============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/ade9e976/tmp/sequence_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/ade9e976/tmp/sequence_refx/sequence.pdb ============================================================================= Error: recognition of atom ATOM 27 1H2' DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 32 2H2' DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 33 OP3 DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 34 3HOP DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 59 1H2' DU A 2 ... failed. Atom erased. Error: recognition of atom ATOM 63 2H2' DU A 2 ... failed. Atom erased. Error: recognition of atom ATOM 88 1H2' DC A 3 ... failed. Atom erased. Error: recognition of atom ATOM 93 2H2' DC A 3 ... failed. Atom erased. Error: recognition of atom ATOM 121 1H2' DG A 4 ... failed. Atom erased. Error: recognition of atom ATOM 126 2H2' DG A 4 ... failed. Atom erased. Error: recognition of atom ATOM 151 1H2' DU A 5 ... failed. Atom erased. Error: recognition of atom ATOM 155 2H2' DU A 5 ... failed. Atom erased. Error: recognition of atom ATOM 182 1H2' DA A 6 ... failed. Atom erased. Error: recognition of atom ATOM 187 2H2' DA A 6 ... failed. Atom erased. Error: recognition of atom ATOM 212 1H2' DU A 7 ... failed. Atom erased. Error: recognition of atom ATOM 216 2H2' DU A 7 ... failed. Atom erased. Error: recognition of atom ATOM 243 1H2' DA A 8 ... failed. Atom erased. Error: recognition of atom ATOM 248 2H2' DA A 8 ... failed. Atom erased. Error: recognition of atom ATOM 276 1H2' DG A 9 ... failed. Atom erased. Error: recognition of atom ATOM 281 2H2' DG A 9 ... failed. Atom erased. Error: recognition of atom ATOM 306 1H2' DC A 10 ... failed. Atom erased. Error: recognition of atom ATOM 311 2H2' DC A 10 ... failed. Atom erased. Error: recognition of atom ATOM 336 1H2' DU A 11 ... failed. Atom erased. Error: recognition of atom ATOM 340 2H2' DU A 11 ... failed. Atom erased. Error: recognition of atom ATOM 367 1H2' DA A 12 ... failed. Atom erased. Error: recognition of atom ATOM 372 2H2' DA A 12 ... failed. Atom erased. Error: recognition of atom ATOM 400 1H2' DG A 13 ... failed. Atom erased. Error: recognition of atom ATOM 429 1H2' DC A 14 ... failed. Atom erased. Error: recognition of atom ATOM 434 2H2' DC A 14 ... failed. Atom erased. Error: recognition of atom ATOM 459 1H2' DU A 15 ... failed. Atom erased. Error: recognition of atom ATOM 463 2H2' DU A 15 ... failed. Atom erased. Error: recognition of atom ATOM 490 1H2' DA A 16 ... failed. Atom erased. Error: recognition of atom ATOM 495 2H2' DA A 16 ... failed. Atom erased. Error: recognition of atom ATOM 523 1H2' DG A 17 ... failed. Atom erased. Error: recognition of atom ATOM 528 2H2' DG A 17 ... failed. Atom erased. Error: recognition of atom ATOM 553 1H2' DC A 18 ... failed. Atom erased. Error: recognition of atom ATOM 558 2H2' DC A 18 ... failed. Atom erased. Error: recognition of atom ATOM 583 1H2' DU A 19 ... failed. Atom erased. Error: recognition of atom ATOM 587 2H2' DU A 19 ... failed. Atom erased. Error: recognition of atom ATOM 614 1H2' DA A 20 ... failed. Atom erased. Error: recognition of atom ATOM 619 2H2' DA A 20 ... failed. Atom erased. Error: recognition of atom ATOM 647 1H2' DG A 21 ... failed. Atom erased. Error: recognition of atom ATOM 652 2H2' DG A 21 ... failed. Atom erased. Error: recognition of atom ATOM 677 1H2' DC A 22 ... failed. Atom erased. Error: recognition of atom ATOM 682 2H2' DC A 22 ... failed. Atom erased. Error: recognition of atom ATOM 707 1H2' DU A 23 ... failed. Atom erased. Error: recognition of atom ATOM 711 2H2' DU A 23 ... failed. Atom erased. Error: recognition of atom ATOM 738 1H2' DA A 24 ... failed. Atom erased. Error: recognition of atom ATOM 743 2H2' DA A 24 ... failed. Atom erased. Missing atom added: HETATM 11 H2'2 DA A 1 2.244 3.515 4.101 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 1 4.172 3.532 3.569 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U A 2 9.996 6.900 1.828 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DC A 3 14.849 8.996 -0.058 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 3 15.216 8.199 -1.854 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 4 19.433 8.283 -4.968 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 4 18.940 7.627 -6.791 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U A 5 19.182 6.283 -13.045 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA A 6 19.111 4.288 -18.210 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 6 17.319 5.175 -18.216 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U A 7 12.956 5.003 -22.005 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA A 8 8.041 5.053 -23.791 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 8 7.748 6.956 -23.253 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 9 2.627 8.791 -23.141 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 9 3.516 10.560 -22.863 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 10 -0.217 13.902 -21.075 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 10 1.122 15.356 -21.373 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U A 11 2.465 21.091 -20.961 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA A 12 3.222 26.099 -18.531 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 12 4.323 25.992 -20.197 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 13 7.809 29.666 -19.789 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 13 8.846 29.249 -21.446 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 14 13.515 31.323 -23.556 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 14 12.969 30.594 -25.336 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U A 15 15.574 30.346 -30.397 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA A 16 17.610 29.144 -34.522 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 16 16.104 28.825 -35.798 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 17 15.211 26.111 -40.409 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 17 13.479 27.109 -40.382 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 18 10.351 24.558 -44.045 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 18 9.062 26.085 -44.099 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U A 19 3.926 27.392 -45.257 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA A 20 -1.562 28.231 -45.474 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 20 -0.891 30.109 -45.336 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 21 -5.023 33.317 -43.996 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 21 -3.659 34.714 -44.430 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 22 -5.054 39.453 -42.473 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 22 -4.130 40.344 -44.006 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U A 23 -2.437 45.558 -43.628 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA A 24 0.747 49.892 -42.192 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 24 1.133 49.496 -44.113 1.00 0.00 H Missing atom added: HETATM 2 OP3 DA A 1 0.001 1.126 -2.377 1.00 0.00 O1- Number of atoms: 736 Number of residues: 24 Building intraresidual bonds... Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. A 2 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. A 5 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. A 7 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. A 11 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. A 15 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. A 19 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. A 23 Building intraresidual angles... Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. A 2 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. A 2 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. A 2 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. A 5 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. A 5 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. A 5 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. A 7 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. A 7 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. A 7 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. A 11 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. A 11 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. A 11 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. A 15 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. A 15 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. A 15 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. A 19 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. A 19 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. A 19 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. A 23 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. A 23 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. A 23 Building intraresidual dihedrals... Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. A 2 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. A 2 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. A 2 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. A 2 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. A 2 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. A 2 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. A 5 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. A 5 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. A 5 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. A 5 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. A 5 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. A 5 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. A 7 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. A 7 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. A 7 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. A 7 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. A 7 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. A 7 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. A 11 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. A 11 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. A 11 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. A 11 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. A 11 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. A 11 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. A 15 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. A 15 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. A 15 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. A 15 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. A 15 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. A 15 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. A 19 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. A 19 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. A 19 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. A 19 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. A 19 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. A 19 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. A 23 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. A 23 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. A 23 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. A 23 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. A 23 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. A 23 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: 795 Number of angles built: 1433 Number of dihedrals built: 2132 Number of impropers built: 161 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- Error: recognition of atom ATOM 23 1H2' DA S 1 ... failed. Atom erased. Error: recognition of atom ATOM 24 2H2' DA S 1 ... failed. Atom erased. Error: recognition of atom ATOM 33 OP3 DA S 1 ... failed. Atom erased. Error: recognition of atom ATOM 34 3HOP DA S 1 ... failed. Atom erased. Error: recognition of atom ATOM 55 1H2' DC S 2 ... failed. Atom erased. Error: recognition of atom ATOM 56 2H2' DC S 2 ... failed. Atom erased. Error: recognition of atom ATOM 88 1H2' DG S 3 ... failed. Atom erased. Error: recognition of atom ATOM 89 2H2' DG S 3 ... failed. Atom erased. Error: recognition of atom ATOM 119 1H2' DT S 4 ... failed. Atom erased. Error: recognition of atom ATOM 120 2H2' DT S 4 ... failed. Atom erased. Error: recognition of atom ATOM 152 1H2' DA S 5 ... failed. Atom erased. Error: recognition of atom ATOM 153 2H2' DA S 5 ... failed. Atom erased. Error: recognition of atom ATOM 182 1H2' DU S 6 ... failed. Atom erased. Error: recognition of atom ATOM 183 2H2' DU S 6 ... failed. Atom erased. Error: recognition of atom ATOM 211 1H2' DC S 7 ... failed. Atom erased. Error: recognition of atom ATOM 212 2H2' DC S 7 ... failed. Atom erased. Error: recognition of atom ATOM 244 1H2' DG S 8 ... failed. Atom erased. Error: recognition of atom ATOM 245 2H2' DG S 8 ... failed. Atom erased. Error: recognition of atom ATOM 274 1H2' DU S 9 ... failed. Atom erased. Error: recognition of atom ATOM 275 2H2' DU S 9 ... failed. Atom erased. Error: recognition of atom ATOM 305 1H2' DA S 10 ... failed. Atom erased. Error: recognition of atom ATOM 306 2H2' DA S 10 ... failed. Atom erased. Error: recognition of atom ATOM 335 1H2' DU S 11 ... failed. Atom erased. Error: recognition of atom ATOM 336 2H2' DU S 11 ... failed. Atom erased. Error: recognition of atom ATOM 366 1H2' DA S 12 ... failed. Atom erased. Error: recognition of atom ATOM 367 2H2' DA S 12 ... failed. Atom erased. Error: recognition of atom ATOM 399 1H2' DG S 13 ... failed. Atom erased. Error: recognition of atom ATOM 400 2H2' DG S 13 ... failed. Atom erased. Error: recognition of atom ATOM 429 1H2' DC S 14 ... failed. Atom erased. Error: recognition of atom ATOM 430 2H2' DC S 14 ... failed. Atom erased. Error: recognition of atom ATOM 459 1H2' DU S 15 ... failed. Atom erased. Error: recognition of atom ATOM 460 2H2' DU S 15 ... failed. Atom erased. Error: recognition of atom ATOM 490 1H2' DA S 16 ... failed. Atom erased. Error: recognition of atom ATOM 491 2H2' DA S 16 ... failed. Atom erased. Error: recognition of atom ATOM 523 1H2' DG S 17 ... failed. Atom erased. Error: recognition of atom ATOM 524 2H2' DG S 17 ... failed. Atom erased. Error: recognition of atom ATOM 553 1H2' DC S 18 ... failed. Atom erased. Error: recognition of atom ATOM 554 2H2' DC S 18 ... failed. Atom erased. Error: recognition of atom ATOM 583 1H2' DU S 19 ... failed. Atom erased. Error: recognition of atom ATOM 584 2H2' DU S 19 ... failed. Atom erased. Error: recognition of atom ATOM 614 1H2' DA S 20 ... failed. Atom erased. Error: recognition of atom ATOM 615 2H2' DA S 20 ... failed. Atom erased. Error: recognition of atom ATOM 647 1H2' DG S 21 ... failed. Atom erased. Error: recognition of atom ATOM 648 2H2' DG S 21 ... failed. Atom erased. Error: recognition of atom ATOM 677 1H2' DC S 22 ... failed. Atom erased. Error: recognition of atom ATOM 678 2H2' DC S 22 ... failed. Atom erased. Error: recognition of atom ATOM 707 1H2' DU S 23 ... failed. Atom erased. Error: recognition of atom ATOM 708 2H2' DU S 23 ... failed. Atom erased. Error: recognition of atom ATOM 738 1H2' DA S 24 ... failed. Atom erased. Error: recognition of atom ATOM 739 2H2' DA S 24 ... failed. Atom erased. Error: recognition of atom ATOM 771 1H2' DG S 25 ... failed. Atom erased. Error: recognition of atom ATOM 772 2H2' DG S 25 ... failed. Atom erased. Error: recognition of atom ATOM 801 1H2' DC S 26 ... failed. Atom erased. Error: recognition of atom ATOM 802 2H2' DC S 26 ... failed. Atom erased. Error: recognition of atom ATOM 831 1H2' DU S 27 ... failed. Atom erased. Error: recognition of atom ATOM 832 2H2' DU S 27 ... failed. Atom erased. Error: recognition of atom ATOM 862 1H2' DA S 28 ... failed. Atom erased. Error: recognition of atom ATOM 863 2H2' DA S 28 ... failed. Atom erased. Error: recognition of atom ATOM 894 1H2' DA S 29 ... failed. Atom erased. Error: recognition of atom ATOM 895 2H2' DA S 29 ... failed. Atom erased. Error: recognition of atom ATOM 924 1H2' DC S 30 ... failed. Atom erased. Error: recognition of atom ATOM 925 2H2' DC S 30 ... failed. Atom erased. Error: recognition of atom ATOM 957 1H2' DG S 31 ... failed. Atom erased. Error: recognition of atom ATOM 958 2H2' DG S 31 ... failed. Atom erased. Error: recognition of atom ATOM 988 1H2' DT S 32 ... failed. Atom erased. Error: recognition of atom ATOM 989 2H2' DT S 32 ... failed. Atom erased. Missing atom added: HETATM 11 H2'2 DA S 1 49.992 45.913 10.718 1.00 0.00 H Missing atom added: HETATM 27 H2' DA S 1 48.447 47.068 11.243 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC S 2 51.339 51.447 13.280 1.00 0.00 H Missing atom added: HETATM 25 H2' DC S 2 49.415 51.583 13.806 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG S 3 49.480 56.827 15.853 1.00 0.00 H Missing atom added: HETATM 28 H2' DG S 3 47.789 55.900 16.377 1.00 0.00 H Missing atom added: HETATM 25 H2' DT S 4 44.497 58.190 17.819 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT S 4 44.267 59.265 19.192 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA S 5 39.336 60.883 20.989 1.00 0.00 H Missing atom added: HETATM 27 H2' DA S 5 39.474 58.957 21.507 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U S 6 35.433 56.720 24.065 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DC S 7 31.432 53.325 26.103 1.00 0.00 H Missing atom added: HETATM 25 H2' DC S 7 33.241 52.653 26.625 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG S 8 31.706 47.631 28.655 1.00 0.00 H Missing atom added: HETATM 28 H2' DG S 8 33.591 48.044 29.178 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U S 9 36.379 44.356 31.733 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA S 10 40.304 40.867 33.762 1.00 0.00 H Missing atom added: HETATM 27 H2' DA S 10 40.714 42.751 34.288 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U S 11 45.223 43.746 36.853 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA S 12 50.024 45.861 38.896 1.00 0.00 H Missing atom added: HETATM 27 H2' DA S 12 48.479 47.018 39.418 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG S 13 51.372 51.394 41.460 1.00 0.00 H Missing atom added: HETATM 28 H2' DG S 13 49.447 51.531 41.982 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC S 14 49.516 56.777 44.030 1.00 0.00 H Missing atom added: HETATM 25 H2' DC S 14 47.820 55.853 44.548 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U S 15 44.111 58.606 47.106 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA S 16 39.364 60.846 49.143 1.00 0.00 H Missing atom added: HETATM 27 H2' DA S 16 39.498 58.920 49.660 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG S 17 34.293 58.234 51.689 1.00 0.00 H Missing atom added: HETATM 28 H2' DG S 17 35.450 56.689 52.210 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC S 18 31.438 53.297 54.239 1.00 0.00 H Missing atom added: HETATM 25 H2' DC S 18 33.245 52.622 54.765 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U S 19 33.585 48.013 