============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/5936b356/tmp/CPMA6_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/5936b356/tmp/CPMA6_refx/CPMA6.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 735 'H5' DC A 24 ... failed. Atom erased. Error: recognition of atom ATOM 739 1H2' DC A 24 ... failed. Atom erased. Error: recognition of atom ATOM 740 2H2' DC A 24 ... failed. Atom erased. Error: recognition of atom ATOM 768 'H5' DG A 25 ... failed. Atom erased. Error: recognition of atom ATOM 772 1H2' DG A 25 ... failed. Atom erased. Error: recognition of atom ATOM 773 2H2' DG A 25 ... failed. Atom erased. Error: recognition of atom ATOM 800 'H5' DA A 26 ... failed. Atom erased. Error: recognition of atom ATOM 804 1H2' DA A 26 ... failed. Atom erased. Error: recognition of atom ATOM 805 2H2' DA A 26 ... failed. Atom erased. Error: recognition of atom ATOM 830 'H5' DC A 27 ... failed. Atom erased. Error: recognition of atom ATOM 834 1H2' DC A 27 ... failed. Atom erased. Error: recognition of atom ATOM 835 2H2' DC A 27 ... failed. Atom erased. Error: recognition of atom ATOM 860 'H5' DC A 28 ... failed. Atom erased. Error: recognition of atom ATOM 864 1H2' DC A 28 ... failed. Atom erased. Error: recognition of atom ATOM 865 2H2' DC A 28 ... failed. Atom erased. Error: recognition of atom ATOM 892 'H5' DA A 29 ... failed. Atom erased. Error: recognition of atom ATOM 896 1H2' DA A 29 ... failed. Atom erased. Error: recognition of atom ATOM 897 2H2' DA A 29 ... failed. Atom erased. Error: recognition of atom ATOM 924 'H5' DA A 30 ... failed. Atom erased. Error: recognition of atom ATOM 928 1H2' DA A 30 ... failed. Atom erased. Error: recognition of atom ATOM 929 2H2' DA A 30 ... failed. Atom erased. Error: recognition of atom ATOM 951 C5M DT A 31 ... failed. Atom erased. Error: recognition of atom ATOM 955 HN3 DT A 31 ... failed. Atom erased. Error: recognition of atom ATOM 956 1HM5 DT A 31 ... failed. Atom erased. Error: recognition of atom ATOM 957 2HM5 DT A 31 ... failed. Atom erased. Error: recognition of atom ATOM 958 3HM5 DT 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 1013 C5M DT A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1017 HN3 DT A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1018 1HM5 DT A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1019 2HM5 DT A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1020 3HM5 DT A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1042 C5M DT A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1046 HN3 DT A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1047 1HM5 DT A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1048 2HM5 DT A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1049 3HM5 DT A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1076 'H5' DA A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1080 1H2' DA A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1081 2H2' DA A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1108 'H5' DA A 36 ... failed. Atom erased. Error: recognition of atom ATOM 1112 1H2' DA A 36 ... failed. Atom erased. Error: recognition of atom ATOM 1113 2H2' DA A 36 ... failed. Atom erased. Error: recognition of atom ATOM 1140 'H5' DA A 37 ... failed. Atom erased. Error: recognition of atom ATOM 1144 1H2' DA A 37 ... failed. Atom erased. Error: recognition of atom ATOM 1145 2H2' DA A 37 ... failed. Atom erased. Error: recognition of atom ATOM 1172 'H5' DA A 38 ... failed. Atom erased. Error: recognition of atom ATOM 1176 1H2' DA A 38 ... failed. Atom erased. Error: recognition of atom ATOM 1177 2H2' DA A 38 ... failed. Atom erased. Error: recognition of atom ATOM 1205 'H5' DG A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1209 1H2' DG A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1210 2H2' DG A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1235 'H5' DC A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1239 1H2' DC A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1240 2H2' DC A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1268 'H5' DG A 41 ... failed. Atom erased. Error: recognition of atom ATOM 1272 1H2' DG A 41 ... failed. Atom erased. Error: recognition of atom ATOM 1273 2H2' DG A 41 ... failed. Atom erased. Error: recognition of atom ATOM 1301 'H5' DG A 42 ... failed. Atom erased. Error: recognition of atom ATOM 1305 1H2' DG A 42 ... failed. Atom erased. Error: recognition of atom ATOM 1306 2H2' DG A 42 ... failed. Atom erased. Error: recognition of atom ATOM 1328 C5M DT A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1332 HN3 DT A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1333 1HM5 DT A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1334 2HM5 DT A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1335 3HM5 DT A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1362 'H5' DA A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1366 1H2' DA A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1367 2H2' DA A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1395 'H5' DG A 45 ... failed. Atom erased. Error: recognition of atom ATOM 1399 1H2' DG A 45 ... failed. Atom erased. Error: recognition of atom ATOM 1400 2H2' DG A 45 ... failed. Atom erased. Error: recognition of atom ATOM 1425 'H5' DC A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1429 1H2' DC A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1430 2H2' DC A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1452 C5M DT A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1456 HN3 DT A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1457 1HM5 DT A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1458 2HM5 DT A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1459 3HM5 DT A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1484 'H5' DC A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1488 1H2' DC A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1489 2H2' DC A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1511 C5M DT A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1515 HN3 DT A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1516 1HM5 DT A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1517 2HM5 DT A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1518 3HM5 DT A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1546 'H5' DG A 50 ... failed. Atom erased. Error: recognition of atom ATOM 1550 1H2' DG A 50 ... failed. Atom erased. Error: recognition of atom ATOM 1551 2H2' DG A 50 ... failed. Atom erased. Error: recognition of atom ATOM 1576 'H5' DC A 51 ... failed. Atom erased. Error: recognition of atom ATOM 1580 1H2' DC A 51 ... failed. Atom erased. Error: recognition of atom ATOM 1581 2H2' DC A 51 ... failed. Atom erased. Error: recognition of atom ATOM 1603 C5M DT A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1607 HN3 DT A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1608 1HM5 DT A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1609 2HM5 DT A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1610 3HM5 DT A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1638 'H5' DG A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1642 1H2' DG A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1643 