============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/050cbb42/tmp/CPMB1_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/050cbb42/tmp/CPMB1_refx/CPMB1.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 738 'H5' DG A 24 ... failed. Atom erased. Error: recognition of atom ATOM 742 1H2' DG A 24 ... failed. Atom erased. Error: recognition of atom ATOM 743 2H2' DG A 24 ... failed. Atom erased. Error: recognition of atom ATOM 771 'H5' DG A 25 ... failed. Atom erased. Error: recognition of atom ATOM 775 1H2' DG A 25 ... failed. Atom erased. Error: recognition of atom ATOM 776 2H2' DG A 25 ... failed. Atom erased. Error: recognition of atom ATOM 804 'H5' DG A 26 ... failed. Atom erased. Error: recognition of atom ATOM 808 1H2' DG A 26 ... failed. Atom erased. Error: recognition of atom ATOM 809 2H2' DG A 26 ... failed. Atom erased. Error: recognition of atom ATOM 834 'H5' DC A 27 ... failed. Atom erased. Error: recognition of atom ATOM 838 1H2' DC A 27 ... failed. Atom erased. Error: recognition of atom ATOM 839 2H2' DC A 27 ... failed. Atom erased. Error: recognition of atom ATOM 867 'H5' DG A 28 ... failed. Atom erased. Error: recognition of atom ATOM 871 1H2' DG A 28 ... failed. Atom erased. Error: recognition of atom ATOM 872 2H2' DG A 28 ... failed. Atom erased. Error: recognition of atom ATOM 894 C5M DT A 29 ... failed. Atom erased. Error: recognition of atom ATOM 898 HN3 DT A 29 ... failed. Atom erased. Error: recognition of atom ATOM 899 1HM5 DT A 29 ... failed. Atom erased. Error: recognition of atom ATOM 900 2HM5 DT A 29 ... failed. Atom erased. Error: recognition of atom ATOM 901 3HM5 DT A 29 ... failed. Atom erased. Error: recognition of atom ATOM 926 'H5' DC A 30 ... failed. Atom erased. Error: recognition of atom ATOM 930 1H2' DC A 30 ... failed. Atom erased. Error: recognition of atom ATOM 931 2H2' DC A 30 ... failed. Atom erased. Error: recognition of atom ATOM 953 C5M DT A 31 ... failed. Atom erased. Error: recognition of atom ATOM 957 HN3 DT A 31 ... failed. Atom erased. Error: recognition of atom ATOM 958 1HM5 DT A 31 ... failed. Atom erased. Error: recognition of atom ATOM 959 2HM5 DT A 31 ... failed. Atom erased. Error: recognition of atom ATOM 960 3HM5 DT A 31 ... failed. Atom erased. Error: recognition of atom ATOM 982 C5M DT A 32 ... failed. Atom erased. Error: recognition of atom ATOM 986 HN3 DT A 32 ... failed. Atom erased. Error: recognition of atom ATOM 987 1HM5 DT A 32 ... failed. Atom erased. Error: recognition of atom ATOM 988 2HM5 DT A 32 ... failed. Atom erased. Error: recognition of atom ATOM 989 3HM5 DT A 32 ... failed. Atom erased. Error: recognition of atom ATOM 1014 'H5' DC A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1018 1H2' DC A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1019 2H2' DC A 33 ... failed. Atom erased. Error: recognition of atom ATOM 1047 'H5' DG A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1051 1H2' DG A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1052 2H2' DG A 34 ... failed. Atom erased. Error: recognition of atom ATOM 1080 'H5' DG A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1084 1H2' DG A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1085 2H2' DG A 35 ... failed. Atom erased. Error: recognition of atom ATOM 1113 'H5' DG A 36 ... failed. Atom erased. Error: recognition of atom ATOM 1117 1H2' DG A 36 ... failed. Atom erased. Error: recognition of atom ATOM 1118 2H2' DG A 36 ... failed. Atom erased. Error: recognition of atom ATOM 1145 'H5' DA A 37 ... failed. Atom erased. Error: recognition of atom ATOM 1149 1H2' DA A 37 ... failed. Atom erased. Error: recognition of atom ATOM 1150 2H2' DA A 37 ... failed. Atom erased. Error: recognition of atom ATOM 1177 'H5' DA A 38 ... failed. Atom erased. Error: recognition of atom ATOM 1181 1H2' DA A 38 ... failed. Atom erased. Error: recognition of atom ATOM 1182 2H2' DA A 38 ... failed. Atom erased. Error: recognition of atom ATOM 1204 C5M DT A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1208 HN3 DT A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1209 1HM5 DT A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1210 2HM5 DT A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1211 3HM5 DT A 39 ... failed. Atom erased. Error: recognition of atom ATOM 1233 C5M DT A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1237 HN3 DT A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1238 1HM5 DT A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1239 2HM5 DT A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1240 3HM5 DT A 40 ... failed. Atom erased. Error: recognition of atom ATOM 1265 'H5' DC A 41 ... failed. Atom erased. Error: recognition of atom ATOM 1269 1H2' DC A 41 ... failed. Atom erased. Error: recognition of atom ATOM 1270 2H2' DC A 41 ... failed. Atom erased. Error: recognition of atom ATOM 1297 'H5' DA A 42 ... failed. Atom erased. Error: recognition of atom ATOM 1301 1H2' DA A 42 ... failed. Atom erased. Error: recognition of atom ATOM 1302 2H2' DA A 42 ... failed. Atom erased. Error: recognition of atom ATOM 1324 C5M DT A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1328 HN3 DT A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1329 1HM5 DT A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1330 2HM5 DT A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1331 3HM5 DT A 43 ... failed. Atom erased. Error: recognition of atom ATOM 1359 'H5' DG A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1363 1H2' DG A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1364 2H2' DG A 44 ... failed. Atom erased. Error: recognition of atom ATOM 1389 'H5' DC A 45 ... failed. Atom erased. Error: recognition of atom ATOM 1393 1H2' DC A 45 ... failed. Atom erased. Error: recognition of atom ATOM 1394 2H2' DC A 45 ... failed. Atom erased. Error: recognition of atom ATOM 1416 C5M DT A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1420 HN3 DT A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1421 1HM5 DT A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1422 2HM5 DT A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1423 3HM5 DT A 46 ... failed. Atom erased. Error: recognition of atom ATOM 1450 'H5' DA A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1454 1H2' DA A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1455 2H2' DA A 47 ... failed. Atom erased. Error: recognition of atom ATOM 1477 C5M DT A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1481 HN3 DT A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1482 1HM5 DT A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1483 2HM5 DT A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1484 3HM5 DT A 48 ... failed. Atom