57.316 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA S 20 34.997 42.957 59.350 1.00 0.00 H Missing atom added: HETATM 27 H2' DA S 20 36.361 44.321 59.877 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG S 21 40.278 40.827 61.915 1.00 0.00 H Missing atom added: HETATM 28 H2' DG S 21 40.687 42.711 62.443 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC S 22 45.867 41.890 64.493 1.00 0.00 H Missing atom added: HETATM 25 H2' DC S 22 45.194 43.698 65.017 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U S 23 48.447 46.967 67.589 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA S 24 51.342 51.336 69.646 1.00 0.00 H Missing atom added: HETATM 27 H2' DA S 24 49.416 51.477 70.163 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG S 25 49.486 56.718 72.216 1.00 0.00 H Missing atom added: HETATM 28 H2' DG S 25 47.789 55.794 72.731 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC S 26 45.007 60.242 74.777 1.00 0.00 H Missing atom added: HETATM 25 H2' DC S 26 44.077 58.549 75.289 1.00 0.00 H Internal Warning: Unresolved atom description: ATOM 11 H2'2 U 1 4.698 -0.290 1.451 1.00 0.00 H in /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb Internal Warning: cannot find atom(s): C4', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: ATOM 25 H2' U S 27 39.458 58.861 77.827 1.00 0.00 H Internal Warning: cannot find atom(s): O3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H3', C3', C2' or H2'2 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or O4' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or N1 in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Internal Warning: cannot find atom(s): H2'2, C2', C1' or H1' in internal /home/ubuntu/rna-tools//opt/qrnas//forcefield/PDB/DU.pdb file Missing atom added: HETATM 11 H2'2 DA S 28 34.246 58.178 79.838 1.00 0.00 H Missing atom added: HETATM 27 H2' DA S 28 35.398 56.630 80.359 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA S 29 31.376 53.241 82.369 1.00 0.00 H Missing atom added: HETATM 27 H2' DA S 29 33.181 52.563 82.898 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC S 30 31.623 47.541 84.906 1.00 0.00 H Missing atom added: HETATM 25 H2' DC S 30 33.507 47.946 85.440 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG S 31 34.909 42.883 87.463 1.00 0.00 H Missing atom added: HETATM 28 H2' DG S 31 36.272 44.245 87.997 1.00 0.00 H Missing atom added: HETATM 25 H2' DT S 32 40.067 42.955 89.443 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT S 32 40.584 41.977 90.811 1.00 0.00 H Missing atom added: HETATM 3 OP3 DA S 1 43.690 41.779 10.531 1.00 0.00 O1- Number of atoms: 990 Number of residues: 32 Building intraresidual bonds... Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. S 6 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. S 9 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. S 11 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. S 15 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. S 19 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. S 23 Warning: Bond expected, but some of the atoms are missing: C2' H2'2, residue No. S 27 Building intraresidual angles... Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. S 6 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. S 6 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. S 6 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. S 9 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. S 9 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. S 9 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. S 11 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. S 11 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. S 11 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. S 15 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. S 15 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. S 15 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. S 19 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. S 19 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. S 19 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. S 23 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. S 23 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. S 23 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C3', residue No. S 27 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' C1', residue No. S 27 Warning: Angle expected, but some of the atoms are missing: H2'2 C2' H2', residue No. S 27 Building intraresidual dihedrals... Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. S 6 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. S 6 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. S 6 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. S 6 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. S 6 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. S 6 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. S 9 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. S 9 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. S 9 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. S 9 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. S 9 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. S 9 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. S 11 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. S 11 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. S 11 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. S 11 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. S 11 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. S 11 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. S 15 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. S 15 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. S 15 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. S 15 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. S 15 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. S 15 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. S 19 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. S 19 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. S 19 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. S 19 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. S 19 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. S 19 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. S 23 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. S 23 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. S 23 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. S 23 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. S 23 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. S 23 Warning: Dihedral expected, but some of the atoms are missing: C4' C3' C2' H2'2, residue No. S 27 Warning: Dihedral expected, but some of the atoms are missing: O3' C3' C2' H2'2, residue No. S 27 Warning: Dihedral expected, but some of the atoms are missing: H3' C3' C2' H2'2, residue No. S 27 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' O4', residue No. S 27 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' N1, residue No. S 27 Warning: Dihedral expected, but some of the atoms are missing: H2'2 C2' C1' H1', residue No. S 27 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: 1069 Number of angles built: 1931 Number of dihedrals built: 2876 Number of impropers built: 215 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- Error: recognition of atom ATOM 1022 1H2' DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 1023 2H2' DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 1032 OP3 DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 1033 3HOP DA A 1 ... failed. Atom erased. Error: recognition of atom ATOM 1054 1H2' DC A 2 ... failed. Atom erased. Error: recognition of atom ATOM 1055 2H2' DC A 2 ... failed. Atom erased. Error: recognition of atom ATOM 1087 1H2' DG A 3 ... failed. Atom erased. Error: recognition of atom ATOM 1088 2H2' DG A 3 ... failed. Atom erased. Error: recognition of atom ATOM 1118 1H2' DT A 4 ... failed. Atom erased. Error: recognition of atom ATOM 1119 2H2' DT A 4 ... failed. Atom erased. Error: recognition of atom ATOM 1150 1H2' DT A 5 ... failed. Atom erased. Error: recognition of atom ATOM 1151 2H2' DT A 5 ... failed. Atom erased. Error: recognition of atom ATOM 1183 1H2' DA A 6 ... failed. Atom erased. Error: recognition of atom ATOM 1184 2H2' DA A 6 ... failed. Atom erased. Error: recognition of atom ATOM 1216 1H2' DG A 7 ... failed. Atom erased. Error: recognition of atom ATOM 1217 2H2' DG A 7 ... failed. Atom erased. Error: recognition of atom ATOM 1246 1H2' DC A 8 ... failed. Atom erased. Error: recognition of atom ATOM 1247 2H2' DC A 8 ... failed. Atom erased. Error: recognition of atom ATOM 1277 1H2' DT A 9 ... failed. Atom erased. Error: recognition of atom ATOM 1278 2H2' DT A 9 ... failed. Atom erased. Error: recognition of atom ATOM 1310 1H2' DA A 10 ... failed. Atom erased. Error: recognition of atom ATOM 1311 2H2' DA A 10 ... failed. Atom erased. Error: recognition of atom ATOM 1343 1H2' DG A 11 ... failed. Atom erased. Error: recognition of atom ATOM 1344 2H2' DG A 11 ... failed. Atom erased. Error: recognition of atom ATOM 1373 1H2' DC A 12 ... failed. Atom erased. Error: recognition of atom ATOM 1374 2H2' DC A 12 ... failed. Atom erased. Error: recognition of atom ATOM 1404 1H2' DT A 13 ... failed. Atom erased. Error: recognition of atom ATOM 1405 2H2' DT A 13 ... failed. Atom erased. Error: recognition of atom ATOM 1437 1H2' DA A 