2H2' DG A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1665 C5M DT A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1669 HN3 DT A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1670 1HM5 DT A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1671 2HM5 DT A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1672 3HM5 DT A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1699 'H5' DA A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1703 1H2' DA A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1704 2H2' DA A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1732 'H5' DG A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1736 1H2' DG A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1737 2H2' DG A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1765 'H5' DG A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1769 1H2' DG A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1770 2H2' DG A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1798 'H5' DG A 58 ... failed. Atom erased. Error: recognition of atom ATOM 1802 1H2' DG A 58 ... failed. Atom erased. Error: recognition of atom ATOM 1803 2H2' DG A 58 ... failed. Atom erased. Error: recognition of atom ATOM 1825 C5M DT A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1829 HN3 DT A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1830 1HM5 DT A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1831 2HM5 DT A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1832 3HM5 DT A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1860 'H5' DG A 60 ... failed. Atom erased. Error: recognition of atom ATOM 1864 1H2' DG A 60 ... failed. Atom erased. Error: recognition of atom ATOM 1865 2H2' DG A 60 ... failed. Atom erased. Error: recognition of atom ATOM 1887 C5M DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1891 HN3 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1892 1HM5 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1893 2HM5 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1894 3HM5 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1919 'H5' DC A 62 ... failed. Atom erased. Error: recognition of atom ATOM 1923 1H2' DC A 62 ... failed. Atom erased. Error: recognition of atom ATOM 1924 2H2' DC A 62 ... failed. Atom erased. Error: recognition of atom ATOM 1952 'H5' DG A 63 ... failed. Atom erased. Error: recognition of atom ATOM 1956 1H2' DG A 63 ... failed. Atom erased. Error: recognition of atom ATOM 1957 2H2' DG A 63 ... failed. Atom erased. Error: recognition of atom ATOM 1984 'H5' DA A 64 ... failed. Atom erased. Error: recognition of atom ATOM 1988 1H2' DA A 64 ... failed. Atom erased. Error: recognition of atom ATOM 1989 2H2' DA A 64 ... failed. Atom erased. Error: recognition of atom ATOM 2014 'H5' DC A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2018 1H2' DC A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2019 2H2' DC A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2047 'H5' DG A 66 ... failed. Atom erased. Error: recognition of atom ATOM 2051 1H2' DG A 66 ... failed. Atom erased. Error: recognition of atom ATOM 2052 2H2' DG A 66 ... failed. Atom erased. Error: recognition of atom ATOM 2079 'H5' DA A 67 ... failed. Atom erased. Error: recognition of atom ATOM 2083 1H2' DA A 67 ... failed. Atom erased. Error: recognition of atom ATOM 2084 2H2' DA A 67 ... failed. Atom erased. Error: recognition of atom ATOM 2112 'H5' DG A 68 ... failed. Atom erased. Error: recognition of atom ATOM 2116 1H2' DG A 68 ... failed. Atom erased. Error: recognition of atom ATOM 2117 2H2' DG A 68 ... failed. Atom erased. Error: recognition of atom ATOM 2145 'H5' DG A 69 ... failed. Atom erased. Error: recognition of atom ATOM 2149 1H2' DG A 69 ... failed. Atom erased. Error: recognition of atom ATOM 2150 2H2' DG A 69 ... failed. Atom erased. Error: recognition of atom ATOM 2172 C5M DT A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2176 HN3 DT A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2177 1HM5 DT A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2178 2HM5 DT A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2179 3HM5 DT A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2204 'H5' DC A 71 ... failed. Atom erased. Error: recognition of atom ATOM 2208 1H2' DC A 71 ... failed. Atom erased. Error: recognition of atom ATOM 2209 2H2' DC A 71 ... failed. Atom erased. Error: recognition of atom ATOM 2231 C5M DT A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2235 HN3 DT A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2236 1HM5 DT A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2237 2HM5 DT A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2238 3HM5 DT A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2265 'H5' DA A 73 ... failed. Atom erased. Error: recognition of atom ATOM 2269 1H2' DA A 73 ... failed. Atom erased. Error: recognition of atom ATOM 2270 2H2' DA A 73 ... failed. Atom erased. Error: recognition of atom ATOM 2298 'H5' DG A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2302 1H2' DG A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2303 2H2' DG A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2330 'H5' DA A 75 ... failed. Atom erased. Error: recognition of atom ATOM 2334 1H2' DA A 75 ... failed. Atom erased. Error: recognition of atom ATOM 2335 2H2' DA A 75 ... failed. Atom erased. Error: recognition of atom ATOM 2362 'H5' DA A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2366 1H2' DA A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2367 2H2' DA A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2389 C5M DT A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2393 HN3 DT A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2394 1HM5 DT A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2395 2HM5 DT A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2396 3HM5 DT A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2423 'H5' DA A 78 ... failed. Atom erased. Error: recognition of atom ATOM 2427 1H2' DA A 78 ... failed. Atom erased. Error: recognition of atom ATOM 2428 2H2' DA A 78 ... failed. Atom erased. Error: recognition of atom ATOM 2453 'H5' DC A 79 ... failed. Atom erased. Error: recognition of atom ATOM 2457 1H2' DC A 79 ... failed. Atom erased. Error: recognition of atom ATOM 2458 2H2' DC A 79 ... failed. Atom erased. Error: recognition of atom ATOM 2483 'H5' DC A 80 ... failed. Atom erased. Error: recognition of atom ATOM 2487 1H2' DC A 80 ... failed. Atom erased. Error: recognition of atom ATOM 2488 2H2' DC A 80 ... failed. Atom erased. Error: recognition of atom ATOM 2515 'H5' DA A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2519 1H2' DA A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2520 2H2' DA A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2548 'H5' DG A 82 ... failed. Atom erased. Error: recognition of atom ATOM 2549 'HO3 DG A 82 ... failed. Atom erased. Error: recognition of atom ATOM 2553 1H2' DG A 82 ... failed. Atom erased. Error: recognition of atom ATOM 2554 2H2' DG A 82 ... failed. Atom erased. Missing atom added: HETATM 1 P DA A 1 0.210 0.713 -2.581 1.00 0.00 P Missing atom added: HETATM 24 H5'2 DA A 1 1.810 -0.813 -0.647 