erased. Error: recognition of atom ATOM 1511 'H5' DA A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1515 1H2' DA A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1516 2H2' DA A 49 ... failed. Atom erased. Error: recognition of atom ATOM 1543 'H5' DA A 50 ... failed. Atom erased. Error: recognition of atom ATOM 1547 1H2' DA A 50 ... failed. Atom erased. Error: recognition of atom ATOM 1548 2H2' DA A 50 ... failed. Atom erased. Error: recognition of atom ATOM 1573 'H5' DC A 51 ... failed. Atom erased. Error: recognition of atom ATOM 1577 1H2' DC A 51 ... failed. Atom erased. Error: recognition of atom ATOM 1578 2H2' DC A 51 ... failed. Atom erased. Error: recognition of atom ATOM 1603 'H5' DC A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1607 1H2' DC A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1608 2H2' DC A 52 ... failed. Atom erased. Error: recognition of atom ATOM 1630 C5M DT A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1634 HN3 DT A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1635 1HM5 DT A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1636 2HM5 DT A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1637 3HM5 DT A 53 ... failed. Atom erased. Error: recognition of atom ATOM 1665 'H5' DG A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1669 1H2' DG A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1670 2H2' DG A 54 ... failed. Atom erased. Error: recognition of atom ATOM 1698 'H5' DG A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1702 1H2' DG A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1703 2H2' DG A 55 ... failed. Atom erased. Error: recognition of atom ATOM 1725 C5M DT A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1729 HN3 DT A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1730 1HM5 DT A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1731 2HM5 DT A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1732 3HM5 DT A 56 ... failed. Atom erased. Error: recognition of atom ATOM 1759 'H5' DA A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1763 1H2' DA A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1764 2H2' DA A 57 ... failed. Atom erased. Error: recognition of atom ATOM 1792 'H5' DG A 58 ... failed. Atom erased. Error: recognition of atom ATOM 1796 1H2' DG A 58 ... failed. Atom erased. Error: recognition of atom ATOM 1797 2H2' DG A 58 ... failed. Atom erased. Error: recognition of atom ATOM 1822 'H5' DC A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1826 1H2' DC A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1827 2H2' DC A 59 ... failed. Atom erased. Error: recognition of atom ATOM 1855 'H5' DG A 60 ... failed. Atom erased. Error: recognition of atom ATOM 1859 1H2' DG A 60 ... failed. Atom erased. Error: recognition of atom ATOM 1860 2H2' DG A 60 ... failed. Atom erased. Error: recognition of atom ATOM 1882 C5M DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1886 HN3 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1887 1HM5 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1888 2HM5 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1889 3HM5 DT A 61 ... failed. Atom erased. Error: recognition of atom ATOM 1914 'H5' DC A 62 ... failed. Atom erased. Error: recognition of atom ATOM 1918 1H2' DC A 62 ... failed. Atom erased. Error: recognition of atom ATOM 1919 2H2' DC A 62 ... failed. Atom erased. Error: recognition of atom ATOM 1947 'H5' DG A 63 ... failed. Atom erased. Error: recognition of atom ATOM 1951 1H2' DG A 63 ... failed. Atom erased. Error: recognition of atom ATOM 1952 2H2' DG A 63 ... failed. Atom erased. Error: recognition of atom ATOM 1979 'H5' DA A 64 ... failed. Atom erased. Error: recognition of atom ATOM 1983 1H2' DA A 64 ... failed. Atom erased. Error: recognition of atom ATOM 1984 2H2' DA A 64 ... failed. Atom erased. Error: recognition of atom ATOM 2009 'H5' DC A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2013 1H2' DC A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2014 2H2' DC A 65 ... failed. Atom erased. Error: recognition of atom ATOM 2042 'H5' DG A 66 ... failed. Atom erased. Error: recognition of atom ATOM 2046 1H2' DG A 66 ... failed. Atom erased. Error: recognition of atom ATOM 2047 2H2' DG A 66 ... failed. Atom erased. Error: recognition of atom ATOM 2074 'H5' DA A 67 ... failed. Atom erased. Error: recognition of atom ATOM 2078 1H2' DA A 67 ... failed. Atom erased. Error: recognition of atom ATOM 2079 2H2' DA A 67 ... failed. Atom erased. Error: recognition of atom ATOM 2107 'H5' DG A 68 ... failed. Atom erased. Error: recognition of atom ATOM 2111 1H2' DG A 68 ... failed. Atom erased. Error: recognition of atom ATOM 2112 2H2' DG A 68 ... failed. Atom erased. Error: recognition of atom ATOM 2140 'H5' DG A 69 ... failed. Atom erased. Error: recognition of atom ATOM 2144 1H2' DG A 69 ... failed. Atom erased. Error: recognition of atom ATOM 2145 2H2' DG A 69 ... failed. Atom erased. Error: recognition of atom ATOM 2167 C5M DT A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2171 HN3 DT A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2172 1HM5 DT A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2173 2HM5 DT A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2174 3HM5 DT A 70 ... failed. Atom erased. Error: recognition of atom ATOM 2199 'H5' DC A 71 ... failed. Atom erased. Error: recognition of atom ATOM 2203 1H2' DC A 71 ... failed. Atom erased. Error: recognition of atom ATOM 2204 2H2' DC A 71 ... failed. Atom erased. Error: recognition of atom ATOM 2226 C5M DT A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2230 HN3 DT A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2231 1HM5 DT A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2232 2HM5 DT A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2233 3HM5 DT A 72 ... failed. Atom erased. Error: recognition of atom ATOM 2260 'H5' DA A 73 ... failed. Atom erased. Error: recognition of atom ATOM 2264 1H2' DA A 73 ... failed. Atom erased. Error: recognition of atom ATOM 2265 2H2' DA A 73 ... failed. Atom erased. Error: recognition of atom ATOM 2293 'H5' DG A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2297 1H2' DG A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2298 2H2' DG A 74 ... failed. Atom erased. Error: recognition of atom ATOM 2325 'H5' DA A 75 ... failed. Atom erased. Error: recognition of atom ATOM 2329 1H2' DA A 75 ... failed. Atom erased. Error: recognition of atom ATOM 2330 2H2' DA A 75 ... failed. Atom erased. Error: recognition of atom ATOM 2357 'H5' DA A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2361 1H2' DA A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2362 2H2' DA A 76 ... failed. Atom