14 ... failed. Atom erased. Error: recognition of atom ATOM 1438 2H2' DA A 14 ... failed. Atom erased. Error: recognition of atom ATOM 1470 1H2' DG A 15 ... failed. Atom erased. Error: recognition of atom ATOM 1471 2H2' DG A 15 ... failed. Atom erased. Error: recognition of atom ATOM 1500 1H2' DC A 16 ... failed. Atom erased. Error: recognition of atom ATOM 1501 2H2' DC A 16 ... failed. Atom erased. Error: recognition of atom ATOM 1531 1H2' DT A 17 ... failed. Atom erased. Error: recognition of atom ATOM 1532 2H2' DT A 17 ... failed. Atom erased. Error: recognition of atom ATOM 1564 1H2' DA A 18 ... failed. Atom erased. Error: recognition of atom ATOM 1565 2H2' DA A 18 ... failed. Atom erased. Error: recognition of atom ATOM 1597 1H2' DG A 19 ... failed. Atom erased. Error: recognition of atom ATOM 1598 2H2' DG A 19 ... failed. Atom erased. Error: recognition of atom ATOM 1627 1H2' DC A 20 ... failed. Atom erased. Error: recognition of atom ATOM 1628 2H2' DC A 20 ... failed. Atom erased. Error: recognition of atom ATOM 1658 1H2' DT A 21 ... failed. Atom erased. Error: recognition of atom ATOM 1659 2H2' DT A 21 ... failed. Atom erased. Error: recognition of atom ATOM 1691 1H2' DA A 22 ... failed. Atom erased. Error: recognition of atom ATOM 1692 2H2' DA A 22 ... failed. Atom erased. Error: recognition of atom ATOM 1722 1H2' DT A 23 ... failed. Atom erased. Error: recognition of atom ATOM 1723 2H2' DT A 23 ... failed. Atom erased. Error: recognition of atom ATOM 1755 1H2' DA A 24 ... failed. Atom erased. Error: recognition of atom ATOM 1756 2H2' DA A 24 ... failed. Atom erased. Error: recognition of atom ATOM 1785 1H2' DC A 25 ... failed. Atom erased. Error: recognition of atom ATOM 1786 2H2' DC A 25 ... failed. Atom erased. Error: recognition of atom ATOM 1818 1H2' DG A 26 ... failed. Atom erased. Error: recognition of atom ATOM 1819 2H2' DG A 26 ... failed. Atom erased. Error: recognition of atom ATOM 1850 1H2' DA A 27 ... failed. Atom erased. Error: recognition of atom ATOM 1851 2H2' DA A 27 ... failed. Atom erased. Error: recognition of atom ATOM 1881 1H2' DT A 28 ... failed. Atom erased. Error: recognition of atom ATOM 1882 2H2' DT A 28 ... failed. Atom erased. Error: recognition of atom ATOM 1914 1H2' DA A 29 ... failed. Atom erased. Error: recognition of atom ATOM 1915 2H2' DA A 29 ... failed. Atom erased. Error: recognition of atom ATOM 1944 1H2' DC A 30 ... failed. Atom erased. Error: recognition of atom ATOM 1945 2H2' DC A 30 ... failed. Atom erased. Error: recognition of atom ATOM 1977 1H2' DG A 31 ... failed. Atom erased. Error: recognition of atom ATOM 1978 2H2' DG A 31 ... failed. Atom erased. Error: recognition of atom ATOM 2008 1H2' DT A 32 ... failed. Atom erased. Error: recognition of atom ATOM 2009 2H2' DT A 32 ... failed. Atom erased. Missing atom added: HETATM 11 H2'2 DA A 1 49.434 44.938 83.148 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 1 47.746 45.870 82.620 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 2 44.952 41.434 80.558 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 2 44.033 43.129 80.033 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 3 39.286 40.912 77.976 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 3 39.432 42.837 77.459 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 4 35.985 44.891 76.021 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 4 34.911 44.659 74.648 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 5 33.597 48.690 73.452 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 5 32.567 49.082 72.081 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 6 31.680 54.219 70.311 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 6 33.566 53.806 69.793 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 7 35.005 58.867 67.795 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 7 36.366 57.501 67.269 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 8 40.316 60.980 65.258 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 8 40.722 59.096 64.727 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 9 44.616 58.093 63.294 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 9 45.591 58.626 61.930 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 10 50.048 55.939 60.144 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 10 48.503 54.788 59.611 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 11 51.385 50.403 57.584 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 11 49.463 50.271 57.051 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 12 49.512 45.021 55.000 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 12 47.821 45.948 54.472 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 13 44.522 43.662 53.023 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 13 44.291 42.582 51.654 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 14 39.350 40.969 49.855 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 14 39.491 42.893 49.331 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 15 34.288 43.584 47.295 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 15 35.446 45.127 46.772 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 16 31.431 48.539 44.726 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 16 33.239 49.212 44.203 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 17 33.663 53.216 42.775 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 17 33.001 54.104 41.409 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 18 35.023 58.898 39.632 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 18 36.385 57.533 39.106 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 19 40.326 61.020 37.085 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 19 40.732 59.135 36.555 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 20 45.927 59.929 34.522 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 20 45.251 58.124 33.993 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 21 47.987 55.185 32.559 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 21 49.091 55.110 31.192 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 22 51.390 50.456 29.404 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 22 49.466 50.321 28.878 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 23 47.924 46.612 27.424 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 23 48.313 45.579 26.055 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 24 45.031 41.549 24.263 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 24 44.107 43.242 23.738 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 25 39.350 41.005 21.703 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 25 39.487 42.929 21.179 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 26 34.277 43.615 19.153 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 26 35.432 45.160 18.628 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 27 31.408 48.567 16.591 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 27 33.215 49.242 16.064 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 28 33.631 53.246 14.635 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 28 32.964 54.134 13.270 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DA A 29 34.976 58.930 11.489 1.00 0.00 H Missing atom added: HETATM 27 H2' DA A 29 36.339 57.566 10.959 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DC A 30 40.270 61.059 8.929 1.00 0.00 H Missing atom added: HETATM 25 H2' DC A 30 40.679 59.175 8.400 1.00 0.00 H Missing atom added: HETATM 11 H2'2 DG A 31 45.868 59.976 6.353 1.00 0.00 H Missing atom added: HETATM 28 H2' DG A 31 45.191 58.170 5.827 1.00 0.00 H Missing atom added: HETATM 25 H2' DT A 32 47.929 55.232 4.383 1.00 0.00 H Missing atom added: HETATM 26 H2'2 DT A 32 49.032 55.157 3.014 1.00 0.00 H Missing atom added: HETATM 1002 OP3 DA A 1 50.597 52.384 83.362 1.00 0.00 O1- Number of atoms: 1018 Number of residues: 32 Building intraresidual bonds... Building intraresidual angles... Building intraresidual dihedrals... 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: 1097 Number of angles built: 1994 Number of dihedrals built: 2974 Number of impropers built: 215 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Building interresidual nonbonded pairs & H-bonds (it may take a while)... Number of electrostatic pairs: 3755077 Number of van der Waals pairs: 295517 Number of H-bonds built: 78 Number of spring restraints: 0 Number of positional restraints: 0 Number of base pairs built: 32 Number of molecules (chains) read: 3 ----------------------------------------------------------------------------- Performing minimization step: 1. Total energy = 19646.5797 kcal/mol (19613.2552 without restraints) Performing minimization step: 2. Total energy = 19582.4945 kcal/mol (19549.2372 without restraints) Performing minimization step: 3. Total energy = 19518.9699 kcal/mol (19485.7786 without restraints) Performing minimization step: 4. Total energy = 19455.9957 kcal/mol (19422.8693 without restraints) Performing minimization step: 5. Total energy = 19393.5626 kcal/mol (19360.4999 without restraints) Performing minimization step: 6. Total energy = 19331.6611 kcal/mol (19298.6611 without restraints) Performing minimization step: 7. Total energy = 19270.2821 kcal/mol (19237.3437 without restraints) Performing minimization step: 8. Total energy = 19209.4168 kcal/mol (19176.5390 without restraints) Performing minimization step: 9. Total energy = 19149.0564 kcal/mol (19116.2381 without restraints) Performing minimization step: 10. Total