680 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 55 -2.197 9.252 -18.257 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 56 0.228 7.354 -26.264 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 56 -1.084 3.269 -26.895 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 56 -2.913 3.883 -26.369 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 57 -3.775 4.764 -30.001 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 57 -7.423 3.238 -27.456 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 57 -8.145 2.849 -29.012 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 57 -8.864 4.861 -23.690 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 57 -5.774 7.757 -25.472 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 57 -5.190 7.882 -24.559 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 57 -6.503 8.568 -25.546 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 57 -5.105 7.799 -26.333 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 58 -10.049 3.952 -31.714 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 58 -13.594 2.610 -29.502 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 58 -13.766 4.515 -28.920 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 59 -15.855 5.547 -31.970 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 59 -16.901 7.830 -28.044 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 59 -18.442 8.169 -28.823 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 59 -14.020 10.112 -25.505 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 59 -12.163 9.122 -29.613 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 59 -11.181 8.847 -29.217 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 59 -12.137 10.172 -29.924 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 59 -12.374 8.503 -30.490 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 60 -20.539 10.397 -30.615 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 60 -21.629 13.047 -27.289 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 60 -19.922 13.937 -27.828 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 61 -22.192 15.986 -30.288 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 61 -19.053 18.730 -28.153 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 61 -20.109 20.047 -28.650 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 61 -14.969 16.551 -27.140 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 61 -16.488 15.800 -31.446 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 61 -16.339 14.719 -31.429 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 61 -15.612 16.275 -31.897 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 61 -17.367 16.030 -32.051 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 62 -20.376 22.678 -30.588 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 62 -17.134 25.113 -29.336 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 62 -16.182 24.212 -30.845 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 63 -17.221 26.985 -33.335 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 63 -13.002 27.850 -33.129 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 63 -12.799 26.529 -34.616 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 64 -12.944 28.975 -37.429 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 64 -8.938 27.570 -38.298 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 64 -9.829 26.290 -39.548 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 65 -9.728 28.707 -42.457 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 65 -9.469 24.194 -43.667 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 65 -8.695 24.777 -45.136 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 65 -12.433 21.107 -42.114 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 65 -14.200 25.361 -41.840 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 65 -14.563 25.281 -40.814 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 65 -15.013 25.112 -42.528 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 65 -13.879 26.387 -42.027 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 66 -9.570 26.018 -48.739 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 66 -9.838 21.878 -49.937 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 66 -11.743 22.042 -49.352 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 67 -12.590 22.761 -53.231 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 67 -14.582 19.008 -53.995 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 67 -16.172 19.961 -53.245 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 68 -17.496 21.194 -56.529 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 68 -20.766 18.452 -55.440 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 68 -21.589 20.043 -54.553 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 69 -23.610 21.295 -57.653 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 69 -27.053 20.788 -54.904 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 69 -26.722 22.707 -54.454 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 70 -29.315 24.101 -56.916 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 70 -31.260 25.767 -53.548 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 70 -30.000 27.304 -53.764 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 71 -32.434 29.612 -55.889 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 71 -31.434 32.574 -52.775 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 71 -29.772 33.015 -53.793 