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 1 2.186 -0.106 3.705 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 1 0.192 -0.168 3.833 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 2 0.305 -4.126 4.513 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 2 -3.512 -3.157 6.789 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 2 -3.234 -4.734 7.517 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 2 -6.929 -1.100 4.775 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 2 -3.704 -2.039 1.659 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 2 -3.630 -1.048 1.209 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 2 -4.412 -2.643 1.087 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 2 -2.725 -2.518 1.637 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 3 -3.679 -7.982 7.451 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 3 -7.532 -6.973 9.291 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 3 -8.310 -7.202 7.464 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 4 -9.087 -10.932 7.820 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 4 -13.140 -9.337 7.367 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 4 -12.888 -9.697 5.417 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 5 -14.512 -13.459 4.975 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 5 -17.227 -11.870 1.788 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 5 -15.563 -12.003 0.689 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 6 -16.887 -15.542 -0.397 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 6 -17.972 -14.213 -4.439 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 6 -16.028 -14.517 -4.792 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 7 -16.732 -18.144 -5.699 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 7 -13.059 -16.378 -8.032 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 7 -13.424 -17.615 -9.229 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 7 -9.871 -13.962 -5.757 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 7 -11.921 -16.959 -2.942 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 7 -12.167 -16.254 -2.146 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 7 -10.964 -17.437 -2.715 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 7 -12.698 -17.725 -2.992 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 8 -12.851 -20.518 -10.805 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 8 -9.240 -19.624 -13.038 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 8 -8.387 -20.240 -11.338 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 9 -8.126 -23.732 -12.689 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 9 -3.926 -22.541 -12.632 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 9 -3.903 -23.243 -10.760 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 10 -2.769 -26.742 -11.735 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 10 0.752 -25.667 -9.373 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 10 -0.235 -26.415 -7.804 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 11 0.830 -30.135 -8.233 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 11 0.019 -28.886 -3.805 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 11 0.946 -30.322 -3.389 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 11 -3.614 -26.870 -2.369 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 11 -4.319 -28.494 -6.625 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 11 -4.724 -27.570 -7.033 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 11 -5.135 -29.134 -6.291 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 11 -3.744 -29.010 -7.392 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 12 1.470 -33.701 -2.774 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 12 -1.041 -32.789 1.041 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 12 -0.438 -34.353 1.574 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 12 -4.883 -30.508 0.645 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 12 -3.567 -31.857 -3.528 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 12 -3.639 -30.900 -4.048 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 12 -4.499 -32.412 -3.668 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 12 -2.743 -32.433 -3.951 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 13 -1.093 -37.852 1.405 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 13 -4.062 -37.344 4.594 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 13 -5.379 -37.452 3.094 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 14 -5.630 -41.503 3.652 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 14 -9.510 -40.379 5.090 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 14 -10.021 -40.242 3.162 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 15 -11.686 -43.774 3.158 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 15 -14.850 -41.299 0.807 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 15 -13.817 -41.651 -0.868 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 16 -14.697 -43.119 -1.168 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 16 -14.458 -45.680 -4.525 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 16 -14.564 -47.277 -3.327 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 17 -16.364 -47.779 -6.409 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 17 -15.495 -47.172 -9.747 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 17 -13.959 -48.433 -9.534 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 18 -18.820 -51.053 -9.978 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 18 -18.226 -48.998 -14.350 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 18 -16.591 -50.075 -14.756 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 19 -15.834 -54.271 -14.861 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 19 -12.949 -53.186 -18.337 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 19 -12.291 -54.418 -16.907 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 20 -12.194 -57.806 -18.222 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 20 -7.959 -58.000 -17.645 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 20 -8.486 -58.684 -15.842 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 21 -8.138 -62.503 -17.963 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 21 -5.561 -62.727 -14.045 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 21 -7.160 -63.292 -12.987 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 22 -5.853 -67.438 -13.260 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 22 -4.820 -67.345 -8.979 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 22 -6.774 -67.110 -8.632 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 23 -7.246 -71.078 -8.101 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 23 -9.362 -69.790 -4.351 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 23 -11.000 -69.538 -5.470 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 24 -13.285 -72.648 -6.587 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 24 -15.256 -71.773 -3.160 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 24 -16.287 -71.273 -4.798 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 25 -18.290 -75.158 -4.113 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 