erased. Error: recognition of atom ATOM 2384 C5M DT A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2388 HN3 DT A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2389 1HM5 DT A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2390 2HM5 DT A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2391 3HM5 DT A 77 ... failed. Atom erased. Error: recognition of atom ATOM 2418 'H5' DA A 78 ... failed. Atom erased. Error: recognition of atom ATOM 2422 1H2' DA A 78 ... failed. Atom erased. Error: recognition of atom ATOM 2423 2H2' DA A 78 ... failed. Atom erased. Error: recognition of atom ATOM 2448 'H5' DC A 79 ... failed. Atom erased. Error: recognition of atom ATOM 2452 1H2' DC A 79 ... failed. Atom erased. Error: recognition of atom ATOM 2453 2H2' DC A 79 ... failed. Atom erased. Error: recognition of atom ATOM 2478 'H5' DC A 80 ... failed. Atom erased. Error: recognition of atom ATOM 2482 1H2' DC A 80 ... failed. Atom erased. Error: recognition of atom ATOM 2483 2H2' DC A 80 ... failed. Atom erased. Error: recognition of atom ATOM 2510 'H5' DA A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2514 1H2' DA A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2515 2H2' DA A 81 ... failed. Atom erased. Error: recognition of atom ATOM 2543 'H5' DG A 82 ... failed. Atom erased. Error: recognition of atom ATOM 2544 'HO3 DG A 82 ... failed. Atom erased. Error: recognition of atom ATOM 2548 1H2' DG A 82 ... failed. Atom erased. Error: recognition of atom ATOM 2549 2H2' DG A 82 ... failed. Atom erased. Missing atom added: HETATM 1 P DA A 1 1.197 0.565 -2.640 1.00 0.00 P Missing atom added: HETATM 24 H5'2 DA A 1 2.445 -0.548 -0.224 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 1 1.745 0.249 4.002 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 1 -0.207 -0.144 3.824 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 2 0.405 -4.029 4.179 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 2 -3.328 -2.401 6.327 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 2 -3.244 -3.853 7.317 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 2 -6.882 -0.959 4.714 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 2 -3.887 -1.946 1.318 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 2 -4.037 -1.027 0.756 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 2 -4.527 -2.730 0.916 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 2 -2.846 -2.253 1.245 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 3 -3.749 -7.536 7.475 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 3 -7.499 -6.492 9.407 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 3 -8.387 -6.768 7.637 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 4 -9.348 -10.469 7.944 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 4 -13.414 -8.965 7.330 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 4 -13.118 -9.274 5.377 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 5 -14.260 -12.981 4.916 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 5 -17.032 -11.344 2.034 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 5 -15.540 -11.537 0.717 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 6 -17.154 -14.833 -0.451 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 6 -18.342 -13.388 -4.356 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 6 -16.416 -13.726 -4.774 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 7 -17.458 -17.154 -5.796 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 7 -14.171 -14.844 -8.267 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 7 -14.636 -15.902 -9.594 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 7 -10.249 -13.773 -7.102 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 7 -12.315 -15.571 -3.398 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 7 -12.021 -14.770 -2.715 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 7 -11.593 -16.391 -3.315 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 7 -13.301 -15.940 -3.106 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 8 -14.412 -18.975 -11.199 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 8 -11.370 -16.929 -13.565 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 8 -10.016 -17.716 -12.323 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 9 -9.338 -21.005 -14.296 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 9 -5.367 -19.370 -14.680 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 9 -4.971 -20.230 -12.919 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 10 -3.733 -23.797 -14.194 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 10 -0.002 -22.474 -12.423 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 10 -0.719 -23.138 -10.679 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 11 0.909 -26.726 -11.635 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 11 1.470 -25.894 -7.086 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 11 2.664 -27.183 -7.173 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 11 -1.828 -25.131 -4.298 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 11 -3.608 -25.361 -8.513 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 11 -4.137 -24.409 -8.488 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 11 -4.288 -26.162 -8.218 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 11 -3.248 -25.549 -9.525 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 12 3.470 -30.333 -7.156 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 12 1.229 -29.219 -3.110 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 12 2.173 -30.528 -2.409 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 12 -2.890 -28.223 -2.534 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 12 -2.209 -28.987 -7.017 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 12 -2.732 -28.094 -7.372 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 12 -2.909 -29.831 -7.029 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 12 -1.386 -29.207 -7.704 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 13 2.444 -34.021 -1.828 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 13 0.130 -33.279 1.826 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 13 -1.494 -33.752 0.761 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 14 -1.385 -37.575 1.698 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 14 -5.271 -36.760 3.598 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 14 -6.023 -37.110 1.779 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 15 -6.541 -40.994 2.619 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 15 -10.788 -39.852 2.115 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 15 -10.462 -40.086 0.157 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 16 -11.536 -43.860 0.367 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 16 -14.968 -42.327 -1.818 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 16 -13.855 -42.582 -3.459 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 17 -15.056 -46.267 -4.139 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 17 -16.778 -44.492 -7.667 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 17 -15.006 -44.806 -8.539 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 18 -15.830 -48.312 -9.971 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 18 -15.300 -46.250 -13.722 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 18 -13.355 -46.684 -13.564 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 19 -13.550 -50.004 -15.495 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 19 -11.019 -47.829 -18.247 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 19 -9.468 -48.503 -17.180 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 20 -8.837 -51.713 -19.195 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 20 -5.093 -49.744 -20.083 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 20 -4.391 -50.598 -18.418 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 21 -3.039 -53.736 -20.254 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 21 0.842 -52.279 -18.722 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 21 0.394 -53.333 -17.083 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 22 1.893 -56.958 -18.124 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 22 4.490 -56.235 -14.723 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 22 3.016 -56.988 -13.602 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 23 4.353 -60.536 -13.546 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 23 4.462 -60.117 -9.189 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 23 2.607 -60.854 -9.298 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 24 1.001 -64.340 -10.676 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 24 -0.435 -65.766 -6.328 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 24 0.144 -63.975 -5.655 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 25 -1.083 -60.812 -5.688 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 25 -2.675 -61.850 -1.682 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 25 -1.428 -60.307 -1.435 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 26 -3.169 -57.199 -0.859 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 26 -0.630 -55.544 2.141 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 26 0.169 -54.627 0.554 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 27 -1.342 -52.660 -2.333 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 27 2.621 -53.310 -2.630 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 27 1.794 -52.746 -4.360 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 28 3.201 -48.501 -4.194 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 28 5.199 -48.972 -8.058 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 28 3.418 -48.659 -8.910 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 29 4.384 -45.066 -9.400 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 29 2.020 -46.620 -13.091 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 29 2.545 -45.103 -13.810 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 29 -2.063 -48.195 -12.626 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 29 -0.515 -47.215 -8.424 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 29 -0.894 -48.124 -7.956 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 29 -1.232 -46.405 -8.271 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 29 0.436 -46.943 -7.965 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 30 1.891 -41.552 -14.022 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 30 -0.920 -42.627 -17.162 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 30 -2.342 -42.526 -15.761 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 31 -2.752 -38.710 -17.074 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 31 -6.905 -40.852 -16.832 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 31 -7.496 -39.341 -17.511 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 31 -8.220 -42.742 -13.129 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 31 -3.896 -41.433 -12.561 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 31 -3.530 -42.369 -12.152 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 31 -4.160 -40.752 -11.755 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 31 -3.139 -40.982 -13.193 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 32 -8.234 -36.068 -17.373 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 32 -11.180 -38.446 -14.506 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 32 -12.351 -37.197 -14.911 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 32 -10.255 -40.598 -10.927 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 32 -6.448 -38.438 -12.304 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 32 -5.785 -39.305 -12.257 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 32 -6.379 -37.886 -11.362 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 32 -6.124 -37.787 -13.119 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 33 -13.627 -34.017 -14.212 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 33 -16.210 -36.044 -11.286 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 33 -14.824 -35.559 -9.929 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 34 -16.556 -32.206 -9.023 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 34 -17.302 -34.338 -5.312 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 34 -15.488 -33.712 -4.752 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 35 -16.722 -30.395 -3.086 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 35 -15.296 -32.239 0.506 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 35 -13.511 -31.450 0.073 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 36 -13.960 -28.209 2.041 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 36 -10.767 -29.839 4.431 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 36 -9.521 -28.951 3.145 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 37 -9.211 -25.628 5.090 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 37 -5.096 -26.891 5.471 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 37 -4.789 -25.986 3.714 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 38 -3.899 -22.320 5.056 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 38 -0.053 -23.277 3.287 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 38 -0.821 -22.670 1.544 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 39 0.462 -18.948 2.561 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 