energy = 19089.1926 kcal/mol (19056.4328 without restraints) Performing minimization step: 11. Total energy = 19029.8176 kcal/mol (18997.1149 without restraints) Performing minimization step: 12. Total energy = 18970.9215 kcal/mol (18938.2762 without restraints) Performing minimization step: 13. Total energy = 18912.4985 kcal/mol (18879.9091 without restraints) Performing minimization step: 14. Total energy = 18854.5404 kcal/mol (18822.0060 without restraints) Performing minimization step: 15. Total energy = 18797.0395 kcal/mol (18764.5590 without restraints) Performing minimization step: 16. Total energy = 18739.9885 kcal/mol (18707.5612 without restraints) Performing minimization step: 17. Total energy = 18683.3802 kcal/mol (18651.0053 without restraints) Performing minimization step: 18. Total energy = 18627.2071 kcal/mol (18594.8838 without restraints) Performing minimization step: 19. Total energy = 18571.4636 kcal/mol (18539.1910 without restraints) Performing minimization step: 20. Total energy = 18516.1425 kcal/mol (18483.9199 without restraints) Performing minimization step: 21. Total energy = 18461.2372 kcal/mol (18429.0639 without restraints) Performing minimization step: 22. Total energy = 18406.7417 kcal/mol (18374.6169 without restraints) Performing minimization step: 23. Total energy = 18352.6494 kcal/mol (18320.5724 without restraints) Performing minimization step: 24. Total energy = 18298.9544 kcal/mol (18266.9244 without restraints) Performing minimization step: 25. Total energy = 18245.6506 kcal/mol (18213.6671 without restraints) Performing minimization step: 26. Total energy = 18192.7326 kcal/mol (18160.7948 without restraints) Performing minimization step: 27. Total energy = 18140.1945 kcal/mol (18108.3018 without restraints) Performing minimization step: 28. Total energy = 18088.0306 kcal/mol (18056.1823 without restraints) Performing minimization step: 29. Total energy = 18036.2360 kcal/mol (18004.4315 without restraints) Performing minimization step: 30. Total energy = 17984.8051 kcal/mol (17953.0438 without restraints) Performing minimization step: 31. Total energy = 17933.7328 kcal/mol (17902.0142 without restraints) Performing minimization step: 32. Total energy = 17883.0142 kcal/mol (17851.3375 without restraints) Performing minimization step: 33. Total energy = 17832.6442 kcal/mol (17801.0090 without restraints) Performing minimization step: 34. Total energy = 17782.6180 kcal/mol (17751.0237 without restraints) Performing minimization step: 35. Total energy = 17732.9307 kcal/mol (17701.3766 without restraints) Performing minimization step: 36. Total energy = 17683.5778 kcal/mol (17652.0635 without restraints) Performing minimization step: 37. Total energy = 17634.5548 kcal/mol (17603.0799 without restraints) Performing minimization step: 38. Total energy = 17585.8578 kcal/mol (17554.4217 without restraints) Performing minimization step: 39. Total energy = 17537.4814 kcal/mol (17506.0835 without restraints) Performing minimization step: 40. Total energy = 17489.4223 kcal/mol (17458.0622 without restraints) Performing minimization step: 41. Total energy = 17441.6758 kcal/mol (17410.3530 without restraints) Performing minimization step: 42. Total energy = 17394.2381 kcal/mol (17362.9520 without restraints) Performing minimization step: 43. Total energy = 17347.1052 kcal/mol (17315.8556 without restraints) Performing minimization step: 44. Total energy = 17300.2732 kcal/mol (17269.0594 without restraints) Performing minimization step: 45. Total energy = 17253.7383 kcal/mol (17222.5600 without restraints) Performing minimization step: 46. Total energy = 17207.4967 kcal/mol (17176.3535 without restraints) Performing minimization step: 47. Total energy = 17161.5448 kcal/mol (17130.4362 without restraints) Performing minimization step: 48. Total energy = 17115.8788 kcal/mol (17084.8044 without restraints) Performing minimization step: 49. Total energy = 17070.4956 kcal/mol (17039.4549 without restraints) Performing minimization step: 50. Total energy = 17025.3914 kcal/mol (16994.3842 without restraints) Performing minimization step: 51. Total energy = 16980.5630 kcal/mol (16949.5890 without restraints) Performing minimization step: 52. Total energy = 16936.0069 kcal/mol (16905.0653 without restraints) Performing minimization step: 53. Total energy = 16891.7195 kcal/mol (16860.8101 without restraints) Performing minimization step: 54. Total energy = 16847.6982 kcal/mol (16816.8207 without restraints) Performing minimization step: 55. Total energy = 16803.9396 kcal/mol (16773.0936 without restraints) Performing minimization step: 56. Total energy = 16760.4408 kcal/mol (16729.6258 without restraints) Performing minimization step: 57. Total energy = 16717.1988 kcal/mol (16686.4147 without restraints) Performing minimization step: 58. Total energy = 16674.2102 kcal/mol (16643.4566 without restraints) Performing minimization step: 59. Total energy = 16631.4726 kcal/mol (16600.7491 without restraints) Performing minimization step: 60. Total energy = 16588.9832 kcal/mol (16558.2894 without restraints) Performing minimization step: 61. Total energy = 16546.7391 kcal/mol (16516.0747 without restraints) Performing minimization step: 62. Total energy = 16504.7371 kcal/mol (16474.1020 without restraints) Performing minimization step: 63. Total energy = 16462.9744 kcal/mol (16432.3681 without restraints) Performing minimization step: 64. Total energy = 16421.4493 kcal/mol (16390.8716 without restraints) Performing minimization step: 65. Total energy = 16380.1588 kcal/mol (16349.6093 without restraints) Performing minimization step: 66. Total energy = 16339.1003 kcal/mol (16308.5788 without restraints) Performing minimization step: 67. Total energy = 16298.2713 kcal/mol (16267.7774 without restraints) Performing minimization step: 68. Total energy = 16257.6694 kcal/mol (16227.2029 without restraints) Performing minimization step: 69. Total energy = 16217.2919 kcal/mol (16186.8524 without restraints) Performing minimization step: 70. Total energy = 16177.1366 kcal/mol (16146.7241 without restraints) Performing minimization step: 71. Total energy = 16137.2013 kcal/mol (16106.8152 without restraints) Performing minimization step: 72. Total energy = 16097.4834 kcal/mol (16067.1236 without restraints) Performing minimization step: 73. Total energy = 16057.9808 kcal/mol (16027.6470 without restraints) Performing minimization step: 74. Total energy = 16018.6918 kcal/mol (15988.3837 without restraints) Performing minimization step: 75. Total energy = 15979.6131 kcal/mol (15949.3306 without restraints) Performing minimization step: 76. Total energy = 15940.7434 kcal/mol (15910.4862 without restraints) Performing minimization step: 77. Total energy = 15902.0804 kcal/mol (15871.8481 without restraints) Performing minimization step: 78. Total energy = 15863.6218 kcal/mol (15833.4144 without restraints) Performing minimization step: 79. Total energy = 15825.3661 kcal/mol (15795.1832 without restraints) Performing minimization step: 80. Total energy = 15787.3109 kcal/mol (15757.1524 without restraints) Performing minimization step: 81. Total energy = 15749.4539 kcal/mol (15719.3195 without restraints) Performing minimization step: 82. Total energy = 15711.7939 kcal/mol (15681.6833 without restraints) Performing minimization step: 83. Total energy = 15674.3285 kcal/mol (15644.2415 without restraints) Performing minimization step: 84. Total energy = 15637.0561 kcal/mol (15606.9926 without restraints) Performing minimization step: 85. Total energy = 15599.9745 kcal/mol (15569.9343 without restraints) Performing minimization step: 86. Total energy = 15563.0818 kcal/mol (15533.0645 without restraints) Performing minimization step: 87. Total energy = 15526.3765 kcal/mol (15496.3821 without restraints) Performing minimization step: 88. Total energy = 15489.8569 kcal/mol (15459.8851 without restraints) Performing minimization step: 89. Total energy = 15453.5211 kcal/mol (15423.5717 without restraints) Performing minimization step: 90. Total energy = 15417.3675 kcal/mol (15387.4403 without restraints) Performing minimization step: 91. Total energy = 15381.3947 kcal/mol (15351.4895 without restraints) Performing minimization step: 92. Total energy = 15345.6002 kcal/mol (15315.7167 without restraints) Performing minimization step: 93. Total energy = 15309.9833 kcal/mol (15280.1217 without restraints) Performing minimization step: 94. Total energy = 15274.5423 kcal/mol (15244.7021 without restraints) Performing minimization step: 95. Total energy = 15239.2747 kcal/mol (15209.4556 without restraints) Performing minimization step: 96. Total energy = 15204.1794 kcal/mol (15174.3814 without restraints) Performing minimization step: 97. Total energy = 15169.2549 kcal/mol (15139.4779 without restraints) Performing minimization step: 98. Total energy = 15134.4999 kcal/mol (15104.7436 without restraints) Performing minimization step: 99. Total energy = 15099.9127 kcal/mol (15070.1770 without restraints) Performing minimization step: 100. Total energy = 15065.4919 kcal/mol (15035.7765 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/ade9e976/tmp/sequence_refx/sequence_refx.pdb ...Done. Performing minimization step: 101. Total energy = 15031.2364 kcal/mol (15001.5413 without restraints) Performing minimization step: 102. Total energy = 14997.1439 kcal/mol (14967.4689 without restraints) Performing minimization step: 103. Total energy = 14963.2137 kcal/mol (14933.5586 without restraints) Performing minimization step: 104. Total energy = 14929.4441 kcal/mol (14899.8087 without restraints) Performing minimization step: 105. Total energy = 14895.8337 kcal/mol (14866.2180 without restraints) Performing minimization step: 106. Total energy = 14862.3813 kcal/mol (14832.7850 without restraints) Performing minimization step: 107. Total energy = 14829.0858 kcal/mol (14799.5087 without restraints) Performing minimization step: 108. Total energy = 14795.9455 kcal/mol (14766.3876 without restraints) Performing minimization step: 109. Total energy = 14762.9595 kcal/mol (14733.4206 without restraints) Performing minimization step: 110. Total energy = 14730.1262 kcal/mol (14700.6061 without restraints) Performing minimization step: 111. Total energy = 14697.4440 kcal/mol (14667.9426 without restraints) Performing minimization step: 112. Total energy = 14664.9121 kcal/mol (14635.4292 without restraints) Performing minimization step: 113. Total energy = 14632.5293 kcal/mol (14603.0646 without restraints) Performing minimization step: 114. Total energy = 14600.2941 kcal/mol (14570.8479 without restraints) Performing minimization step: 115. Total energy = 14568.2056 kcal/mol (14538.7776 without restraints) Performing minimization step: 116. Total energy = 14536.2621 kcal/mol (14506.8521 without restraints) Performing minimization step: 117. Total energy = 14504.4631 kcal/mol (14475.0710 without restraints) Performing minimization step: 118. Total energy = 14472.8074 kcal/mol (14443.4330 without restraints) Performing minimization step: 119. Total energy = 14441.2934 kcal/mol (14411.9367 without restraints) Performing minimization step: 120. Total energy = 14409.9204 kcal/mol (14380.5811 without restraints) Performing minimization step: 121. Total energy = 14378.6870 kcal/mol (14349.3651 without restraints) Performing minimization step: 122. Total energy = 14347.5924 kcal/mol (14318.2877 without restraints) Performing minimization step: 123. Total energy = 14316.6352 kcal/mol (14287.3476 without restraints) Performing minimization step: 124. Total energy = 14285.8149 kcal/mol (14256.5443 without restraints) Performing minimization step: 125. Total energy = 14255.1296 kcal/mol (14225.8760 without restraints) Performing minimization step: 126. Total energy = 14224.5792 kcal/mol (14195.3423 without restraints) Performing minimization step: 127. Total energy = 14194.1621 kcal/mol (14164.9417 without restraints) Performing minimization step: 128. Total energy = 14163.8767 kcal/mol (14134.6730 without restraints) Performing minimization step: 129. Total energy = 14133.7231 kcal/mol (14104.5358 without restraints) Performing minimization step: 130. Total energy = 14103.7000 kcal/mol (14074.5290 without restraints) Performing minimization step: 131. Total energy = 14073.8063 kcal/mol (14044.6516 without restraints) Performing minimization step: 132. Total energy = 14044.0411 kcal/mol (14014.9023 without restraints) Performing minimization step: 133. Total energy = 14014.4035 kcal/mol (13985.2807 without restraints) Performing minimization step: 134. Total energy = 13984.8923 kcal/mol (13955.7854 without restraints) Performing minimization step: 135. Total energy = 13955.5067 kcal/mol (13926.4156 without restraints) Performing minimization step: 136. Total energy = 13926.2459 kcal/mol (13897.1705 without restraints) Performing minimization step: 137. Total energy = 13897.1089 kcal/mol (13868.0491 without restraints) Performing minimization step: 138. Total energy = 13868.0947 kcal/mol (13839.0503 without restraints) Performing minimization step: 139. Total energy = 13839.2029 kcal/mol (13810.1740 without restraints) Performing minimization step: 140. Total energy = 13810.4323 kcal/mol (13781.4185 without restraints) Performing minimization step: 141. Total energy = 13781.7820 kcal/mol (13752.7834 without restraints) Performing minimization step: 142. Total energy = 13753.2510 kcal/mol (13724.2674 without restraints) Performing minimization step: 143. Total energy = 13724.8387 kcal/mol (13695.8701 without restraints) Performing minimization step: 144. Total energy = 13696.5442 kcal/mol (13667.5906 without restraints) Performing minimization step: 145. Total energy = 13668.3668 kcal/mol (13639.4279 without restraints) Performing minimization step: 146. Total energy = 13640.3058 kcal/mol (13611.3817 without restraints) Performing minimization step: 147. Total energy = 13612.3600 kcal/mol (13583.4505 without restraints) Performing minimization step: 148. Total energy = 13584.5281 kcal/mol (13555.6331 without restraints) Performing minimization step: 149. Total energy = 13556.8106 kcal/mol (13527.9300 without restraints) Performing minimization step: 150. Total energy = 13529.2060 kcal/mol (13500.3398 without restraints) Performing minimization step: 151. Total energy = 13501.7138 kcal/mol (13472.8618 without restraints) Performing minimization step: 152. Total energy = 13474.3330 kcal/mol (13445.4952 without restraints) Performing minimization step: 153. Total energy = 13447.0629 kcal/mol (13418.2393 without restraints) Performing minimization step: 154. Total energy = 13419.9030 kcal/mol (13391.0933 without restraints) Performing minimization step: 155. Total energy = 13392.8523 kcal/mol (13364.0566 without restraints) Performing minimization step: 156. Total energy = 13365.9099 kcal/mol (13337.1281 without restraints) Performing minimization step: 157. Total energy = 13339.0756 kcal/mol (13310.3075 without restraints) Performing minimization step: 158. Total energy = 13312.3484 kcal/mol (13283.5940 without restraints) Performing minimization step: 159. Total energy = 13285.7276 kcal/mol (13256.9868 without restraints) Performing minimization step: 160. Total energy = 13259.2126 kcal/mol (13230.4853 without restraints) Performing minimization step: 161. Total energy = 13232.8025 kcal/mol (13204.0887 without restraints) Performing minimization step: 162. Total energy = 13206.4969 kcal/mol (13177.7965 without restraints) Performing minimization step: 163. Total energy = 13180.2947 kcal/mol (13151.6076 without restraints) Performing minimization step: 164. Total energy = 13154.1959 kcal/mol (13125.5221 without restraints) Performing minimization step: 165. Total energy = 13128.1995 kcal/mol (13099.5388 without restraints) Performing minimization step: 166. Total energy = 13102.3052 kcal/mol (13073.6577 without restraints) Performing minimization step: 167. Total energy = 13076.5117 kcal/mol (13047.8771 without restraints) Performing minimization step: 168. Total energy = 13050.8186 kcal/mol (13022.1970 without restraints) Performing minimization step: 169. Total energy = 13025.2253 kcal/mol (12996.6166 without restraints) Performing minimization step: 170. Total energy = 12999.7313 kcal/mol (12971.1354 without restraints) Performing minimization step: 171. Total energy = 12974.3358 kcal/mol (12945.7527 without restraints) Performing minimization step: 172. Total energy = 12949.0384 kcal/mol (12920.4680 without restraints) Performing minimization step: 173. Total energy = 12923.8386 kcal/mol (12895.2808 without restraints) Performing minimization step: 174. Total energy = 12898.7351 kcal/mol (12870.1898 without restraints) Performing minimization step: 175. Total energy = 12873.7279 kcal/mol (12845.1951 without restraints) Performing minimization step: 176. Total energy = 12848.8164 kcal/mol (12820.2960 without restraints) Performing minimization step: 177. Total energy = 12824.0000 kcal/mol (12795.4920 without restraints) Performing minimization step: 178. Total energy = 12799.2783 kcal/mol (12770.7826 without restraints) Performing minimization step: 179. Total energy = 12774.6504 kcal/mol (12746.1669 without restraints) Performing minimization step: 180. Total energy = 12750.1159 kcal/mol (12721.6445 without restraints) Performing minimization step: 181. Total energy = 12725.6742 kcal/mol (12697.2149 without restraints) Performing minimization step: 182. Total energy = 12701.3260 kcal/mol (12672.8774 without restraints) Performing minimization step: 183. Total energy = 12677.0670 kcal/mol (12648.6315 without restraints) Performing minimization step: 184. Total energy = 12652.9001 kcal/mol (12624.4768 without restraints) Performing minimization step: 185. Total energy = 12628.8244 kcal/mol (12600.4130 without restraints) Performing minimization step: 186. Total energy = 12604.8387 kcal/mol (12576.4392 without restraints) Performing minimization step: 187. Total energy = 12580.9429 kcal/mol (12552.5552 without restraints) Performing minimization step: 188. Total energy = 12557.1358 kcal/mol (12528.7598 without restraints) Performing minimization step: 189. Total energy = 12533.4172 kcal/mol (12505.0527 without restraints) Performing minimization step: 190. Total energy = 12509.7867 kcal/mol (12481.4339 without restraints) Performing minimization step: 191. Total energy = 12486.2435 kcal/mol (12457.9023 without restraints) Performing minimization step: 192. Total energy = 12462.7880 kcal/mol (12434.4582 without restraints) Performing minimization step: 193. Total energy = 12439.4187 kcal/mol (12411.1003 without restraints) Performing minimization step: 194. Total energy = 12416.1355 kcal/mol (12387.8285 without restraints) Performing minimization step: 195. Total energy = 12392.9382 kcal/mol (12364.6425 without restraints) Performing minimization step: 196. Total energy = 12369.8255 kcal/mol (12341.5411 without restraints) Performing