25 -21.308 -71.387 -3.865 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 25 -21.486 -71.441 -5.856 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 26 -24.197 -73.723 -7.132 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 26 -24.633 -70.709 -10.417 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 26 -23.419 -71.929 -11.434 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 27 -26.821 -73.479 -12.858 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 27 -24.666 -71.676 -16.554 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 27 -23.691 -73.417 -16.667 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 28 -27.322 -73.900 -19.150 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 28 -25.331 -72.357 -22.822 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 28 -24.305 -74.067 -22.681 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 29 -26.445 -76.335 -25.144 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 29 -24.556 -75.676 -28.662 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 29 -22.825 -75.526 -27.673 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 30 -23.682 -79.982 -28.011 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 30 -23.320 -79.970 -32.434 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 30 -21.392 -79.541 -32.123 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 31 -20.512 -83.575 -31.773 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 31 -17.066 -81.261 -33.885 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 31 -16.520 -82.855 -34.391 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 31 -16.226 -76.823 -32.373 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 31 -17.592 -79.621 -28.980 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 31 -18.391 -78.979 -28.608 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 31 -16.683 -79.436 -28.402 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 31 -17.885 -80.665 -28.860 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 32 -14.881 -86.061 -33.688 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 32 -12.551 -86.384 -37.416 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 32 -11.548 -84.828 -36.662 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 33 -9.114 -88.021 -33.768 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 33 -7.517 -83.730 -35.683 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 33 -5.834 -84.232 -35.567 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 33 -7.881 -79.690 -35.212 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 33 -10.817 -81.986 -32.441 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 33 -11.631 -81.262 -32.554 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 33 -10.274 -81.759 -31.514 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 33 -11.252 -82.988 -32.350 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 34 -2.480 -86.179 -33.379 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 34 -2.759 -81.551 -35.125 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 34 -1.008 -81.401 -35.053 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 34 -5.760 -78.466 -34.407 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 34 -5.569 -81.592 -31.001 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 34 -6.643 -81.754 -30.895 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 34 -5.246 -80.843 -30.272 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 34 -5.046 -82.530 -30.801 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 35 2.457 -81.085 -33.082 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 35 2.053 -77.025 -35.207 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 35 0.976 -76.433 -33.630 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 36 4.970 -75.008 -32.256 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 36 2.389 -71.260 -33.177 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 36 1.490 -71.535 -31.413 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 37 4.349 -68.765 -30.518 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 37 0.245 -66.676 -30.124 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 37 0.144 -67.408 -28.266 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 38 1.973 -63.445 -27.825 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 38 -2.476 -63.370 -26.233 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 38 -1.874 -64.306 -24.573 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 39 -1.428 -60.842 -22.916 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 39 -4.968 -62.177 -20.714 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 39 -3.604 -62.903 -19.445 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 40 -2.570 -59.970 -16.537 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 40 -2.490 -62.412 -13.354 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 40 -0.833 -63.051 -14.271 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 41 0.199 -60.494 -11.502 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 41 0.865 -63.616 -8.559 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 41 2.596 -63.803 -9.540 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 42 4.470 -61.570 -7.307 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 42 6.626 -65.308 -6.511 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 42 7.785 -64.783 -8.052 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 43 10.312 -62.843 -6.128 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 43 11.276 -64.488 -10.902 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 43 12.911 -65.030 -10.547 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 43 10.064 -61.969 -13.891 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 43 7.236 -60.702 -10.531 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 43 6.292 -60.896 -11.037 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 43 7.506 -59.652 -10.653 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 43 7.134 -60.928 -9.471 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 44 13.299 -60.317 -8.435 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 44 14.288 -57.461 -11.121 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 44 14.575 -59.045 -12.306 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 45 11.498 -59.114 -14.349 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 45 14.330 -60.432 -17.752 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 45 13.931 -62.304 -17.173 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 46 11.750 -62.435 -20.330 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 46 13.989 -66.217 -21.341 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 46 12.760 -67.023 -19.986 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 47 11.126 -67.045 -23.920 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 47 13.297 -67.883 -21.338 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 47 13.971 -69.454 -20.926 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 47 17.669 -70.514 -24.515 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 47 16.793 -66.082 -23.696 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 47 16.800 -65.728 -24.728 