39 1.175 -19.728 -1.983 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 39 2.243 -18.333 -1.880 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 39 -2.016 -20.766 -4.820 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 39 -3.863 -20.641 -0.626 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 39 -4.328 -21.626 -0.652 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 39 -4.592 -19.888 -0.932 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 39 -3.528 -20.426 0.388 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 40 2.726 -15.099 -1.884 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 40 0.619 -16.367 -5.962 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 40 1.436 -14.963 -6.638 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 40 -3.309 -17.897 -6.573 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 40 -2.846 -16.901 -2.115 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 40 -3.265 -17.835 -1.730 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 40 -3.643 -16.150 -2.161 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 40 -2.076 -16.550 -1.423 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 41 1.312 -11.505 -7.196 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 41 -1.105 -12.345 -10.720 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 41 -2.684 -11.884 -9.584 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 42 -2.665 -8.075 -10.597 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 42 -6.323 -9.214 -12.698 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 42 -7.221 -8.987 -10.926 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 43 -7.759 -5.192 -11.836 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 43 -11.243 -7.289 -9.490 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 43 -12.235 -5.959 -10.074 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 43 -11.121 -9.103 -5.624 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 43 -6.886 -7.578 -6.596 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 43 -6.369 -8.501 -6.326 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 43 -6.867 -6.895 -5.742 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 43 -6.366 -7.111 -7.435 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 44 -13.366 -2.701 -9.613 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 44 -16.630 -4.610 -7.446 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 44 -15.612 -4.249 -5.764 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 45 -16.774 -0.510 -4.790 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 45 -18.030 -2.516 -1.168 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 45 -16.150 -2.285 -0.528 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 46 -17.734 1.082 1.062 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 46 -15.019 -0.877 4.259 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 46 -15.716 0.365 5.293 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 46 -10.884 -2.126 3.315 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 46 -12.537 -0.269 -0.487 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 46 -12.345 -1.105 -1.151 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 46 -11.707 0.431 -0.517 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 46 -13.456 0.231 -0.775 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 47 -15.596 3.457 6.768 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 47 -12.486 1.417 9.474 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 47 -11.119 1.981 8.128 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 48 -10.894 5.764 10.279 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 48 -6.930 4.703 8.370 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 48 -6.166 5.726 9.581 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 48 -5.307 4.235 4.608 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 48 -9.881 4.762 4.212 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 48 -10.063 3.831 3.676 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 48 -9.777 5.579 3.495 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 48 -10.723 4.970 4.872 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 49 -5.570 9.267 10.794 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 49 -4.588 9.397 6.527 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 49 -5.237 11.180 7.155 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 50 -1.428 13.212 10.507 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 50 -2.313 17.424 10.214 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 50 -3.796 17.038 11.498 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 51 1.086 15.210 14.171 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 51 4.724 18.042 13.350 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 51 3.597 19.560 14.001 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 52 5.425 18.302 18.167 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 52 3.878 19.111 22.274 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 52 1.943 18.632 22.115 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 53 3.586 15.895 24.678 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 53 0.640 18.662 27.014 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 53 1.061 17.633 28.378 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 53 -3.213 19.903 25.082 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 53 -0.991 17.047 22.254 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 53 -0.989 17.677 21.367 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 53 -1.848 16.373 22.221 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 53 -0.072 16.462 22.287 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 54 0.319 14.826 30.276 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 54 -3.330 17.042 31.743 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 54 -4.407 16.146 30.317 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 55 -5.664 12.987 29.918 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 55 -9.045 16.255 31.207 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 55 -9.790 15.350 29.587 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 56 -11.238 12.276 32.266 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 56 -11.841 12.990 27.300 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 56 -13.580 13.220 27.436 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 56 -10.122 11.104 23.828 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 56 -7.438 10.176 27.418 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 56 -6.496 10.493 26.965 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 56 -7.563 9.099 27.262 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 56 -7.399 10.374 28.492 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 57 -14.876 11.696 26.959 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 57 -17.344 7.914 24.627 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 57 -15.744 6.715 24.649 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 58 -16.121 6.245 30.277 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 58 -11.611 6.022 29.144 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 58 -12.261 7.912 29.126 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 59 -9.193 8.287 32.566 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 59 -8.341 3.121 33.098 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 59 -9.093 2.991 31.250 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 60 -8.752 3.019 29.523 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 60 -9.555 1.294 25.440 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 60 -7.834 0.293 25.625 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 61 -7.622 -2.774 27.642 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 61 -6.010 -3.794 24.820 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 61 -6.545 -5.466 24.716 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 61 -2.191 -2.206 25.805 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 61 -4.719 -0.473 29.132 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 61 -4.309 0.534 29.064 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 61 -4.179 -1.035 29.895 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 61 -5.772 -0.418 29.401 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 62 -6.093 -8.659 26.558 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 62 -1.583 -8.553 25.475 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 62 -1.274 -7.821 27.309 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 63 -2.942 -10.436 31.130 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 63 1.149 -9.268 31.331 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 63 0.688 -10.633 32.717 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 64 -0.061 -12.961 33.356 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 64 1.677 -13.922 37.115 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 64 3.464 -13.567 36.292 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 65 -0.443 -9.027 38.205 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 65 0.445 -8.589 42.771 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 65 2.071 -7.492 42.386 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 66 -0.612 -4.967 38.489 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 66 1.213 -4.204 37.068 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 66 0.625 -5.954 36.301 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 67 -0.808 -0.244 34.961 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 67 2.551 -2.192 33.379 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 67 0.842 -2.546 32.403 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 68 0.506 3.228 33.305 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 68 -0.858 5.181 35.757 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 68 0.828 6.167 35.329 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 69 -1.113 6.321 29.043 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 69 2.540 8.088 27.064 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 69 3.417 9.150 28.513 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 70 4.248 3.961 26.988 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 70 7.869 6.255 29.527 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 70 9.218 5.507 28.680 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 70 8.649 8.806 32.735 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 70 4.640 6.647 33.392 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 70 4.028 7.529 33.608 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 70 4.998 6.227 34.339 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 70 4.014 5.900 32.893 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 71 10.248 1.212 26.111 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 71 10.472 -3.392 25.211 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 71 8.475 -3.386 25.134 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 72 9.745 -1.989 20.796 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 72 5.968 -4.628 21.042 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 72 6.246 -5.031 19.352 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 72 2.252 -4.769 22.728 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 72 4.679 -1.688 25.112 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 72 4.690 -2.193 26.083 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 72 3.836 -0.986 25.092 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 72 5.607 -1.117 25.004 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 73 4.483 -2.371 17.849 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 73 1.514 -5.360 16.261 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 73 0.391 -3.998 17.198 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 74 0.288 -3.361 12.464 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 74 -3.828 -5.557 13.260 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 74 -4.524 -3.867 14.070 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 75 -6.511 -1.893 11.505 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 75 -9.501 -0.325 14.306 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 75 -8.220 1.201 14.471 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 76 -5.356 2.463 11.454 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 76 -4.611 4.466 15.714 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 76 -2.994 4.957 14.646 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DT A 77 -7.632 7.277 13.456 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 77 -10.009 6.938 15.652 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 77 -11.172 7.903 14.751 1.00 0.00 H Missing atom added: HETATM 28 H3 DT A 77 -10.072 7.742 19.726 1.00 0.00 H Missing atom added: HETATM 19 C7 DT A 77 -5.630 7.451 18.493 1.00 0.00 C Missing atom added: HETATM 30 H72 DT A 77 -5.314 6.805 19.308 1.00 0.00 H Missing atom added: HETATM 29 H71 DT A 77 -5.448 8.492 18.757 1.00 0.00 H Missing atom added: HETATM 31 H73 DT A 77 -5.076 7.202 17.591 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 78 -12.325 11.663 14.141 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 78 -15.355 12.121 16.964 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 78 -13.826 