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 72 -31.680 35.813 -55.594 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 72 -29.330 38.502 -53.130 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 72 -27.995 38.405 -54.615 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 73 -27.846 39.275 -57.830 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 73 -24.561 41.277 -55.542 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 73 -23.737 40.379 -57.126 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 74 -23.237 43.786 -58.665 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 74 -19.427 41.945 -59.882 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 74 -18.984 43.560 -60.419 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 74 -19.106 37.909 -61.635 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 74 -23.457 38.649 -60.453 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 74 -23.593 37.832 -59.744 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 74 -23.778 38.323 -61.445 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 74 -24.066 39.499 -60.142 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 75 -18.966 45.691 -63.088 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 75 -15.636 43.459 -65.043 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 75 -17.128 42.546 -66.010 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 76 -16.908 44.953 -69.022 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 76 -18.648 40.511 -69.886 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 76 -18.634 41.027 -71.568 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 76 -22.104 38.477 -68.667 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 76 -22.065 42.613 -66.612 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 76 -22.274 42.245 -65.598 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 76 -23.020 42.907 -67.072 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 76 -21.439 43.511 -66.526 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 77 -20.244 43.145 -72.281 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 77 -19.574 43.492 -76.170 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 77 -18.044 42.689 -75.164 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 78 -23.366 40.224 -75.031 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 78 -22.901 35.936 -74.848 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 78 -23.225 36.823 -73.085 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 79 -27.262 36.144 -71.593 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 79 -29.041 36.198 -69.364 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 79 -28.510 34.329 -69.834 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 80 -24.586 32.227 -68.789 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 80 -22.447 29.957 -71.843 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 80 -21.058 31.237 -71.188 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 81 -19.872 28.471 -68.098 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 81 -17.359 32.145 -68.365 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 81 -16.084 31.198 -67.609 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 81 -17.686 36.321 -67.963 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 81 -21.468 34.152 -66.396 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 81 -22.194 34.701 -66.990 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 81 -21.362 34.620 -65.418 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 81 -21.796 33.123 -66.275 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 82 -14.350 29.873 -64.762 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 82 -12.725 34.277 -64.650 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 82 -14.170 34.660 -63.323 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 83 -14.034 33.850 -59.786 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 83 -14.630 37.380 -58.803 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 83 -16.106 36.316 -57.975 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 84 -15.718 35.961 -54.191 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 84 -17.344 39.182 -52.734 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 84 -18.534 37.641 -52.282 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 85 -16.456 38.518 -48.122 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 85 -20.808 40.350 -47.799 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 85 -21.545 38.495 -47.694 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 86 -21.823 38.613 -43.968 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 86 -26.159 37.773 -44.518 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 86 -25.696 35.839 -44.732 1.00 0.00 H Number of atoms: 2733 Number of residues: 86 Building intraresidual bonds... Warning: Bond expected, but some of the atoms are missing: P OP2, residue No. A 1 Warning: Bond expected, but some of the atoms are missing: P OP1, residue No. A 1 Building intraresidual angles... Warning: Angle expected, but some of the atoms are missing: OP2 P O5', residue No. A 1 Warning: Angle expected, but some of the atoms are missing: OP1 P O5', residue No. A 1 Warning: Angle expected, but some of the atoms are missing: OP1 P OP2, residue No. A 1 Building intraresidual dihedrals... Warning: Dihedral expected, but some of the atoms are missing: OP2 P O5' C5', residue No. A 1 Warning: Dihedral expected, but some of the atoms are