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 47 17.786 -65.939 -23.261 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 47 16.067 -65.502 -23.124 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 48 12.960 -72.940 -18.191 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 48 13.309 -72.043 -13.835 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 48 11.445 -71.321 -13.857 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 49 9.806 -75.197 -14.598 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 49 6.803 -71.380 -13.196 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 49 5.722 -72.604 -12.541 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 49 5.776 -68.014 -15.655 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 49 8.160 -71.001 -18.207 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 49 8.725 -70.284 -18.791 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 49 7.262 -71.296 -18.741 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 49 8.769 -71.871 -17.990 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 50 2.880 -74.011 -13.316 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 50 0.774 -72.920 -10.558 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 50 -0.058 -72.281 -12.259 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 51 -3.222 -74.246 -12.755 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 51 -5.923 -70.720 -13.024 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 51 -5.319 -70.841 -14.926 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 52 -8.232 -72.822 -15.897 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 52 -7.465 -70.782 -20.054 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 52 -9.144 -71.216 -20.348 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 52 -3.352 -70.766 -21.776 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 52 -3.127 -73.626 -18.242 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 52 -2.345 -73.116 -17.675 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 52 -2.664 -74.386 -18.880 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 52 -3.808 -74.119 -17.544 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 53 -11.414 -72.155 -20.841 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 53 -15.420 -70.797 -21.977 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 53 -15.667 -70.675 -19.997 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 54 -14.442 -66.994 -20.671 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 54 -13.787 -67.483 -17.267 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 54 -14.891 -66.951 -16.005 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 54 -17.011 -71.487 -14.001 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 54 -12.865 -71.858 -16.019 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 54 -13.015 -72.869 -16.410 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 54 -12.349 -71.925 -15.055 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 54 -12.233 -71.302 -16.717 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 55 -18.995 -63.038 -19.364 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 55 -23.218 -62.397 -19.793 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 55 -23.240 -63.054 -17.905 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 56 -22.791 -60.323 -14.667 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 56 -24.396 -62.651 -11.637 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 56 -22.540 -63.394 -11.588 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 57 -22.385 -60.292 -8.927 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 57 -23.052 -63.028 -5.648 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 57 -21.056 -63.147 -5.618 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 58 -20.299 -60.471 -3.072 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 58 -18.416 -63.650 -0.868 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 58 -16.742 -63.252 -1.886 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 59 -15.003 -60.797 0.389 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 59 -12.102 -61.883 -3.315 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 59 -10.787 -61.425 -2.240 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 59 -12.413 -60.911 -7.323 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 59 -16.484 -59.742 -5.536 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 59 -17.118 -60.277 -6.250 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 59 -16.352 -58.712 -5.887 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 59 -16.991 -59.718 -4.567 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 60 -8.342 -59.245 -0.268 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 60 -4.985 -60.842 -2.582 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 60 -5.663 -59.760 -4.121 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 61 -2.961 -57.162 -3.070 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 61 -3.997 -57.618 -7.831 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 61 -2.567 -56.617 -8.054 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 61 -8.078 -57.423 -9.375 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 61 -8.205 -56.536 -4.881 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 61 -8.989 -57.240 -4.625 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 61 -8.628 -55.549 -5.046 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 61 -7.467 -56.496 -4.087 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 62 -1.015 -53.459 -8.622 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 62 -2.764 -53.476 -12.831 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 62 -4.359 -52.572 -12.036 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 63 -4.921 -49.286 -11.215 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 63 -8.056 -48.889 -13.792 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 63 -8.400 -48.012 -12.029 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 64 -5.440 -44.672 -15.096 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 64 -9.290 -44.851 -17.923 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 64 -10.327 -43.862 -16.531 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 65 -9.666 -40.613 -14.901 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 65 -12.634 -40.915 -13.569 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 65 -11.537 -40.676 -11.915 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 66 -13.392 -36.837 -12.035 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 66 -16.378 -38.093 -9.121 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 66 -14.863 -38.103 -7.815 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 67 -14.609 -32.213 -11.698 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 67 -16.698 -30.287 -14.930 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 67 -18.230 -31.294 -14.133 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 68 -19.904 -28.607 -12.026 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 68 -23.601 -29.923 -13.492 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 68 -23.656 -30.930 -11.765 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 69 -25.576 -28.446 -9.786 