minimization step: 197. Total energy = 12346.7975 kcal/mol (12318.5243 without restraints) Performing minimization step: 198. Total energy = 12323.8540 kcal/mol (12295.5921 without restraints) Performing minimization step: 199. Total energy = 12300.9941 kcal/mol (12272.7434 without restraints) Performing minimization step: 200. Total energy = 12278.2178 kcal/mol (12249.9781 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/ade9e976/tmp/sequence_refx/sequence_refx.pdb ...Done. Performing minimization step: 201. Total energy = 12255.5241 kcal/mol (12227.2954 without restraints) Performing minimization step: 202. Total energy = 12232.9129 kcal/mol (12204.6952 without restraints) Performing minimization step: 203. Total energy = 12210.3838 kcal/mol (12182.1771 without restraints) Performing minimization step: 204. Total energy = 12187.9364 kcal/mol (12159.7405 without restraints) Performing minimization step: 205. Total energy = 12165.5699 kcal/mol (12137.3849 without restraints) Performing minimization step: 206. Total energy = 12143.2840 kcal/mol (12115.1098 without restraints) Performing minimization step: 207. Total energy = 12121.0783 kcal/mol (12092.9147 without restraints) Performing minimization step: 208. Total energy = 12098.9527 kcal/mol (12070.8000 without restraints) Performing minimization step: 209. Total energy = 12076.9058 kcal/mol (12048.7638 without restraints) Performing minimization step: 210. Total energy = 12054.9382 kcal/mol (12026.8068 without restraints) Performing minimization step: 211. Total energy = 12033.0493 kcal/mol (12004.9284 without restraints) Performing minimization step: 212. Total energy = 12011.2385 kcal/mol (11983.1282 without restraints) Performing minimization step: 213. Total energy = 11989.5052 kcal/mol (11961.4054 without restraints) Performing minimization step: 214. Total energy = 11967.8495 kcal/mol (11939.7601 without restraints) Performing minimization step: 215. Total energy = 11946.2702 kcal/mol (11918.1911 without restraints) Performing minimization step: 216. Total energy = 11924.7679 kcal/mol (11896.6992 without restraints) Performing minimization step: 217. Total energy = 11903.3418 kcal/mol (11875.2834 without restraints) Performing minimization step: 218. Total energy = 11881.9915 kcal/mol (11853.9435 without restraints) Performing minimization step: 219. Total energy = 11860.7165 kcal/mol (11832.6788 without restraints) Performing minimization step: 220. Total energy = 11839.5164 kcal/mol (11811.4888 without restraints) Performing minimization step: 221. Total energy = 11818.3913 kcal/mol (11790.3739 without restraints) Performing minimization step: 222. Total energy = 11797.3403 kcal/mol (11769.3330 without restraints) Performing minimization step: 223. Total energy = 11776.3633 kcal/mol (11748.3661 without restraints) Performing minimization step: 224. Total energy = 11755.4598 kcal/mol (11727.4726 without restraints) Performing minimization step: 225. Total energy = 11734.6295 kcal/mol (11706.6524 without restraints) Performing minimization step: 226. Total energy = 11713.8721 kcal/mol (11685.9050 without restraints) Performing minimization step: 227. Total energy = 11693.1873 kcal/mol (11665.2301 without restraints) Performing minimization step: 228. Total energy = 11672.5745 kcal/mol (11644.6272 without restraints) Performing minimization step: 229. Total energy = 11652.0329 kcal/mol (11624.0954 without restraints) Performing minimization step: 230. Total energy = 11631.5633 kcal/mol (11603.6357 without restraints) Performing minimization step: 231. Total energy = 11611.1648 kcal/mol (11583.2470 without restraints) Performing minimization step: 232. Total energy = 11590.8370 kcal/mol (11562.9289 without restraints) Performing minimization step: 233. Total energy = 11570.5797 kcal/mol (11542.6814 without restraints) Performing minimization step: 234. Total energy = 11550.3923 kcal/mol (11522.5036 without restraints) Performing minimization step: 235. Total energy = 11530.2745 kcal/mol (11502.3955 without restraints) Performing minimization step: 236. Total energy = 11510.2262 kcal/mol (11482.3569 without restraints) Performing minimization step: 237. Total energy = 11490.2470 kcal/mol (11462.3872 without restraints) Performing minimization step: 238. Total energy = 11470.3365 kcal/mol (11442.4863 without restraints) Performing minimization step: 239. Total energy = 11450.4947 kcal/mol (11422.6540 without restraints) Performing minimization step: 240. Total energy = 11430.7207 kcal/mol (11402.8894 without restraints) Performing minimization step: 241. Total energy = 11411.0145 kcal/mol (11383.1927 without restraints) Performing minimization step: 242. Total energy = 11391.3757 kcal/mol (11363.5633 without restraints) Performing minimization step: 243. Total energy = 11371.8042 kcal/mol (11344.0013 without restraints) Performing minimization step: 244. Total energy = 11352.2997 kcal/mol (11324.5061 without restraints) Performing minimization step: 245. Total energy = 11332.8615 kcal/mol (11305.0773 without restraints) Performing minimization step: 246. Total energy = 11313.4898 kcal/mol (11285.7149 without restraints) Performing minimization step: 247. Total energy = 11294.1845 kcal/mol (11266.4189 without restraints) Performing minimization step: 248. Total energy = 11274.9444 kcal/mol (11247.1880 without restraints) Performing minimization step: 249. Total energy = 11255.7698 kcal/mol (11228.0226 without restraints) Performing minimization step: 250. Total energy = 11236.6602 kcal/mol (11208.9222 without restraints) Performing minimization step: 251. Total energy = 11217.6155 kcal/mol (11189.8866 without restraints) Performing minimization step: 252. Total energy = 11198.6353 kcal/mol (11170.9156 without restraints) Performing minimization step: 253. Total energy = 11179.7193 kcal/mol (11152.0087 without restraints) Performing minimization step: 254. Total energy = 11160.8671 kcal/mol (11133.1656 without restraints) Performing minimization step: 255. Total energy = 11142.0789 kcal/mol (11114.3864 without restraints) Performing minimization step: 256. Total energy = 11123.3540 kcal/mol (11095.6705 without restraints) Performing minimization step: 257. Total energy = 11104.6922 kcal/mol (11077.0176 without restraints) Performing minimization step: 258. Total energy = 11086.0932 kcal/mol (11058.4278 without restraints) Performing minimization step: 259. Total energy = 11067.5570 kcal/mol (11039.9003 without restraints) Performing minimization step: 260. Total energy = 11049.0829 kcal/mol (11021.4352 without restraints) Performing minimization step: 261. Total energy = 11030.6708 kcal/mol (11003.0320 without restraints) Performing minimization step: 262. Total energy = 11012.3205 kcal/mol (10984.6906 without restraints) Performing minimization step: 263. Total energy = 10994.0317 kcal/mol (10966.4106 without restraints) Performing minimization step: 264. Total energy = 10975.8043 kcal/mol (10948.1918 without restraints) Performing minimization step: 265. Total energy = 10957.6377 kcal/mol (10930.0343 without restraints) Performing minimization step: 266. Total energy = 10939.5323 kcal/mol (10911.9375 without restraints) Performing minimization step: 267. Total energy = 10921.4868 kcal/mol (10893.9007 without restraints) Performing minimization step: 268. Total energy = 10903.5019 kcal/mol (10875.9245 without restraints) Performing minimization step: 269. Total energy = 10885.5763 kcal/mol (10858.0077 without restraints) Performing minimization step: 270. Total energy = 10867.7110 kcal/mol (10840.1510 without restraints) Performing minimization step: 271. Total energy = 10849.9049 kcal/mol (10822.3535 without restraints) Performing minimization step: 272. Total energy = 10832.1582 kcal/mol (10804.6155 without restraints) Performing minimization step: 273. Total energy = 10814.4706 kcal/mol (10786.9364 without restraints) Performing minimization step: 274. Total energy = 10796.8418 kcal/mol (10769.3162 without restraints) Performing minimization step: 275. Total energy = 10779.2709 kcal/mol (10751.7538 without restraints) Performing minimization step: 276. Total energy = 10761.7587 kcal/mol (10734.2502 without restraints) Performing minimization step: 277. Total energy = 10744.3049 kcal/mol (10716.8048 without restraints) Performing minimization step: 278. Total energy = 10726.9084 kcal/mol (10699.4169 without restraints) Performing minimization step: 279. Total energy = 10709.5697 kcal/mol (10682.0866 without restraints) Performing minimization step: 280. Total energy = 10692.2885 kcal/mol (10664.8138 without restraints) Performing minimization step: 281. Total energy = 10675.0642 kcal/mol (10647.5979 without restraints) Performing minimization step: 282. Total energy = 10657.8968 kcal/mol (10630.4389 without restraints) Performing minimization step: 283. Total energy = 10640.7861 kcal/mol (10613.3366 without restraints) Performing minimization step: 284. Total energy = 10623.7318 kcal/mol (10596.2906 without restraints) Performing minimization step: 285. Total energy = 10606.7337 kcal/mol (10579.3007 without restraints) Performing minimization step: 286. Total energy = 10589.7916 kcal/mol (10562.3669 without restraints) Performing minimization step: 287. Total energy = 10572.9051 kcal/mol (10545.4889 without restraints) Performing minimization step: 288. Total energy = 10556.0742 kcal/mol (10528.6662 without restraints) Performing minimization step: 289. Total energy = 