12.706 18.111 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 79 -14.373 16.464 17.180 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 79 -15.444 16.775 21.333 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 79 -13.478 16.896 21.676 1.00 0.00 H Missing atom added: HETATM 22 H5'2 DC A 80 -14.096 20.734 21.882 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 80 -13.134 21.427 25.851 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 80 -11.275 21.608 25.139 1.00 0.00 H Missing atom added: HETATM 24 H5'2 DA A 81 -11.647 25.627 24.394 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 81 -8.573 25.722 27.568 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 81 -7.262 25.354 26.104 1.00 0.00 H Missing atom added: HETATM 25 H5'2 DG A 82 -5.730 27.798 24.475 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 82 -2.689 27.434 26.802 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 82 -2.116 26.768 25.006 1.00 0.00 H Number of atoms: 2607 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: 2815 Number of angles built: 5110 Number of dihedrals built: 7639 Number of impropers built: 560 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Building interresidual nonbonded pairs & H-bonds (it may take a while)... Number of electrostatic pairs: 3388996 Number of van der Waals pairs: 315757 Number of H-bonds built: 66 Number of spring restraints: 0 Number of positional restraints: 0 Number of base pairs built: 18 Number of molecules (chains) read: 1 ----------------------------------------------------------------------------- Performing minimization step: 1. Total energy = 225888.1295 kcal/mol (225108.8241 without restraints) Performing minimization step: 2. Total energy = 219610.4513 kcal/mol (218872.4958 without restraints) Performing minimization step: 3. Total energy = 213668.1008 kcal/mol (212967.9981 without restraints) Performing minimization step: 4. Total energy = 208033.1495 kcal/mol (207367.7976 without restraints) Performing minimization step: 5. Total energy = 202680.7920 kcal/mol (202047.4320 without restraints) Performing minimization step: 6. Total energy = 197588.9361 kcal/mol (196985.1073 without restraints) Performing minimization step: 7. Total energy = 192737.8505 kcal/mol (192161.3519 without restraints) Performing minimization step: 8. Total energy = 188109.8618 kcal/mol (187558.7194 without restraints) Performing minimization step: 9. Total energy = 183689.0952 kcal/mol (183161.5330 without restraints) Performing minimization step: 10. Total energy = 179461.2503 kcal/mol (178955.6661 without restraints) Performing minimization step: 11. Total energy = 175413.4089 kcal/mol (174928.3534 without restraints) Performing minimization step: 12. Total energy = 171533.8694 kcal/mol (171068.0279 without restraints) Performing minimization step: 13. Total energy = 167812.0033 kcal/mol (167364.1802 without restraints) Performing minimization step: 14. Total energy = 164238.1319 kcal/mol (163807.2367 without restraints) Performing minimization step: 15. Total energy = 160803.4182 kcal/mol (160388.4542 without restraints) Performing minimization step: 16. Total energy = 157499.7736 kcal/mol (157099.8273 without restraints) Performing minimization step: 17. Total energy = 154319.7771 kcal/mol (153934.0093 without restraints) Performing minimization step: 18. Total energy = 151256.6034 kcal/mol (150884.2415 without restraints) Performing minimization step: 19. Total energy = 148303.9613 kcal/mol (147944.2920 without restraints) Performing minimization step: 20. Total energy = 145456.0390 kcal/mol (145108.4030 without restraints) Performing minimization step: 21. Total energy = 142707.4559 kcal/mol (142371.2421 without restraints) Performing minimization step: 22. Total energy = 140053.2199 kcal/mol (139727.8605 without restraints) Performing minimization step: 23. Total energy = 137488.6911 kcal/mol (137173.6580 without restraints) Performing minimization step: 24. Total energy = 135009.5480 kcal/mol (134704.3489 without restraints) Performing minimization step: 25. Total energy = 132611.7584 kcal/mol (132315.9335 without restraints) Performing minimization step: 26. Total energy = 130291.5534 kcal/mol (130004.6726 without restraints) Performing minimization step: 27. Total energy = 128045.4043 kcal/mol (127767.0644 without restraints) Performing minimization step: 28. Total energy = 125870.0017 kcal/mol (125599.8244 without restraints) Performing minimization step: 29. Total energy = 123762.2373 kcal/mol (123499.8670 without restraints) Performing minimization step: 30. Total energy = 121719.1873 kcal/mol (121464.2893 without restraints) Performing minimization step: 31. Total energy = 119738.0978 kcal/mol (119490.3565 without restraints) Performing minimization step: 32. Total energy = 117816.3714 kcal/mol (117575.4891 without restraints) Performing minimization step: 33. Total energy = 115951.5550 kcal/mol (115717.2501 without restraints) Performing minimization step: 34. Total energy = 114141.3290 kcal/mol (113913.3354 without restraints) Performing minimization step: 35. Total energy = 112383.4984 kcal/mol (112161.5639 without restraints) Performing minimization step: 36. Total energy = 110675.9827 kcal/mol (110459.8683 without restraints) Performing minimization step: 37. Total energy = 109016.8089 kcal/mol (108806.2878 without restraints) Performing minimization step: 38. Total energy = 107404.1041 kcal/mol (107198.9609 without restraints) Performing minimization step: 39. Total energy = 105836.0885 kcal/mol (105636.1183 without restraints) Performing minimization step: 40. Total energy = 104311.0694 kcal/mol (104116.0775 without restraints) Performing minimization step: 41. Total energy = 102827.4366 kcal/mol (102637.2374 without restraints) Performing minimization step: 42. Total energy = 101383.6550 kcal/mol (101198.0717 without restraints) Performing minimization step: 43. Total energy = 99978.2630 kcal/mol (99797.1273 without restraints) Performing minimization step: 44. Total energy = 98609.8662 kcal/mol (98433.0174 without restraints) Performing minimization step: 45. Total energy = 97277.1343 kcal/mol (97104.4189 without restraints) Performing minimization step: 46. Total energy = 95978.7967 kcal/mol (95810.0681 without restraints) Performing minimization step: 47. Total energy = 94713.6406 kcal/mol (94548.7589 without restraints) Performing minimization step: 48. Total energy = 93480.5058 kcal/mol (93319.3373 without restraints) Performing minimization step: 49. Total energy = 92278.2838 kcal/mol (92120.7003 without restraints) Performing minimization step: 50. Total energy = 91105.9139 kcal/mol (90951.7932 without restraints) Performing