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 69 -28.339 -31.597 -9.861 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 69 -27.444 -32.174 -8.169 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 70 -30.945 -30.112 -7.370 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 70 -30.600 -33.670 -4.839 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 70 -32.208 -33.236 -4.273 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 70 -27.160 -35.101 -2.562 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 70 -25.770 -31.706 -5.312 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 70 -24.989 -32.226 -5.866 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 70 -25.327 -31.196 -4.453 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 70 -26.243 -30.968 -5.961 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 71 -34.263 -31.559 -2.083 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 71 -33.530 -34.783 0.814 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 71 -32.006 -33.656 1.449 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 72 -33.936 -31.773 4.410 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 72 -29.215 -32.159 4.918 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 72 -29.500 -31.382 6.470 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 72 -25.975 -30.530 3.006 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 72 -29.783 -29.356 0.660 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 72 -29.392 -29.618 -0.332 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 72 -29.621 -28.280 0.819 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 72 -30.865 -29.542 0.661 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 73 -30.656 -28.719 6.691 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 73 -30.950 -28.026 10.451 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 73 -31.158 -29.954 9.967 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 74 -26.596 -26.757 8.598 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 74 -22.935 -29.218 8.938 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 74 -23.555 -28.958 7.055 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 75 -21.741 -26.315 4.638 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 75 -20.752 -25.414 2.252 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 75 -19.362 -26.617 3.038 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 76 -19.346 -31.212 3.041 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 76 -18.234 -33.390 6.615 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 76 -20.025 -34.195 6.241 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 77 -18.035 -36.932 4.231 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 77 -22.988 -37.817 4.961 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 77 -22.624 -39.526 4.762 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 77 -26.150 -35.309 3.326 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 77 -22.162 -33.676 1.735 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 77 -22.356 -32.655 2.028 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 77 -22.475 -33.850 0.714 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 77 -21.117 -33.920 1.860 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 78 -22.758 -42.474 3.081 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 78 -27.342 -41.477 2.724 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 78 -26.964 -40.770 0.893 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 79 -25.901 -42.162 -2.078 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 79 -29.116 -40.475 -4.312 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 79 -27.412 -39.928 -5.202 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 80 -27.191 -41.655 -8.610 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 80 -30.036 -39.167 -10.314 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 80 -28.226 -39.185 -11.163 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 81 -30.111 -41.897 -14.486 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 81 -29.195 -37.840 -16.615 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 81 -27.245 -38.272 -16.541 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 82 -27.149 -39.311 -20.037 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 82 -23.948 -36.285 -20.655 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 82 -22.642 -37.640 -19.980 1.00 0.00 H Number of atoms: 2609 Number of residues: 82 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: 2819 Number of angles built: 5115 Number of dihedrals built: 7647 Number of impropers built: 562 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Building interresidual nonbonded pairs & H-bonds (it may take a while)... Number of electrostatic pairs: 3394202 Number of van der Waals pairs: 301505 Number of H-bonds built: 57 Number of spring restraints: 0 Number of positional restraints: 0 Number of base pairs built: 9 Number of molecules (chains) read: 1 ----------------------------------------------------------------------------- Performing minimization step: 1. Total energy = 86203.7346 kcal/mol (86024.0142 without restraints) Performing minimization step: 2. Total energy = 84781.1533 kcal/mol (84606.0885 without restraints) Performing minimization step: 3. Total energy = 83397.3576 kcal/mol (83226.7940 without restraints) Performing minimization step: 4. Total energy = 82051.0659 kcal/mol (81884.8554 without restraints) Performing minimization step: 5. Total energy = 80741.0493 kcal/mol (80579.0498 without restraints) Performing minimization step: 6. Total energy = 79466.1287 kcal/mol (79308.2039 without restraints) Performing minimization step: 7. Total energy = 78225.1724 kcal/mol (78071.1915 without restraints) Performing minimization step: 8. Total energy = 77017.0938 kcal/mol (76866.9310 without restraints) Performing minimization step: 9. Total energy = 75840.8487 kcal/mol (75694.3833 without restraints) Performing minimization step: 10. Total energy = 74695.4339 kcal/mol (74552.5497 without restraints) Performing minimization step: 11. Total energy = 73579.8844 kcal/mol (73440.4698 without restraints) Performing minimization step: 12. Total energy = 72493.2722 kcal/mol (72357.2198 without restraints) Performing minimization step: 13. Total energy = 71434.7044 kcal/mol (71301.9107 without restraints) Performing minimization step: 14. Total energy = 70403.3211 kcal/mol (70273.6867 without restraints) Performing minimization step: 15. Total energy = 69398.2945 kcal/mol (69271.7233 without restraints) Performing minimization step: 16. Total energy = 68418.8274 kcal/mol (68295.2271 without restraints) Performing minimization step: 17. Total energy = 67464.1511 kcal/mol (67343.4327 without restraints) Performing minimization step: 18. Total energy = 66533.5247 kcal/mol (66415.6024 without restraints) Performing minimization step: 19. Total energy = 65626.2340 kcal/mol (65511.0249 without restraints) Performing minimization step: 20. Total energy = 64741.5898 kcal/mol (64629.0140 without restraints) Performing minimization step: 21. Total energy = 63878.9273 kcal/mol (63768.9077 without restraints) Performing minimization step: 22. Total