missing: OP1 P O5' C5', residue No. A 1 Building intraresidual impropers... Building interresidual bonds... Building interresidual angles... Internal Warning: unknown atoms in angle: H5 C2 N* Internal Warning: unknown atoms in angle: H5 C2 NB Internal Warning: unknown atoms in angle: N* C2 NB Internal Warning: unknown atoms in angle: CB N* C2 Internal Warning: unknown atoms in angle: C2 N* CT Internal Warning: unknown atoms in angle: CB NB C2 Internal Warning: unknown atoms in angle: C1 C NA Internal Warning: unknown atoms in angle: C1 C O Internal Warning: unknown atoms in angle: C1 CA N2 Internal Warning: unknown atoms in angle: C1 CA NC Internal Warning: unknown atoms in angle: C C1 C1 Internal Warning: unknown atoms in angle: C C1 CT Internal Warning: unknown atoms in angle: C C1 HA Internal Warning: unknown atoms in angle: C C1 H4 Internal Warning: unknown atoms in angle: CA C1 C1 Internal Warning: unknown atoms in angle: CA C1 HA Internal Warning: unknown atoms in angle: CA C1 H4 Internal Warning: unknown atoms in angle: C1 C1 CT Internal Warning: unknown atoms in angle: C1 C1 HA Internal Warning: unknown atoms in angle: C1 C1 H4 Internal Warning: unknown atoms in angle: C1 C1 N* Internal Warning: unknown atoms in angle: H4 C1 N* Internal Warning: unknown atoms in angle: H1 CT C1 Internal Warning: unknown atoms in angle: HC CT C1 Internal Warning: unknown atoms in angle: C N* C1 Internal Warning: unknown atoms in angle: C1 N* CT Building interresidual dihedrals... Internal Warning: unknown atom(s) in dihedral: X C2 N* X Internal Warning: unknown atom(s) in dihedral: X C2 NB X Internal Warning: unknown atom(s) in dihedral: X C C1 X Internal Warning: unknown atom(s) in dihedral: X CA C1 X Internal Warning: unknown atom(s) in dihedral: X C1 C1 X Internal Warning: unknown atom(s) in dihedral: X C1 CT X Internal Warning: unknown atom(s) in dihedral: X C1 N* X Internal Warning: unknown atom(s) in dihedral: HC CT C1 C1 Internal Warning: unknown atom(s) in dihedral: HC CT C1 C1 Internal Warning: unknown atom(s) in dihedral: C1 C1 C O Internal Warning: unknown atom(s) in dihedral: C1 C1 C O Internal Warning: unknown atom(s) in dihedral: OS CT N* C2 Internal Warning: unknown atom(s) in dihedral: OS CT N* C2 Internal Warning: unknown atom(s) in dihedral: OS CT N* C2 Internal Warning: unknown atom(s) in dihedral: OS CT N* C1 Internal Warning: unknown atom(s) in dihedral: OS CT N* C1 Internal Warning: unknown atom(s) in dihedral: OS CT N* C1 Internal Warning: unknown atom(s) in dihedral: OS CT N* C1 Number of bonds built: 2950 Number of angles built: 5357 Number of dihedrals built: 8007 Number of impropers built: 585 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Building interresidual nonbonded pairs & H-bonds (it may take a while)... Number of electrostatic pairs: 3724971 Number of van der Waals pairs: 322195 Number of H-bonds built: 40 Number of spring restraints: 0 Number of positional restraints: 0 Number of base pairs built: 7 Number of molecules (chains) read: 1 ----------------------------------------------------------------------------- Performing minimization step: 1. Total energy = 183849.6850 kcal/mol (183481.2550 without restraints) Performing minimization step: 2. Total energy = 180841.4323 kcal/mol (180483.9656 without restraints) Performing minimization step: 3. Total energy = 177923.8588 kcal/mol (177576.8386 without restraints) Performing minimization step: 4. Total energy = 175092.7231 kcal/mol (174755.6648 without restraints) Performing minimization step: 5. Total energy = 172344.0463 kcal/mol (172016.4949 without restraints) Performing minimization step: 6. Total energy = 169674.0926 kcal/mol (169355.6209 without restraints) Performing minimization step: 7. Total energy = 167079.3524 kcal/mol (166769.5589 without restraints) Performing minimization step: 8. Total energy = 164556.5262 kcal/mol (164255.0334 without restraints) Performing minimization step: 9. Total energy = 162102.5101 kcal/mol (161808.9625 without restraints) Performing minimization step: 10. Total energy = 159714.3820 kcal/mol (159428.4452 without restraints) Performing minimization step: 11. Total energy = 157389.3896 kcal/mol (157110.7481 without restraints) Performing minimization step: 12. Total energy = 155124.9383 kcal/mol (154853.2949 without restraints) Performing minimization step: 13. Total energy = 152918.5808 kcal/mol (152653.6549 without restraints) Performing minimization step: 14. Total energy = 150768.0071 kcal/mol (150509.5339 without restraints) Performing minimization step: 15. Total energy = 148671.0355 kcal/mol (148418.7648 without restraints) Performing minimization step: 16. Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to C15MA2_refx.pdb Traceback (most recent call last): File "/home/ubuntu/miniconda3/bin/rna_refinement.py", line 7, in exec(compile(f.read(), __file__, 'exec')) File "/home/ubuntu/rna-tools/rna_tools/tools/rna_refinement/rna_refinement.py", line 181, in q.run(args.fn, output_file, steps=args.steps, interactive=args.interactive, verbose=args.verbose) File "/home/ubuntu/rna-tools/rna_tools/tools/rna_refinement/rna_refinement.py", line 156, in run copyfile(qrnas_outputfile, outputfile) File "/home/ubuntu/miniconda3/lib/python3.8/shutil.py", line 264, in copyfile with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst: FileNotFoundError: [Errno 2] No such file or directory: '/home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/9b512edd/tmp/C15MA2_refx/C15MA2_refx.pdb' DONE!