10539.2989 kcal/mol (10511.8991 without restraints) Performing minimization step: 290. Total energy = 10522.5786 kcal/mol (10495.1871 without restraints) Performing minimization step: 291. Total energy = 10505.9133 kcal/mol (10478.5300 without restraints) Performing minimization step: 292. Total energy = 10489.3030 kcal/mol (10461.9279 without restraints) Performing minimization step: 293. Total energy = 10472.7471 kcal/mol (10445.3801 without restraints) Performing minimization step: 294. Total energy = 10456.2453 kcal/mol (10428.8865 without restraints) Performing minimization step: 295. Total energy = 10439.7975 kcal/mol (10412.4468 without restraints) Performing minimization step: 296. Total energy = 10423.4035 kcal/mol (10396.0609 without restraints) Performing minimization step: 297. Total energy = 10407.0630 kcal/mol (10379.7285 without restraints) Performing minimization step: 298. Total energy = 10390.7760 kcal/mol (10363.4496 without restraints) Performing minimization step: 299. Total energy = 10374.5421 kcal/mol (10347.2236 without restraints) Performing minimization step: 300. Total energy = 10358.3617 kcal/mol (10331.0514 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/ade9e976/tmp/sequence_refx/sequence_refx.pdb ...Done. Performing minimization step: 301. Total energy = 10342.2338 kcal/mol (10314.9315 without restraints) Performing minimization step: 302. Total energy = 10326.1589 kcal/mol (10298.8647 without restraints) Performing minimization step: 303. Total energy = 10310.1364 kcal/mol (10282.8501 without restraints) Performing minimization step: 304. Total energy = 10294.1659 kcal/mol (10266.8875 without restraints) Performing minimization step: 305. Total energy = 10278.2479 kcal/mol (10250.9772 without restraints) Performing minimization step: 306. Total energy = 10262.3814 kcal/mol (10235.1188 without restraints) Performing minimization step: 307. Total energy = 10246.5667 kcal/mol (10219.3121 without restraints) Performing minimization step: 308. Total energy = 10230.8038 kcal/mol (10203.5571 without restraints) Performing minimization step: 309. Total energy = 10215.0919 kcal/mol (10187.8531 without restraints) Performing minimization step: 310. Total energy = 10199.4311 kcal/mol (10172.2003 without restraints) Performing minimization step: 311. Total energy = 10183.8210 kcal/mol (10156.5979 without restraints) Performing minimization step: 312. Total energy = 10168.2618 kcal/mol (10141.0466 without restraints) Performing minimization step: 313. Total energy = 10152.7533 kcal/mol (10125.5459 without restraints) Performing minimization step: 314. Total energy = 10137.2950 kcal/mol (10110.0954 without restraints) Performing minimization step: 315. Total energy = 10121.8870 kcal/mol (10094.6952 without restraints) Performing minimization step: 316. Total energy = 10106.5291 kcal/mol (10079.3451 without restraints) Performing minimization step: 317. Total energy = 10091.2212 kcal/mol (10064.0449 without restraints) Performing minimization step: 318. Total energy = 10075.9627 kcal/mol (10048.7942 without restraints) Performing minimization step: 319. Total energy = 10060.7535 kcal/mol (10033.5927 without restraints) Performing minimization step: 320. Total energy = 10045.5939 kcal/mol (10018.4408 without restraints) Performing minimization step: 321. Total energy = 10030.4833 kcal/mol (10003.3379 without restraints) Performing minimization step: 322. Total energy = 10015.4219 kcal/mol (9988.2842 without restraints) Performing minimization step: 323. Total energy = 10000.4091 kcal/mol (9973.2790 without restraints) Performing minimization step: 324. Total energy = 9985.4448 kcal/mol (9958.3224 without restraints) Performing minimization step: 325. Total energy = 9970.5293 kcal/mol (9943.4145 without restraints) Performing minimization step: 326. Total energy = 9955.6613 kcal/mol (9928.5542 without restraints) Performing minimization step: 327. Total energy = 9940.8416 kcal/mol (9913.7421 without restraints) Performing minimization step: 328. Total energy = 9926.0701 kcal/mol (9898.9782 without restraints) Performing minimization step: 329. Total energy = 9911.3464 kcal/mol (9884.2621 without restraints) Performing minimization step: 330. Total energy = 9896.6703 kcal/mol (9869.5936 without restraints) Performing minimization step: 331. Total energy = 9882.0416 kcal/mol (9854.9725 without restraints) Performing minimization step: 332. Total energy = 9867.4602 kcal/mol (9840.3985 without restraints) Performing minimization step: 333. Total energy = 9852.9257 kcal/mol (9825.8715 without restraints) Performing minimization step: 334. Total energy = 9838.4379 kcal/mol (9811.3914 without restraints) Performing minimization step: 335. Total energy = 9823.9973 kcal/mol (9796.9582 without restraints) Performing minimization step: 336. Total energy = 9809.6031 kcal/mol (9782.5715 without restraints) Performing minimization step: 337. Total energy = 9795.2554 kcal/mol (9768.2313 without restraints) Performing minimization step: 338. Total energy = 9780.9541 kcal/mol (9753.9374 without restraints) Performing minimization step: 339. Total energy = 9766.6988 kcal/mol (9739.6896 without restraints) Performing minimization step: 340. Total energy = 9752.4892 kcal/mol (9725.4875 without restraints) Performing minimization step: 341. Total energy = 9738.3255 kcal/mol (9711.3312 without restraints) Performing minimization step: 342. Total energy = 9724.2076 kcal/mol (9697.2206 without restraints) Performing minimization step: 343. Total energy = 9710.1352 kcal/mol (9683.1557 without restraints) Performing minimization step: 344. Total energy = 9696.1086 kcal/mol (9669.1365 without restraints) Performing minimization step: 345. Total energy = 9682.1267 kcal/mol (9655.1620 without restraints) Performing minimization step: 346. Total energy = 9668.1898 kcal/mol (9641.2325 without restraints) Performing minimization step: 347. Total energy = 9654.2973 kcal/mol (9627.3473 without restraints) Performing minimization step: 348. Total energy = 9640.4503 kcal/mol (9613.5077 without restraints) Performing minimization step: 349. Total energy = 9626.6475 kcal/mol (9599.7123 without restraints) Performing minimization step: 350. Total energy = 9612.8891 kcal/mol (9585.9611 without restraints) Performing minimization step: 351. Total energy = 9599.1743 kcal/mol (9572.2536 without restraints) Performing minimization step: 352. Total energy = 9585.5043 kcal/mol (9558.5910 without restraints) Performing minimization step: 353. Total energy = 9571.8777 kcal/mol (9544.9715 without restraints) Performing minimization step: 354. Total energy = 9558.2953 kcal/mol (9531.3966 without restraints) Performing minimization step: 355. Total energy = 9544.7573 kcal/mol (9517.8658 without restraints) Performing minimization step: 356. Total energy = 9531.2625 kcal/mol (9504.3783 without restraints) Performing minimization step: 357. Total energy = 9517.8112 kcal/mol (9490.9342 without restraints) Performing minimization step: 358. Total energy = 9504.4028 kcal/mol (9477.5329 without restraints) Performing minimization step: 359. Total energy = 9491.0379 kcal/mol (9464.1754 without restraints) Performing minimization step: 360. Total energy = 9477.7158 kcal/mol (9450.8606 without restraints) Performing minimization step: 361. Total energy = 9464.4366 kcal/mol (9437.5886 without restraints) Performing minimization step: 362. Total energy = 9451.2003 kcal/mol (9424.3595 without restraints) Performing minimization step: 363. Total energy = 9438.0063 kcal/mol (9411.1726 without restraints) Performing minimization step: 364. Total energy = 9424.8546 kcal/mol (9398.0280 without restraints) Performing minimization step: 365. Total energy = 9411.7451 kcal/mol (9384.9258 without restraints) Performing minimization step: 366. Total energy = 9398.6777 kcal/mol (9371.8655 without restraints) Performing minimization step: 367. Total energy = 9385.6524 kcal/mol (9358.8474 without restraints) Performing minimization step: 368. Total energy = 9372.6689 kcal/mol (9345.8709 without restraints) Performing minimization step: 369. Total energy = 9359.7268 kcal/mol (9332.9360 without restraints) Performing minimization step: 370. Total energy = 9346.8268 kcal/mol (9320.0432 without restraints) Performing minimization step: 371. Total energy = 9333.9678 kcal/mol (9307.1913 without restraints) Performing minimization step: 372. Total energy = 9321.1497 kcal/mol (9294.3803 without restraints) Performing minimization step: 373. Total energy = 9308.3737 kcal/mol (9281.6114 without restraints) Performing minimization step: 374. Total energy = 9295.6382 kcal/mol (9268.8830 without restraints) Performing minimization step: 375. Total energy = 9282.9436 kcal/mol (9256.1955 without restraints) Performing minimization step: 376. Total energy = 9270.2899 kcal/mol (9243.5489 without restraints) Performing minimization step: 377. Total energy = 9257.6771 kcal/mol (9230.9431 without restraints) Performing minimization step: 378. Total energy = 9245.1047 kcal/mol (9218.3776 without restraints) Performing minimization step: 379. Total energy = 9232.5725 kcal/mol (9205.8526 without restraints) Performing minimization step: 380. Total energy = 9220.0806 kcal/mol (9193.3678 without restraints) Performing minimization step: 381. Total energy = 9207.6288 kcal/mol (9180.9230 without restraints) Performing minimization step: 382. Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to sequence_refx.pdb DONE!