energy = 63037.6045 kcal/mol (62930.0667 without restraints) Performing minimization step: 23. Total energy = 62217.0020 kcal/mol (62111.8741 without restraints) Performing minimization step: 24. Total energy = 61416.5213 kcal/mol (61313.7339 without restraints) Performing minimization step: 25. Total energy = 60635.5843 kcal/mol (60535.0704 without restraints) Performing minimization step: 26. Total energy = 59873.6325 kcal/mol (59775.3273 without restraints) Performing minimization step: 27. Total energy = 59130.1259 kcal/mol (59033.9666 without restraints) Performing minimization step: 28. Total energy = 58404.5426 kcal/mol (58310.4689 without restraints) Performing minimization step: 29. Total energy = 57696.3782 kcal/mol (57604.3313 without restraints) Performing minimization step: 30. Total energy = 57005.1440 kcal/mol (56915.0673 without restraints) Performing minimization step: 31. Total energy = 56330.3678 kcal/mol (56242.2064 without restraints) Performing minimization step: 32. Total energy = 55671.5924 kcal/mol (55585.2933 without restraints) Performing minimization step: 33. Total energy = 55028.3758 kcal/mol (54943.8875 without restraints) Performing minimization step: 34. Total energy = 54400.2888 kcal/mol (54317.5616 without restraints) Performing minimization step: 35. Total energy = 53786.9173 kcal/mol (53705.9031 without restraints) Performing minimization step: 36. Total energy = 53187.8597 kcal/mol (53108.5118 without restraints) Performing minimization step: 37. Total energy = 52602.7261 kcal/mol (52524.9993 without restraints) Performing minimization step: 38. Total energy = 52031.1399 kcal/mol (51954.9903 without restraints) Performing minimization step: 39. Total energy = 51472.7358 kcal/mol (51398.1210 without restraints) Performing minimization step: 40. Total energy = 50927.1590 kcal/mol (50854.0379 without restraints) Performing minimization step: 41. Total energy = 50394.0665 kcal/mol (50322.3991 without restraints) Performing minimization step: 42. Total energy = 49873.1256 kcal/mol (49802.8732 without restraints) Performing minimization step: 43. Total energy = 49364.0125 kcal/mol (49295.1376 without restraints) Performing minimization step: 44. Total energy = 48866.4149 kcal/mol (48798.8811 without restraints) Performing minimization step: 45. Total energy = 48380.0288 kcal/mol (48313.8007 without restraints) Performing minimization step: 46. Total energy = 47904.5590 kcal/mol (47839.6025 without restraints) Performing minimization step: 47. Total energy = 47439.7197 kcal/mol (47376.0014 without restraints) Performing minimization step: 48. Total energy = 46985.2333 kcal/mol (46922.7209 without restraints) Performing minimization step: 49. Total energy = 46540.8302 kcal/mol (46479.4924 without restraints) Performing minimization step: 50. Total energy = 46106.2488 kcal/mol (46046.0552 without restraints) Performing minimization step: 51. Total energy = 45681.2350 kcal/mol (45622.1561 without restraints) Performing minimization step: 52. Total energy = 45265.5423 kcal/mol (45207.5493 without restraints) Performing minimization step: 53. Total energy = 44858.9311 kcal/mol (44801.9963 without restraints) Performing minimization step: 54. Total energy = 44461.1686 kcal/mol (44405.2647 without restraints) Performing minimization step: 55. Total energy = 44072.0285 kcal/mol (44017.1294 without restraints) Performing minimization step: 56. Total energy = 43691.2917 kcal/mol (43637.3717 without restraints) Performing minimization step: 57. Total energy = 43318.7441 kcal/mol (43265.7785 without restraints) Performing minimization step: 58. Total energy = 42954.1791 kcal/mol (42902.1437 without restraints) Performing minimization step: 59. Total energy = 42597.3944 kcal/mol (42546.2656 without restraints) Performing minimization step: 60. Total energy = 42248.1941 kcal/mol (42197.9493 without restraints) Performing minimization step: 61. Total energy = 41906.3881 kcal/mol (41857.0050 without restraints) Performing minimization step: 62. Total energy = 41571.7910 kcal/mol (41523.2481 without restraints) Performing minimization step: 63. Total energy = 41244.2228 kcal/mol (41196.4992 without restraints) Performing minimization step: 64. Total energy = 40923.5083 kcal/mol (40876.5836 without restraints) Performing minimization step: 65. Total energy = 40609.4773 kcal/mol (40563.3317 without restraints) Performing minimization step: 66. Total energy = 40301.9642 kcal/mol (40256.5784 without restraints) Performing minimization step: 67. Total energy = 40000.8081 kcal/mol (39956.1632 without restraints) Performing minimization step: 68. Total energy = 39705.8516 kcal/mol (39661.9296 without restraints) Performing minimization step: 69. Total energy = 39416.9427 kcal/mol (39373.7256 without restraints) Performing minimization step: 70. Total energy = 39133.9328 kcal/mol (39091.4035 without restraints) Performing minimization step: 71. Total energy = 38856.6776 kcal/mol (38814.8192 without restraints) Performing minimization step: 72. Total energy = 38585.0365 kcal/mol (38543.8327 without restraints) Performing minimization step: 73. Total energy = 38318.8730 kcal/mol (38278.3079 without restraints) Performing minimization step: 74. Total energy = 38058.0533 kcal/mol (38018.1113 without restraints) Performing minimization step: 75. Total energy = 37802.4484 kcal/mol (37763.1144 without restraints) Performing minimization step: 76. Total energy = 37551.9319 kcal/mol (37513.1913 without restraints) Performing minimization step: 77. Total energy = 37306.3810 kcal/mol (37268.2195 without restraints) Performing minimization step: 78. Total energy = 37065.6758 kcal/mol (37028.0794 without restraints) Performing minimization step: 79. Total energy = 36829.7003 kcal/mol (36792.6555 without restraints) Performing minimization step: 80. Total energy = 36598.3406 kcal/mol (36561.8341 without restraints) Performing minimization step: 81. Total energy = 36371.4866 kcal/mol (36335.5055 without restraints) Performing minimization step: 82. Total energy = 36149.0304 kcal/mol (36113.5623 without restraints) Performing minimization step: 83. Total energy = 35930.8671 kcal/mol (35895.8996 without restraints) Performing minimization step: 84. Total energy = 35716.8948 kcal/mol (35682.4162 without restraints) Performing minimization step: 85. Total energy = 35507.0139 kcal/mol (35473.0125 without restraints) Performing minimization step: 86. Total energy = 35301.1273 kcal/mol (35267.5919 without restraints) Performing minimization step: 87. Total energy = 35099.1402 kcal/mol (35066.0597 without restraints) Performing minimization step: 88. Total energy = 34900.9614 kcal/mol (34868.3251 without restraints) Performing minimization step: 89. Total energy = 34706.5007 kcal/mol (34674.2981 without restraints) Performing minimization step: 90. Total energy = 34515.6706 kcal/mol (34483.8916 without restraints) Performing minimization step: 91. Total energy = 34328.3858 kcal/mol (34297.0203 without restraints) Performing minimization step: 92. Total energy = 34144.5634 kcal/mol (34113.6019 without restraints) Performing minimization step: 93. Total energy = 33964.1223 kcal/mol (33933.5553 without restraints) Performing minimization step: 