minimization step: 51. Total energy = 89962.3811 kcal/mol (89811.6058 without restraints) Performing minimization step: 52. Total energy = 88846.7133 kcal/mol (88699.1713 without restraints) Performing minimization step: 53. Total energy = 87757.9800 kcal/mol (87613.5638 without restraints) Performing minimization step: 54. Total energy = 86695.2897 kcal/mol (86553.8962 without restraints) Performing minimization step: 55. Total energy = 85657.7873 kcal/mol (85519.3177 without restraints) Performing minimization step: 56. Total energy = 84644.6536 kcal/mol (84509.0133 without restraints) Performing minimization step: 57. Total energy = 83655.1030 kcal/mol (83522.2011 without restraints) Performing minimization step: 58. Total energy = 82688.3815 kcal/mol (82558.1309 without restraints) Performing minimization step: 59. Total energy = 81743.7654 kcal/mol (81616.0825 without restraints) Performing minimization step: 60. Total energy = 80820.5610 kcal/mol (80695.3654 without restraints) Performing minimization step: 61. Total energy = 79918.1011 kcal/mol (79795.3157 without restraints) Performing minimization step: 62. Total energy = 79035.7453 kcal/mol (78915.2961 without restraints) Performing minimization step: 63. Total energy = 78172.8781 kcal/mol (78054.6939 without restraints) Performing minimization step: 64. Total energy = 77328.9087 kcal/mol (77212.9210 without restraints) Performing minimization step: 65. Total energy = 76503.2685 kcal/mol (76389.4116 without restraints) Performing minimization step: 66. Total energy = 75695.4109 kcal/mol (75583.6215 without restraints) Performing minimization step: 67. Total energy = 74904.8102 kcal/mol (74795.0275 without restraints) Performing minimization step: 68. Total energy = 74130.9608 kcal/mol (74023.1261 without restraints) Performing minimization step: 69. Total energy = 73373.3759 kcal/mol (73267.4331 without restraints) Performing minimization step: 70. Total energy = 72631.5871 kcal/mol (72527.4817 without restraints) Performing minimization step: 71. Total energy = 71905.1434 kcal/mol (71802.8233 without restraints) Performing minimization step: 72. Total energy = 71193.6101 kcal/mol (71093.0250 without restraints) Performing minimization step: 73. Total energy = 70496.5688 kcal/mol (70397.6701 without restraints) Performing minimization step: 74. Total energy = 69813.6164 kcal/mol (69716.3575 without restraints) Performing minimization step: 75. Total energy = 69144.3636 kcal/mol (69048.6994 without restraints) Performing minimization step: 76. Total energy = 68488.4359 kcal/mol (68394.3229 without restraints) Performing minimization step: 77. Total energy = 67845.4716 kcal/mol (67752.8680 without restraints) Performing minimization step: 78. Total energy = 67215.1222 kcal/mol (67123.9874 without restraints) Performing minimization step: 79. Total energy = 66597.0509 kcal/mol (66507.3460 without restraints) Performing minimization step: 80. Total energy = 65990.9325 kcal/mol (65902.6198 without restraints) Performing minimization step: 81. Total energy = 65396.4544 kcal/mol (65309.4977 without restraints) Performing minimization step: 82. Total energy = 64813.3128 kcal/mol (64727.6766 without restraints) Performing minimization step: 83. Total energy = 64241.2151 kcal/mol (64156.8656 without restraints) Performing minimization step: 84. Total energy = 63679.8785 kcal/mol (63596.7830 without restraints) Performing minimization step: 85. Total energy = 63129.0298 kcal/mol (63047.1565 without restraints) Performing minimization step: 86. Total energy = 62588.4046 kcal/mol (62507.7228 without restraints) Performing minimization step: 87. Total energy = 62057.7473 kcal/mol (61978.2273 without restraints) Performing minimization step: 88. Total energy = 61536.8106 kcal/mol (61458.4238 without restraints) Performing minimization step: 89. Total energy = 61025.3552 kcal/mol (60948.0737 without restraints) Performing minimization step: 90. Total energy = 60523.1496 kcal/mol (60446.9465 without restraints) Performing minimization step: 91. Total energy = 60029.9693 kcal/mol (59954.8186 without restraints) Performing minimization step: 92. Total energy = 59545.5971 kcal/mol (59471.4735 without restraints) Performing minimization step: 93. Total energy = 59069.8228 kcal/mol (58996.7022 without restraints) Performing minimization step: 94. Total energy = 58602.4428 kcal/mol (58530.3013 without restraints) Performing minimization step: 95. Total energy = 58143.2592 kcal/mol (58072.0737 without restraints) Performing minimization step: 96. Total energy = 57692.0803 kcal/mol (57621.8286 without restraints) Performing minimization step: 97. Total energy = 57248.7204 kcal/mol (57179.3810 without restraints) Performing minimization step: 98. Total energy = 56812.9992 kcal/mol (56744.5510 without restraints) Performing minimization step: 99. Total energy = 56384.7418 kcal/mol (56317.1646 without restraints) Performing minimization step: 100. Total energy = 55963.7784 kcal/mol (55897.0525 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/050cbb42/tmp/CPMB1_refx/CPMB1_refx.pdb ...Done. Performing minimization step: 101. Total energy = 55549.9450 kcal/mol (55484.0511 without restraints) Performing minimization step: 102. Total energy = 55143.0813 kcal/mol (55078.0009 without restraints) Performing minimization step: 103. Total energy = 54743.0317 kcal/mol (54678.7467 without restraints) Performing minimization step: 104. Total energy = 54349.6457 kcal/mol (54286.1386 without restraints) Performing minimization step: 105. Total energy = 53962.7765 kcal/mol (53900.0303 without restraints) Performing minimization step: 106. Total energy = 53582.2820 kcal/mol (53520.2800 without restraints) Performing minimization step: 107. Total energy = 53208.0228 kcal/mol (53146.7489 without restraints) Performing minimization step: 108. Total energy = 52839.8650 kcal/mol (52779.3035 without restraints) Performing minimization step: 109. Total energy = 52477.6776 kcal/mol (52417.8133 without restraints) Performing minimization step: 110. Total energy = 52121.3326 kcal/mol (52062.1507 without restraints) Performing minimization step: 111. Total energy = 51770.7062 kcal/mol (51712.1922 without restraints) Performing minimization step: 112. Total energy = 51425.6778 kcal/mol (51367.8177 without restraints) Performing minimization step: 113. Total energy = 51086.1303 kcal/mol (51028.9104 without restraints) Performing minimization step: 114. Total energy = 50751.9491 kcal/mol (50695.3560 without restraints) Performing minimization step: 115. Total energy = 50423.0228 kcal/mol (50367.0436 without restraints) Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to CPMB1_refx.pdb DONE!