94. Total energy = 33786.9837 kcal/mol (33756.8021 without restraints) Performing minimization step: 95. Total energy = 33613.0704 kcal/mol (33583.2650 without restraints) Performing minimization step: 96. Total energy = 33442.3072 kcal/mol (33412.8693 without restraints) Performing minimization step: 97. Total energy = 33274.6210 kcal/mol (33245.5423 without restraints) Performing minimization step: 98. Total energy = 33109.9406 kcal/mol (33081.2126 without restraints) Performing minimization step: 99. Total energy = 32948.1961 kcal/mol (32919.8107 without restraints) Performing minimization step: 100. Total energy = 32789.3200 kcal/mol (32761.2693 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/5936b356/tmp/CPMA6_refx/CPMA6_refx.pdb ...Done. Performing minimization step: 101. Total energy = 32633.2459 kcal/mol (32605.5221 without restraints) Performing minimization step: 102. Total energy = 32479.9090 kcal/mol (32452.5046 without restraints) Performing minimization step: 103. Total energy = 32329.2463 kcal/mol (32302.1542 without restraints) Performing minimization step: 104. Total energy = 32181.1969 kcal/mol (32154.4097 without restraints) Performing minimization step: 105. Total energy = 32035.7005 kcal/mol (32009.2113 without restraints) Performing minimization step: 106. Total energy = 31892.6986 kcal/mol (31866.5005 without restraints) Performing minimization step: 107. Total energy = 31752.1337 kcal/mol (31726.2202 without restraints) Performing minimization step: 108. Total energy = 31613.9510 kcal/mol (31588.3155 without restraints) Performing minimization step: 109. Total energy = 31478.0958 kcal/mol (31452.7320 without restraints) Performing minimization step: 110. Total energy = 31344.5151 kcal/mol (31319.4168 without restraints) Performing minimization step: 111. Total energy = 31213.1571 kcal/mol (31188.3183 without restraints) Performing minimization step: 112. Total energy = 31083.9716 kcal/mol (31059.3864 without restraints) Performing minimization step: 113. Total energy = 30956.9089 kcal/mol (30932.5715 without restraints) Performing minimization step: 114. Total energy = 30831.9213 kcal/mol (30807.8262 without restraints) Performing minimization step: 115. Total energy = 30708.9616 kcal/mol (30685.1034 without restraints) Performing minimization step: 116. Total energy = 30587.9840 kcal/mol (30564.3571 without restraints) Performing minimization step: 117. Total energy = 30468.9440 kcal/mol (30445.5434 without restraints) Performing minimization step: 118. Total energy = 30351.7980 kcal/mol (30328.6185 without restraints) Performing minimization step: 119. Total energy = 30236.5033 kcal/mol (30213.5400 without restraints) Performing minimization step: 120. Total energy = 30123.0187 kcal/mol (30100.2668 without restraints) Performing minimization step: 121. Total energy = 30011.3030 kcal/mol (29988.7577 without restraints) Performing minimization step: 122. Total energy = 29901.3168 kcal/mol (29878.9735 without restraints) Performing minimization step: 123. Total energy = 29793.0215 kcal/mol (29770.8756 without restraints) Performing minimization step: 124. Total energy = 29686.3793 kcal/mol (29664.4266 without restraints) Performing minimization step: 125. Total energy = 29581.3535 kcal/mol (29559.5895 without restraints) Performing minimization step: 126. Total energy = 29477.9076 kcal/mol (29456.3283 without restraints) Performing minimization step: 127. Total energy = 29376.0072 kcal/mol (29354.6084 without restraints) Performing minimization step: 128. Total energy = 29275.6177 kcal/mol (29254.3954 without restraints) Performing minimization step: 129. Total energy = 29176.7055 kcal/mol (29155.6557 without restraints) Performing minimization step: 130. Total energy = 29079.2379 kcal/mol (29058.3570 without restraints) Performing minimization step: 131. Total energy = 28983.1832 kcal/mol (28962.4674 without restraints) Performing minimization step: 132. Total energy = 28888.5099 kcal/mol (28867.9555 without restraints) Performing minimization step: 133. Total energy = 28795.1879 kcal/mol (28774.7914 without restraints) Performing minimization step: 134. Total energy = 28703.1870 kcal/mol (28682.9449 without restraints) Performing minimization step: 135. Total energy = 28612.4786 kcal/mol (28592.3875 without restraints) Performing minimization step: 136. Total energy = 28523.0339 kcal/mol (28503.0905 without restraints) Performing minimization step: 137. Total energy = 28434.8254 kcal/mol (28415.0266 without restraints) Performing minimization step: 138. Total energy = 28347.8266 kcal/mol (28328.1691 without restraints) Performing minimization step: 139. Total energy = 28262.0100 kcal/mol (28242.4908 without restraints) Performing minimization step: 140. Total energy = 28177.3505 kcal/mol (28157.9665 without restraints) Performing minimization step: 141. Total energy = 28093.8229 kcal/mol (28074.5713 without restraints) Performing minimization step: 142. Total energy = 28011.4024 kcal/mol (27992.2803 without restraints) Performing minimization step: 143. Total energy = 27930.0654 kcal/mol (27911.0699 without restraints) Performing minimization step: 144. Total energy = 27849.7881 kcal/mol (27830.9165 without restraints) Performing minimization step: 145. Total energy = 27770.5476 kcal/mol (27751.7973 without restraints) Performing minimization step: 146. Total energy = 27692.3219 kcal/mol (27673.6902 without restraints) Performing minimization step: 147. Total energy = 27615.0885 kcal/mol (27596.5730 without restraints) Performing minimization step: 148. Total energy = 27538.8265 kcal/mol (27520.4246 without restraints) Performing minimization step: 149. Total energy = 27463.5148 kcal/mol (27445.2240 without restraints) Performing minimization step: 150. Total energy = 27389.1329 kcal/mol (27370.9510 without restraints) Performing minimization step: 151. Total energy = 27315.6614 kcal/mol (27297.5860 without restraints) Performing minimization step: 152. Total energy = 27243.0811 kcal/mol (27225.1100 without restraints) Performing minimization step: 153. Total energy = 27171.3724 kcal/mol (27153.5034 without restraints) Performing minimization step: 154. Total energy = 27100.5168 kcal/mol (27082.7476 without restraints) Performing minimization step: 155. Total energy = 27030.4964 kcal/mol (27012.8250 without restraints) Performing minimization step: 156. Total energy = 26961.2937 kcal/mol (26943.7180 without restraints) Performing minimization step: 157. Total energy = 26892.8915 kcal/mol (26875.4095 without restraints) Performing minimization step: 158. Total energy = 26825.2726 kcal/mol (26807.8824 without restraints) Performing minimization step: 159. Total energy = 26758.4211 kcal/mol (26741.1208 without restraints) Performing minimization step: 160. Total energy = 26692.3205 kcal/mol (26675.1081 without restraints) Performing minimization step: 161. Total energy = 26626.9551 kcal/mol (26609.8289 without restraints) Performing minimization step: 162. Total energy = 26562.3097 kcal/mol (26545.2678 without restraints) Performing minimization step: 163. Total energy = 26498.3690 kcal/mol (26481.4096 without restraints) Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to CPMA6_refx.pdb DONE!